https://murray.cds.caltech.edu/api.php?action=feedcontributions&feedformat=atom&user=Murray Murray Wiki - User contributions [en] 2026-05-10T19:11:58Z User contributions MediaWiki 1.44.2 https://murray.cds.caltech.edu/index.php?title=Bio&diff=27241 Bio 2026-03-20T20:12:37Z <p>Murray: </p> <hr /> <div><br /> {| width=100% padding=0 border=0<br /> |-<br /> | colspan=2 |<br /> {{RMM short bio}}<br /> | rowspan = 2 | <br /> [[Image:Murray-26Oct2021.jpg|150px|right]]<br /> |-<br /> | width=50% |<br /> Longer versions:<br /> * [[Expanded bio]]<br /> * [[Biographical Sketch]]<br /> * [[RMM photos]]<br /> | width=50% |<br /> Variants<br /> * [[http:www.eas.caltech.edu/people/murray|Caltech bio]]<br /> * [[http:en.wikipedia.org/wiki/Richard_M._Murray|Wikipedia bio]]<br /> * [[http:www.linkedin.com/in/murrayrm/|LinkedIn]]<br /> |}</div> Murray https://murray.cds.caltech.edu/index.php?title=RMM_research_meetings,_Mar_2026&diff=27240 RMM research meetings, Mar 2026 2026-03-17T18:08:09Z <p>Murray: </p> <hr /> <div>Please sign up for a time to meet.<br /> <br /> 18 Mar (Wed)<br /> * 4:15 pm: Open<br /> * 5:00 pm: Sal<br /> <br /> 20 Mar (Fri)<br /> * 2:00 pm: Miki<br /> * 2:45 pm: Zach M.<br /> * 3:30 pm: Leo<br /> * 4:15 pm: Han</div> Murray https://murray.cds.caltech.edu/index.php?title=RMM_research_meetings,_Mar_2026&diff=27235 RMM research meetings, Mar 2026 2026-03-15T14:39:45Z <p>Murray: </p> <hr /> <div>Please sign up for a time to meet.<br /> <br /> 18 Mar (Wed)<br /> * 3:30 pm: Open<br /> * 4:15 pm: Open<br /> * 5:00 pm: Open<br /> <br /> 20 Mar (Fri)<br /> * 2:00 pm: Miki<br /> * 2:45 pm: Open<br /> * 3:30 pm: Open<br /> * 4:15 pm: Open</div> Murray https://murray.cds.caltech.edu/index.php?title=RMM_research_meetings,_Mar_2026&diff=27234 RMM research meetings, Mar 2026 2026-03-15T11:21:26Z <p>Murray: Created page with &quot;Please sign up for a time to meet. 18 Mar (Wed) * 3:30 pm: Open * 4:15 pm: Open * 5:00 pm: Open 20 Mar (Fri) * 2:00 pm: Open * 2:45 pm: Open * 3:30 pm: Open * 4:15 pm: Open&quot;</p> <hr /> <div>Please sign up for a time to meet.<br /> <br /> 18 Mar (Wed)<br /> * 3:30 pm: Open<br /> * 4:15 pm: Open<br /> * 5:00 pm: Open<br /> <br /> 20 Mar (Fri)<br /> * 2:00 pm: Open<br /> * 2:45 pm: Open<br /> * 3:30 pm: Open<br /> * 4:15 pm: Open</div> Murray https://murray.cds.caltech.edu/index.php?title=Main_Page&diff=27228 Main Page 2026-02-15T01:35:42Z <p>Murray: </p> <hr /> <div>&lt;table border=1 width=100%&gt;<br /> &lt;tr&gt;<br /> &lt;td align=center width=150px&gt; [[Image:Murray-26Oct2021.jpg|150px]]&lt;/td&gt;<br /> &lt;td align=center&gt;<br /> &lt;font size=5&gt;<br /> &lt;b&gt;Richard M. Murray&lt;/b&gt;<br /> &lt;/font&gt;<br /> <br /> &lt;font size=3&gt;<br /> Thomas E. and Doris Everhart Professor of &lt;br&gt;<br /> Control &amp; Dynamical Systems and Bioengineering<br /> <br /> California Institute of Technology<br /> &lt;/font&gt;<br /> &lt;br&gt;&lt;hr&gt;<br /> &lt;table width=100%&gt; __NOTOC__<br /> &lt;tr&gt;<br /> &lt;td width=20% align=center&gt; [[Papers]]&lt;/td&gt;<br /> &lt;td width=20% align=center&gt; [[Research Overview|Research]]&lt;/td&gt;<br /> &lt;td width=20% align=center&gt; [[#Group|Group]]&lt;/td&gt;<br /> &lt;td width=20% align=center&gt; [[#Teaching|Teaching]]&lt;/td&gt;<br /> &lt;td width=20% align=center&gt; [[#Contact|Contact]]&lt;/td&gt;<br /> &lt;/tr&gt;&lt;/table&gt;&lt;/td&gt;<br /> &lt;td align=center width=160px&gt;<br /> Quick Links:<br /> <br /> &lt;!-- [[Group Schedule]] &lt;br&gt; --&gt;<br /> &lt;!-- [[E/SEC 103, Winter 2025|E/SEC 103]] &lt;br&gt; --&gt;<br /> [https://fbswiki.org/wiki/index.php/Feedback_Systems:_An_Introduction_for_Scientists_and_Engineers ''Feedback Systems''] &lt;br&gt;<br /> [[http:python-control.org|python-control]] &lt;br&gt;<br /> [[http:syncellwiki.org|SynCell wiki]]<br /> &lt;!-- [https://fbswiki.org/wiki/index.php/Biomolecular_Feedback_Systems ''Biomolecular Feedback Systems''] --&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;&lt;/table&gt;<br /> &lt;br&gt;<br /> &lt;!-- '''Prospective graduate students''': Students in my group come through the [[http:www.cds.caltech.edu|CDS]], [[http:www.cms.caltech.edu/academics/grad_cms|CMS]], [[http:be.caltech.edu|BE]], [[http:/www.its.caltech.edu/~biochem|BMB]], [[http:www.cms.caltech.edu/academics/grad_acm|ACM]], [[http:www.cms.caltech.edu/academics/grad_cs|CS]] and [[http:www.me.caltech.edu|ME]] graduate programs at Caltech. Some of my students also come from the CNS and EE departments, but I do not actively participate in admissions decisions in those programs. Please take a look at my current [[Research Overview|research interests]] to get a sense of what my group is currently working on. --&gt;<br /> &lt;!-- '''Prospective postdocs''': I typically make decisions about postdocs in the April-May timeframe, when I know what my grants look like for fall. Please take a look at my current [[Research Overview|research interests]] to see what projects we are currently working on. --&gt;<br /> &lt;!-- Caltech has several postdoc programs that admit exceptionally qualified postdocs for independent study at Caltech:<br /> * Caltech [[http:cmi.caltech.edu|Center for the Mathematics of Information (CMI)]] postdocs - applications due mid-December<br /> * Caltech [[http:www.its.caltech.edu/~bi/fellows.html|Beckman Fellows program]] - applications due early January<br /> --&gt;<br /> '''Note: I am currently sabbatical through Dec 2026''', and I am not starting any new students or postdocs in my group nor hosting visitors or SURF students during this time. If you are interested in the work we are doing in my group, I encourage you to take a look at some of my [[Collaborators|collaborators at Caltech]].<br /> == Research ==<br /> My group's research is in the application of feedback and control to networked systems, with applications in biology and autonomy. Current projects include design and implementation of synthetic cells and verification and testing of safety-critical systems (see my [[Research Overview|research overview]] for more details).<br /> <br /> {| border=1 style=&quot;float: right&quot;<br /> |-<br /> |<br /> [[Preprint archive]] &lt;br&gt;<br /> [http://thesis.library.caltech.edu/view/advisor/Murray-R-M.html Caltech theses]&lt;br&gt;<br /> [http://scholar.google.com/scholar?q=author:richard-m-murray Google Scholar]<br /> |}<br /> Active projects:<br /> {{#ask:<br /> [[Category:Active projects]]<br /> | ?agency = <br /> | format = ul<br /> | sort=Start date<br /> | order=descending<br /> }}<br /> [[Projects|&lt;nowiki&gt;[Archive]&lt;/nowiki&gt;]]<br /> <br /> == Group ==<br /> <br /> &lt;blockquote&gt;<br /> {| width=100% border=0 cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=33% | <br /> {|<br /> {{group entry|Sal Ibarra*|BE}}<br /> {{group entry|Leo Li*|CNS}}<br /> |}<br /> | width=33% | <br /> {|<br /> {{group entry|Zach Martinez*|BE}}<br /> {{group entry|Nikos Mynhier*|BE}}<br /> |}<br /> | width=33% | <br /> {|<br /> {{group entry|Miki Yun#|EAS}}<br /> {{group entry|Han Zhang*|BE}}<br /> |}<br /> |}<br /> &lt;font size=&quot;-2&quot;&gt;<br /> {| width=100%<br /> |-<br /> | * co-advised students || + visiting researchers <br /> | ° rotation students || † undergraduates || # research staff<br /> |}<br /> &lt;/font&gt;<br /> &lt;!-- 0 MS student; 0 PhD students (+5 joint); 0 postdoc --&gt;<br /> &lt;/blockquote&gt;<br /> <br /> ==== Former graduate students: ====<br /> &lt;!-- 87 PhD students (72 primary; 15 joint); 41 postdocs (incl. 1 visiting); 7 MS students --&gt;<br /> <br /> * Matthieu Kratz - PhD in Bioengineering, Oct 2025<br /> * [[http:mandralis.github.io/|Ioannis Mandralis]] - PhD in Aerospace, Oct 2025<br /> * Manisha Kapasiawala - PhD in Bioengineering, Aug 2025<br /> * Blade Olson* - PhD in Bioengineering, Aug 2025<br /> * Elin Larsson - PhD in Bioengineering, May 2025<br /> <br /> &lt;blockquote&gt;<br /> {| width=100% border=0 cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=33% | <br /> &lt;table&gt;<br /> {{PhD alum|Ania Baetica |thesis=CaltechTHESIS:06042018-171639726}}<br /> {{PhD alum|Julia Badger (Braman) |url=http:www.linkedin.com/in/julia-badger-b690094/ |thesis=CaltechETD:etd-05292009-111937}}<br /> {{PhD alum|Apurva Badithela|option=Control and Dynamical Systems|completed=May 2024|thesis=CaltechTHESIS:06022024-014038700|url=http:abadithela.github.io}}<br /> {{PhD alum|Dionysios Barmpoutis |option= |completed= |thesis=CaltechTHESIS:12102011-161913831}}<br /> {{PhD alum|Robert Behnken |url=http:www.linkedin.com/in/bob-behnken-2b6aa81a2/ |thesis=CaltechETD:etd-07102006-085216}}<br /> {{PhD alum|Robert Bodenheimer |url=http:engineering.vanderbilt.edu/bio/robert-bodenheimer}}<br /> {{PhD alum|Francesco Bullo |url=http:fbullo.github.io |thesis=CaltechETD:etd-02072008-100242}}<br /> {{PhD alum|Karena Cai |option=CDS |completed=Mar 2021 |thesis=CaltechTHESIS:04022021-033321217}}<br /> {{PhD alum|John Carson |thesis=CaltechETD:etd-05072008-131735}}<br /> {{PhD alum|Andrea Censi |url=http:censi.science |thesis=CaltechTHESIS:10282012-082208075}}<br /> {{PhD alum|Richard Cheng* |option=ME |completed=Feb 2021 |url=http:www.linkedin.com/in/richard-cheng-83838088/ |thesis=CaltechTHESIS:01052021-195655093}}<br /> {{PhD alum|Samuel Clamons |option=BE |completed=Sep 2021 |thesis=CaltechTHESIS:09262021-022402778}}<br /> {{PhD alum|Benson Christalin# }}<br /> {{PhD alum|Tim Chung* |url=http:www.linkedin.com/in/timothy-h-chung/}}<br /> {{PhD alum|Lars Cremean |url=http:www.cds.caltech.edu/~lars |thesis=CaltechETD:etd-05242006-190748}}<br /> {{PhD alum|Nadine Dabby* }}<br /> {{PhD alum|Raff D'Andrea* |url=http:www.mae.cornell.edu/Raff}}<br /> {{PhD alum|Sumanth Dathathri |thesis=CaltechTHESIS:04292020-165136662}}<br /> {{PhD alum|Samantha (Feakins) Daly# |url=http:www.its.caltech.edu/~feakins/index.html}}<br /> {{PhD alum|Emzo de los Santos |option= |completed= |thesis=CaltechTHESIS:05182015-163708506}}<br /> {{PhD alum|Domitilla Del Vecchio | url=http:www.mit.edu/~ddv/ | thesis=CaltechETD:etd-05272005-113928}}<br /> {{PhD alum|Mary Dunlop |url=http:www.cds.caltech.edu/~mjdunlop |thesis=CaltechETD:etd-05302008-141602}}<br /> {{PhD alum|William Dunbar |url=http:www.soe.ucsc.edu/~dunbar/ |thesis=CaltechETD:etd-05282004-170123}}<br /> {{PhD alum|Michael Epstein |url=http:www.cds.caltech.edu/~epstein/ |thesis=CaltechETD:etd-12192007-153619}}<br /> {{PhD alum|Alex Fax |url=http:www.cds.caltech.edu/~fax |thesis=CaltechETD:etd-10242005-105000}}<br /> {{PhD alum|Ioannis Filippidis |thesis=CaltechTHESIS:07202018-115217471}}<br /> {{PhD alum|Anthony Fragoso |option= |completed= |thesis=CaltechTHESIS:10242017-193520989}}<br /> {{PhD alum|Sawyer Fuller |url=http:www.media.mit.edu/~minster/ (thesis)}}<br /> {{PhD alum|Melvin Flores |thesis=CaltechETD:etd-02192008-153449}}<br /> {{PhD alum|Elisa Franco |url=http:samueli.ucla.edu/people/elisa-franco/ |option= |completed= |thesis=CaltechTHESIS:10192011-161454857}}<br /> &lt;/table&gt;<br /> | width=33% | <br /> &lt;table&gt;<br /> {{PhD alum|Jimmy Fung |url=http:www.cds.caltech.edu/~fung |thesis=05272005-165938}}<br /> {{PhD alum| Marcella Gomez | url=http:caltech.academia.edu/MarcellaGomez | option=CDS | completed= | thesis=CaltechTHESIS:08282014-165029252}}<br /> {{PhD alum|Martha Grover (Gallivan) | url=http:grover.chbe.gatech.edu | thesis=CaltechETD:etd-10222002-115711}}<br /> {{PhD alum|Shaobin Guo |option= |completed= |thesis=CaltechTHESIS:03082017-163613964}}<br /> {{PhD alum|Vijay Gupta |url=http:ee.nd.edu/faculty/vgupta/ |thesis=CaltechETD:etd-08172006-130145}}<br /> {{PhD alum|Sonja Glavaski*}}<br /> {{PhD alum|Josefine Graebener|option=Aerospace Engineering|completed=April 2024|thesis=CaltechTHESIS:05312024-094443866}}<br /> {{PhD alum|Shuo Han | url=http:fling.seas.upenn.edu/~hanshuo/cgi-bin/wordpress/ | thesis=CaltechTHESIS:10162013-111333269}}<br /> {{PhD alum|Adam Hayes*}}<br /> {{PhD alum|Sean Humbert |url=http:www.avl.umd.edu/people/director.html |thesis=CaltechETD:etd-06072005-163739}}<br /> {{PhD alum|Victoria Hsiao |option=BE |completed=May 2016 |thesis=CaltechTHESIS:05082016-170628018}}<br /> {{PhD alum|Ali Jadbabaie* |url=http:www.seas.upenn.edu/~jadbabai |thesis=CaltechTHESIS:10262010-112027161}}<br /> {{PhD alum|Zhipu Jin |url=http:www.cds.caltech.edu/~jzp |thesis=CaltechETD:etd-09182006-162259}}<br /> {{PhD alum|Vanessa Jonsson |option= |completed= |thesis=CaltechTHESIS:10132015-121212703}}<br /> {{PhD alum|Zoila Jurado|option=Mechanical Engineering|completed=May 2024|thesis=CaltechTHESIS:06032024-141219249|url=http:www.linkedin.com/in/zoila-jurado-93005b83/}}<br /> {{PhD alum|Scott Kelly |url=http:www.coe.uncc.edu/~skelly52/ |thesis=CaltechETD:etd-08122005-152639}}<br /> {{PhD alum|Dmitriy Kogan# |url=http:www.linkedin.com/pub/1/446/a84 }}<br /> {{PhD alum|Javad Lavaei* |url=http:www.ee.columbia.edu/~lavaei |thesis=CaltechTHESIS:05132011-113642762}}<br /> {{PhD alum|Andrew Lewis |url=http:www.mast.queensu.ca/~andrew/ |thesis=CaltechETD:etd-07132006-143133}}<br /> {{PhD alum|[[http:scottman.net/ |Scott Livingston]] |option=CDS |completed=Dec 2015 |thesis=CaltechTHESIS:12312015-131513787}}<br /> {{PhD alum|[[http:jpmarken.github.io/|John Marken]] |option=BE|completed=May 2023|thesis=CaltechTHESIS:05292023-181810775}}<br /> {{PhD alum|Reed McCardell |option=BE |completed=May 2021 |thesis=CaltechTHESIS:05082021-185615529}}<br /> {{PhD alum|Robert M'Closkey | url=http:www.seas.ucla.edu/~mcloskey/ | thesis=CaltechETD:etd-10172007-104556}}<br /> {{PhD alum|Joseph Meyerowitz|option=BMB|completed=Dec 2022|thesis=CaltechTHESIS:12022022-073109279}}<br /> {{PhD alum|Mark Milam |url=http:www.cds.caltech.edu/~milam/ |thesis=CaltechETD:etd-06022003-114340}}<br /> {{PhD alum|Michiel van Nieuwstadt |thesis=CaltechETD:etd-01172008-085534}}<br /> {{PhD alum|Ayush Pandey |option=CDS |completed=Jun 2023 |thesis=CaltechTHESIS:06062023-021337351|url=http:ayush-pandey.github.io}}<br /> {{PhD alum|Ivan Papusha |option= |completed= |thesis=CaltechTHESIS:06032016-102336160}}<br /> {{PhD alum|James Parkin |option=BE |completed=Mar 2021 |thesis=CaltechTHESIS:03262021-160841703}}<br /> {{PhD alum|Tung Phan |thesis=CaltechTHESIS:01132021-065636010}}<br /> &lt;/table&gt;<br /> | width=33% | <br /> &lt;table&gt;<br /> {{PhD alum|William Poole |option=CNS |completed=Aug 2021 |thesis=CaltechTHESIS:11102021-210013472}}<br /> {{PhD alum|Muruhan Rathinam | url=http:www.math.umbc.edu/~muruhan/ | thesis=CaltechETD:etd-01152008-082733}}<br /> {{PhD alum|Xinying (Cindy) Ren |option=CDS |completed=Jun 2021 |thesis=CaltechTHESIS:05262021-072231177}}<br /> {{PhD alum|Clancy Rowley* |url=http:weblamp.princeton.edu/cwrowley/}}<br /> {{PhD alum|Ben Shapiro |url=http:www.glue.umd.edu/~benshap/ |thesis=CaltechETD:etd-02272008-083040}}<br /> {{PhD alum|Ling Shi |url=http:www.cds.caltech.edu/~shiling/ |thesis=CaltechETD:etd-08272008-121822}}<br /> {{PhD alum|Andrey Shur |option=BE |completed=Dec 2021 |thesis=CaltechTHESIS:12212021-193826426}}<br /> {{PhD alum|Vipul Singhal |thesis=CaltechTHESIS:08262018-213846283}}<br /> {{PhD alum|Demetri Spanos |url=http:www.cds.caltech.edu/~demetri |thesis=CaltechETD:etd-06262006-171822}}<br /> {{PhD alum|Zachary Sun |option= |completed= |thesis=CaltechTHESIS:10012015-221355676/}}<br /> {{PhD alum|Sudipto Sur | url=http:alumnus.caltech.edu/~sur/ |thesis=CaltechETD:etd-01172008-092801}}<br /> {{PhD alum|Anandh Swaminathan |thesis=CaltechTHESIS:12132017-121914940}}<br /> {{PhD alum|Anu Thubagere* |option= |completed= |thesis=CaltechTHESIS:06082017-194534497}}<br /> {{PhD alum|Amber Thweatt#}}<br /> {{PhD alum|Jorge Tierno*}}<br /> {{PhD alum|Abhishek Tiwari |url=http:www.cds.caltech.edu/~atiwari/ |thesis=CaltechETD:etd-05202007-135411}}<br /> {{PhD alum|Pete Trautman |option= |completed= |thesis=CaltechTHESIS:05182013-191132413}}<br /> {{PhD alum|Stephanie Tsuei#}}<br /> {{PhD alum|David van Gogh#}}<br /> {{PhD alum|Tony Vanelli# |thesis=CaltechETD:etd-01162008-152619}}<br /> {{PhD alum|Ophelia Venturelli |thesis=CaltechTHESIS:06072013-095239958}}<br /> {{PhD alum|Yong Wang |url=http:www.mech.pku.edu.cn/robot/teacher/wangyong/ |thesis=CaltechETD:etd-06282005-103901}}<br /> {{PhD alum|Steve Waydo* |url=http:www.cds.caltech.edu/~waydo |thesis=CaltechETD:etd-11022007-104734}}<br /> {{PhD alum|Rory Williams |option= |completed=Dec 2021 |thesis=CaltechTHESIS:01042022-184525578}}<br /> {{PhD alum|Eric Wolff |option=CDS |completed= |thesis=CaltechTHESIS:02172014-121159358}}<br /> {{PhD alum|Nok Wongpiromsarn |url=http:robotics.caltech.edu/~nok |thesis=CaltechTHESIS:05272010-153304667}}<br /> {{PhD alum|Yong Wu |option= |completed= |thesis=CaltechTHESIS:08302017-121452132}}<br /> {{PhD alum|Huan (Mumu) Xu |url=http:www.aero.umd.edu/~mumu |thesis=CaltechTHESIS:05312013-103940337}}<br /> {{PhD alum|Enoch Yeung |option=CDS |completed=Jan 2016 |thesis=CaltechTHESIS:05272016-145559554}}<br /> {{PhD alum|Simon Yeung |url=http:www.linkedin.com/pub/3/a32/258 |thesis=CaltechETD:etd-02272008-083453}}<br /> &lt;/table&gt;<br /> |}<br /> &lt;font size=&quot;-2&quot;&gt;# Masters or Engineers degree &amp;nbsp;&amp;nbsp; * Co-advised student&lt;/font&gt;<br /> &lt;/blockquote&gt;<br /> <br /> ==== Former postdocs: ====<br /> * Kazu Echigo (2025) - CMS Postdoctoral Fellow<br /> * [[http:yzhang952.github.io|Yan Zhang]] (2022-24) - Presidential Postdoctoral Fellow<br /> * Inigo Incer (2022-24) - CMS Postdoctoral Fellow<br /> * Chelsea Hu (2018-22) - BE Postdoctoral Fellow<br /> * Ersin Das (2021-22) - CMS Postdoctoral Fellow<br /> <br /> &lt;blockquote&gt;<br /> {| width=100% border=0 cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=33% | <br /> &lt;table&gt;<br /> {{Postdoc alum|Raktim Bhattacharya|years=2002-04}}<br /> &lt;tr&gt;&lt;td&gt;[http://www.niu.edu/faculty/coller.shtml Brianno Coller] (1995-97) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Noel du Toit (2011)&lt;/td&gt;&lt;/tr&gt;<br /> {{Postdoc alum|Chuchu Fan|years=2019-20|title=CMS Postdoctoral Fellow}}<br /> &lt;tr&gt;&lt;td&gt;Samira Farahani (2014-15) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;David Garcia (2020-21) &lt;/td&gt;&lt;/tr&gt;<br /> {{Postdoc alum|Jin Ge|years=2016-18|title=CMS Postdoctoral Fellow}}<br /> &lt;tr&gt;&lt;td&gt;Leopold Green (2018-21) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Sofie Haesaert (2016-18) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Yutaka Hori (2013-16) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.ece.louisville.edu/~t0inan01/ Tamer Inanc] (2002-04)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Jongmin Kim (2010-14)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;/table&gt;<br /> | width=33% | <br /> &lt;table&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://soslab.ee.washington.edu/mw/index.php/User:Klavins Eric Klavins]* (2001-03)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://cc.ee.ntu.edu.tw/~fengli/ Feng-Li Lian] (2001-02)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Jun Liu (2011-2012)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Michaelle Mayalu (2017-22) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Catherine McGhan (2014-16)&lt;/td&gt;&lt;/tr&gt;<br /> {{Postdoc alum|John McManus*|years=2018-19|title=Visiting Postdoctoral Fellow}}<br /> &lt;tr&gt;&lt;td&gt;Yilin Mo (2013-15)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.aa.washington.edu/faculty/morgansen/ Kristi Morgansen] (1999-2001)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www-sop.inria.fr/icare/personnel/morin/morin-personnel.html Pascal Morin] (1996-97)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.ece.ucsb.edu/~ymostofi/ Yasamin Mostofi] (2004-06)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Reza Olfati-Saber (2001-04)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.cds.caltech.edu/~izi/ Yizhar Or] (2007-09)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;/table&gt;<br /> | width=33% | <br /> &lt;table&gt;<br /> &lt;tr&gt;&lt;td&gt;Necmiye Ozay (2010-13)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Pavithra Prabhakar (2011-12)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://cas.ensmp.fr/~petit/ Nicolas Petit] (2001-02)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Vasu Raman (2013-15)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.ee.kth.se/php/index.php?action=people&amp;cmd=extended&amp;peopleid=768 Henrik Sandberg] (2005-07)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Shaunak Sen (2011-12)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://me.nmsu.edu/~shashi/ B. N. Shashikanth*] (1998-2000)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Dan Siegal (2012-15)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[[http:www.its.caltech.edu/~astraw/|Andrew Straw*]] (2010)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Willem Sluis (1994-96)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.cds.caltech.edu/~herb/ Herbert Streumper] (1997-99)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Ufuk Topcu (2008-12)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;/table&gt;<br /> |}<br /> &lt;/blockquote&gt;<br /> '''Additional group alumni:''' &amp;nbsp; [[SURF alumni|SURF]] &amp;nbsp;&amp;nbsp; [[Undergraduate alumni|Undergrads]] &amp;nbsp;&amp;nbsp; [[Visitors]]<br /> <br /> == Teaching ==<br /> The list below is the courses that I have taught at Caltech (or at least most of them). The course links will take you to the (current) course homepage, where you can find the syllabus, handouts, and homework sets. The links for specific terms take you to the course homepage for that term. Links to [[Teaching Archive|older courses]] are available on a separate page.<br /> <br /> &lt;!--<br /> * BE/APh 162 - Physical Biology Laboratory ([http://www.rpgroup.caltech.edu/courses/aph162/2009/ Wi09])<br /> --&gt;<br /> * [[ACM/EE 116]] - Probability and Random Processes ([[ACM/EE_116,_Fall_2011|Fa11]])<br /> * [[BE 107]] - Exploring Biological Principles Through Bio-Inspired Design ([[BE 107, Spring 2015|Sp15]], [[BE 107, Spring 2016|Sp16]], [[BE 107, Spring 2019|Sp19]])<br /> * [[BE 150/Bi 250b]] - Systems Biology ([[Bi/BE_250c_Winter_2011|Wi11]], [[BE_150/Bi_250b_Winter_2012|Wi12]], [[BE_150/Bi_250b_Winter_2013|Wi13]], [[BE 150/Bi 250 Spring 2014|Sp14]])<br /> * [[BE/EE/MedE 189a]] - Design and Construction of Biodevices ([[BE/EE/MedE 189a, Fall 2024|Fa24]])<br /> * [[Bi/BE/CS 183]] - Introduction to Computational Biology and Bioinformatics ([[Bi/BE/CS 183, Winter 2024|Wi24]])<br /> * [[CS/EE/ME 75]] - Introduction to Multi-Disciplinary Systems Engineering (04-05, 06-07, 10-11, [[CS/EE/ME 75, 2015-16|15-16]])<br /> * [[CDS 90]] - Senior Thesis in Control and Dynamical Systems (2004-2014, 2020-2024)<br /> * [[CDS 101|CDS 101/110]] - Analysis and Design of Feedback Systems (Fa97, Fa01, [[http:www.cds.caltech.edu/~murray/courses/cds101/fa02|Fa02]], [[http:www.cds.caltech.edu/~murray/courses/cds101/fa03/|Fa03]], [[http:www.cds.caltech.edu/~murray/courses/cds101/fa04/|Fa04]], [[CDS 101/110a, Fall 2006|Fa06]], [[CDS 101/110a, Fall 2007|Fa07]], [[CDS 101/110a, Fall 2008|Fa08]], [[CDS 101/110a, Fall 2012|Fa12]], [[CDS 101/110, Fall 2015|Fa15]], [[CDS 110/ChE 130, Spring 2024|Sp24]])<br /> * [[CDS 112]] - Optimization-Based Control (Wi98, Wi02, Wi03, Wi04, [[CDS 110b, Winter 2006|Wi06]], [[CDS 110b, Winter 2007|Wi07]], [[CDS 110b, Winter 2008|Wi08]], [[CDS 112/Ae 103a, Winter 2022|Wi22]], [[CDS 112/Ae 103b, Winter 2023|Wi23]])<br /> * [[CDS 131]] - Linear Systems Theory ([[CDS 131, Fall 2018|Fa18]], [[CDS 131, Fall 2019|Fa19]], [[CDS 131, Fall 2020|Fa20]])<br /> * [[CDS 140]] - Differential Equations and Dynamical Systems ([[AM 101b/AM 125b/CDS 140a, Winter 2011|Wi11]], [[AM 101b/AM 125b/CDS 140a, Winter 2013|Wi13]], [[ACM 101b/AM 125b/CDS 140a, Winter 2014|Wi14]], [[CDS 140, Winter 2015|Wi15]])<br /> * [[CDS 240]] - Nonlinear Dynamical Systems ([[CDS 140b, Spring 2014|Sp14]], [[CDS 240, Spring 2016|Sp16]])<br /> * [[CDS 202]] - Geometry of Nonlinear Systems (Wi93, Wi94, [[http:www.cds.caltech.edu/~murray/courses/cds202/wi04/|Wi04]], [[CDS 202, Winter 2009|Wi09]], [[CDS 202, Spring 2013|Sp13]])<br /> * [[http:www.cds.caltech.edu/cs142|CS 142]] - Distributed Computing ([[CS 142, Fall 2017|Fa17]], [[CS 142, Fall 2019|Fa19]])<br /> * CS 143 - Communication Networks ([http://courses.cms.caltech.edu/cs143/ Fa18])<br /> * [[CMS 273]] - Frontiers in Computing and Mathematical Sciences ([[CMS 273, Winter 2019|Wi19]], [[CMS 273, Winter 2020|Wi20]], [[CMS 273, Winter 2021|Wi21]])<br /> * [[E/SEC 103]] - Management of Technology ([[E/SEC 103, Spring 2020|Sp20]], [[E/SEC 103, Spring 2023|Sp23]], [[E/SEC 103, Winter 2024|Wi24]], [[E/SEC 103, Winter 2025|Wi25]])<br /> * [[Courses#Older_courses_(not_on_this_wiki)|Older courses]] (not taught in the last 15 years)<br /> * [[:Category:Guest lectures|Guest lectures]] - some individual lectures I have given in various courses<br /> <br /> == Contact ==<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ==== Mailing Address ====<br /> Richard M. Murray&lt;br&gt;<br /> Control and Dynamical Systems 107-81&lt;br&gt;<br /> California Institute of Technology&lt;br&gt;<br /> 1200 E. California Blvd&lt;br&gt;<br /> Pasadena, CA 91125 USA<br /> | width=50% |<br /> <br /> ==== Contact information ====<br /> E-mail: murray@cds.caltech.edu &lt;br&gt;<br /> Office: 109 Steele Lab, (626) 395-6460 &lt;br&gt;<br /> Asst: Nuvia Alvarez, x2464 &lt;br&gt;<br /> Labs: 108, 116, 136 Keck<br /> |- valign=bottom<br /> |<br /> <br /> ==== Other links ====<br /> [http://www.caltech.edu Caltech]&lt;br&gt;<br /> [http://www.eas.caltech.edu Engineering and Applied Science]&lt;br&gt;<br /> [http://cms.caltech.edu Computing and Mathematical Sciences]&lt;br&gt;<br /> |<br /> [http://be.caltech.edu/ Bioengineering]&lt;br&gt;<br /> [http://www.cds.caltech.edu Control and Dynamical Systems]&lt;br&gt;<br /> [http://www.linkedin.com/in/murrayrm LinkedIn]<br /> |}</div> Murray https://murray.cds.caltech.edu/index.php?title=Main_Page&diff=27227 Main Page 2026-02-15T01:35:14Z <p>Murray: </p> <hr /> <div>&lt;table border=1 width=100%&gt;<br /> &lt;tr&gt;<br /> &lt;td align=center width=150px&gt; [[Image:Murray-26Oct2021.jpg|150px]]&lt;/td&gt;<br /> &lt;td align=center&gt;<br /> &lt;font size=5&gt;<br /> &lt;b&gt;Richard M. Murray&lt;/b&gt;<br /> &lt;/font&gt;<br /> <br /> &lt;font size=3&gt;<br /> Thomas E. and Doris Everhart Professor of &lt;br&gt;<br /> Control &amp; Dynamical Systems and Bioengineering<br /> <br /> California Institute of Technology<br /> &lt;/font&gt;<br /> &lt;br&gt;&lt;hr&gt;<br /> &lt;table width=100%&gt; __NOTOC__<br /> &lt;tr&gt;<br /> &lt;td width=20% align=center&gt; [[Papers]]&lt;/td&gt;<br /> &lt;td width=20% align=center&gt; [[Research Overview|Research]]&lt;/td&gt;<br /> &lt;td width=20% align=center&gt; [[#Group|Group]]&lt;/td&gt;<br /> &lt;td width=20% align=center&gt; [[#Teaching|Teaching]]&lt;/td&gt;<br /> &lt;td width=20% align=center&gt; [[#Contact|Contact]]&lt;/td&gt;<br /> &lt;/tr&gt;&lt;/table&gt;&lt;/td&gt;<br /> &lt;td align=center width=160px&gt;<br /> Quick Links:<br /> <br /> &lt;!-- [[Group Schedule]] &lt;br&gt; --&gt;<br /> &lt;!-- [[E/SEC 103, Winter 2025|E/SEC 103]] &lt;br&gt; --&gt;<br /> [https://fbswiki.org/wiki/index.php/Feedback_Systems:_An_Introduction_for_Scientists_and_Engineers ''Feedback Systems''] &lt;br&gt;<br /> [[http:python-control.org|python-control]] &lt;br&gt;<br /> [[http:devcellwiki.org|DevCell wiki]]<br /> &lt;!-- [https://fbswiki.org/wiki/index.php/Biomolecular_Feedback_Systems ''Biomolecular Feedback Systems''] --&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;&lt;/table&gt;<br /> &lt;br&gt;<br /> &lt;!-- '''Prospective graduate students''': Students in my group come through the [[http:www.cds.caltech.edu|CDS]], [[http:www.cms.caltech.edu/academics/grad_cms|CMS]], [[http:be.caltech.edu|BE]], [[http:/www.its.caltech.edu/~biochem|BMB]], [[http:www.cms.caltech.edu/academics/grad_acm|ACM]], [[http:www.cms.caltech.edu/academics/grad_cs|CS]] and [[http:www.me.caltech.edu|ME]] graduate programs at Caltech. Some of my students also come from the CNS and EE departments, but I do not actively participate in admissions decisions in those programs. Please take a look at my current [[Research Overview|research interests]] to get a sense of what my group is currently working on. --&gt;<br /> &lt;!-- '''Prospective postdocs''': I typically make decisions about postdocs in the April-May timeframe, when I know what my grants look like for fall. Please take a look at my current [[Research Overview|research interests]] to see what projects we are currently working on. --&gt;<br /> &lt;!-- Caltech has several postdoc programs that admit exceptionally qualified postdocs for independent study at Caltech:<br /> * Caltech [[http:cmi.caltech.edu|Center for the Mathematics of Information (CMI)]] postdocs - applications due mid-December<br /> * Caltech [[http:www.its.caltech.edu/~bi/fellows.html|Beckman Fellows program]] - applications due early January<br /> --&gt;<br /> '''Note: I am currently sabbatical through Dec 2026''', and I am not starting any new students or postdocs in my group nor hosting visitors or SURF students during this time. If you are interested in the work we are doing in my group, I encourage you to take a look at some of my [[Collaborators|collaborators at Caltech]].<br /> == Research ==<br /> My group's research is in the application of feedback and control to networked systems, with applications in biology and autonomy. Current projects include design and implementation of synthetic cells and verification and testing of safety-critical systems (see my [[Research Overview|research overview]] for more details).<br /> <br /> {| border=1 style=&quot;float: right&quot;<br /> |-<br /> |<br /> [[Preprint archive]] &lt;br&gt;<br /> [http://thesis.library.caltech.edu/view/advisor/Murray-R-M.html Caltech theses]&lt;br&gt;<br /> [http://scholar.google.com/scholar?q=author:richard-m-murray Google Scholar]<br /> |}<br /> Active projects:<br /> {{#ask:<br /> [[Category:Active projects]]<br /> | ?agency = <br /> | format = ul<br /> | sort=Start date<br /> | order=descending<br /> }}<br /> [[Projects|&lt;nowiki&gt;[Archive]&lt;/nowiki&gt;]]<br /> <br /> == Group ==<br /> <br /> &lt;blockquote&gt;<br /> {| width=100% border=0 cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=33% | <br /> {|<br /> {{group entry|Sal Ibarra*|BE}}<br /> {{group entry|Leo Li*|CNS}}<br /> |}<br /> | width=33% | <br /> {|<br /> {{group entry|Zach Martinez*|BE}}<br /> {{group entry|Nikos Mynhier*|BE}}<br /> |}<br /> | width=33% | <br /> {|<br /> {{group entry|Miki Yun#|EAS}}<br /> {{group entry|Han Zhang*|BE}}<br /> |}<br /> |}<br /> &lt;font size=&quot;-2&quot;&gt;<br /> {| width=100%<br /> |-<br /> | * co-advised students || + visiting researchers <br /> | ° rotation students || † undergraduates || # research staff<br /> |}<br /> &lt;/font&gt;<br /> &lt;!-- 0 MS student; 0 PhD students (+5 joint); 0 postdoc --&gt;<br /> &lt;/blockquote&gt;<br /> <br /> ==== Former graduate students: ====<br /> &lt;!-- 87 PhD students (72 primary; 15 joint); 41 postdocs (incl. 1 visiting); 7 MS students --&gt;<br /> <br /> * Matthieu Kratz - PhD in Bioengineering, Oct 2025<br /> * [[http:mandralis.github.io/|Ioannis Mandralis]] - PhD in Aerospace, Oct 2025<br /> * Manisha Kapasiawala - PhD in Bioengineering, Aug 2025<br /> * Blade Olson* - PhD in Bioengineering, Aug 2025<br /> * Elin Larsson - PhD in Bioengineering, May 2025<br /> <br /> &lt;blockquote&gt;<br /> {| width=100% border=0 cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=33% | <br /> &lt;table&gt;<br /> {{PhD alum|Ania Baetica |thesis=CaltechTHESIS:06042018-171639726}}<br /> {{PhD alum|Julia Badger (Braman) |url=http:www.linkedin.com/in/julia-badger-b690094/ |thesis=CaltechETD:etd-05292009-111937}}<br /> {{PhD alum|Apurva Badithela|option=Control and Dynamical Systems|completed=May 2024|thesis=CaltechTHESIS:06022024-014038700|url=http:abadithela.github.io}}<br /> {{PhD alum|Dionysios Barmpoutis |option= |completed= |thesis=CaltechTHESIS:12102011-161913831}}<br /> {{PhD alum|Robert Behnken |url=http:www.linkedin.com/in/bob-behnken-2b6aa81a2/ |thesis=CaltechETD:etd-07102006-085216}}<br /> {{PhD alum|Robert Bodenheimer |url=http:engineering.vanderbilt.edu/bio/robert-bodenheimer}}<br /> {{PhD alum|Francesco Bullo |url=http:fbullo.github.io |thesis=CaltechETD:etd-02072008-100242}}<br /> {{PhD alum|Karena Cai |option=CDS |completed=Mar 2021 |thesis=CaltechTHESIS:04022021-033321217}}<br /> {{PhD alum|John Carson |thesis=CaltechETD:etd-05072008-131735}}<br /> {{PhD alum|Andrea Censi |url=http:censi.science |thesis=CaltechTHESIS:10282012-082208075}}<br /> {{PhD alum|Richard Cheng* |option=ME |completed=Feb 2021 |url=http:www.linkedin.com/in/richard-cheng-83838088/ |thesis=CaltechTHESIS:01052021-195655093}}<br /> {{PhD alum|Samuel Clamons |option=BE |completed=Sep 2021 |thesis=CaltechTHESIS:09262021-022402778}}<br /> {{PhD alum|Benson Christalin# }}<br /> {{PhD alum|Tim Chung* |url=http:www.linkedin.com/in/timothy-h-chung/}}<br /> {{PhD alum|Lars Cremean |url=http:www.cds.caltech.edu/~lars |thesis=CaltechETD:etd-05242006-190748}}<br /> {{PhD alum|Nadine Dabby* }}<br /> {{PhD alum|Raff D'Andrea* |url=http:www.mae.cornell.edu/Raff}}<br /> {{PhD alum|Sumanth Dathathri |thesis=CaltechTHESIS:04292020-165136662}}<br /> {{PhD alum|Samantha (Feakins) Daly# |url=http:www.its.caltech.edu/~feakins/index.html}}<br /> {{PhD alum|Emzo de los Santos |option= |completed= |thesis=CaltechTHESIS:05182015-163708506}}<br /> {{PhD alum|Domitilla Del Vecchio | url=http:www.mit.edu/~ddv/ | thesis=CaltechETD:etd-05272005-113928}}<br /> {{PhD alum|Mary Dunlop |url=http:www.cds.caltech.edu/~mjdunlop |thesis=CaltechETD:etd-05302008-141602}}<br /> {{PhD alum|William Dunbar |url=http:www.soe.ucsc.edu/~dunbar/ |thesis=CaltechETD:etd-05282004-170123}}<br /> {{PhD alum|Michael Epstein |url=http:www.cds.caltech.edu/~epstein/ |thesis=CaltechETD:etd-12192007-153619}}<br /> {{PhD alum|Alex Fax |url=http:www.cds.caltech.edu/~fax |thesis=CaltechETD:etd-10242005-105000}}<br /> {{PhD alum|Ioannis Filippidis |thesis=CaltechTHESIS:07202018-115217471}}<br /> {{PhD alum|Anthony Fragoso |option= |completed= |thesis=CaltechTHESIS:10242017-193520989}}<br /> {{PhD alum|Sawyer Fuller |url=http:www.media.mit.edu/~minster/ (thesis)}}<br /> {{PhD alum|Melvin Flores |thesis=CaltechETD:etd-02192008-153449}}<br /> {{PhD alum|Elisa Franco |url=http:samueli.ucla.edu/people/elisa-franco/ |option= |completed= |thesis=CaltechTHESIS:10192011-161454857}}<br /> &lt;/table&gt;<br /> | width=33% | <br /> &lt;table&gt;<br /> {{PhD alum|Jimmy Fung |url=http:www.cds.caltech.edu/~fung |thesis=05272005-165938}}<br /> {{PhD alum| Marcella Gomez | url=http:caltech.academia.edu/MarcellaGomez | option=CDS | completed= | thesis=CaltechTHESIS:08282014-165029252}}<br /> {{PhD alum|Martha Grover (Gallivan) | url=http:grover.chbe.gatech.edu | thesis=CaltechETD:etd-10222002-115711}}<br /> {{PhD alum|Shaobin Guo |option= |completed= |thesis=CaltechTHESIS:03082017-163613964}}<br /> {{PhD alum|Vijay Gupta |url=http:ee.nd.edu/faculty/vgupta/ |thesis=CaltechETD:etd-08172006-130145}}<br /> {{PhD alum|Sonja Glavaski*}}<br /> {{PhD alum|Josefine Graebener|option=Aerospace Engineering|completed=April 2024|thesis=CaltechTHESIS:05312024-094443866}}<br /> {{PhD alum|Shuo Han | url=http:fling.seas.upenn.edu/~hanshuo/cgi-bin/wordpress/ | thesis=CaltechTHESIS:10162013-111333269}}<br /> {{PhD alum|Adam Hayes*}}<br /> {{PhD alum|Sean Humbert |url=http:www.avl.umd.edu/people/director.html |thesis=CaltechETD:etd-06072005-163739}}<br /> {{PhD alum|Victoria Hsiao |option=BE |completed=May 2016 |thesis=CaltechTHESIS:05082016-170628018}}<br /> {{PhD alum|Ali Jadbabaie* |url=http:www.seas.upenn.edu/~jadbabai |thesis=CaltechTHESIS:10262010-112027161}}<br /> {{PhD alum|Zhipu Jin |url=http:www.cds.caltech.edu/~jzp |thesis=CaltechETD:etd-09182006-162259}}<br /> {{PhD alum|Vanessa Jonsson |option= |completed= |thesis=CaltechTHESIS:10132015-121212703}}<br /> {{PhD alum|Zoila Jurado|option=Mechanical Engineering|completed=May 2024|thesis=CaltechTHESIS:06032024-141219249|url=http:www.linkedin.com/in/zoila-jurado-93005b83/}}<br /> {{PhD alum|Scott Kelly |url=http:www.coe.uncc.edu/~skelly52/ |thesis=CaltechETD:etd-08122005-152639}}<br /> {{PhD alum|Dmitriy Kogan# |url=http:www.linkedin.com/pub/1/446/a84 }}<br /> {{PhD alum|Javad Lavaei* |url=http:www.ee.columbia.edu/~lavaei |thesis=CaltechTHESIS:05132011-113642762}}<br /> {{PhD alum|Andrew Lewis |url=http:www.mast.queensu.ca/~andrew/ |thesis=CaltechETD:etd-07132006-143133}}<br /> {{PhD alum|[[http:scottman.net/ |Scott Livingston]] |option=CDS |completed=Dec 2015 |thesis=CaltechTHESIS:12312015-131513787}}<br /> {{PhD alum|[[http:jpmarken.github.io/|John Marken]] |option=BE|completed=May 2023|thesis=CaltechTHESIS:05292023-181810775}}<br /> {{PhD alum|Reed McCardell |option=BE |completed=May 2021 |thesis=CaltechTHESIS:05082021-185615529}}<br /> {{PhD alum|Robert M'Closkey | url=http:www.seas.ucla.edu/~mcloskey/ | thesis=CaltechETD:etd-10172007-104556}}<br /> {{PhD alum|Joseph Meyerowitz|option=BMB|completed=Dec 2022|thesis=CaltechTHESIS:12022022-073109279}}<br /> {{PhD alum|Mark Milam |url=http:www.cds.caltech.edu/~milam/ |thesis=CaltechETD:etd-06022003-114340}}<br /> {{PhD alum|Michiel van Nieuwstadt |thesis=CaltechETD:etd-01172008-085534}}<br /> {{PhD alum|Ayush Pandey |option=CDS |completed=Jun 2023 |thesis=CaltechTHESIS:06062023-021337351|url=http:ayush-pandey.github.io}}<br /> {{PhD alum|Ivan Papusha |option= |completed= |thesis=CaltechTHESIS:06032016-102336160}}<br /> {{PhD alum|James Parkin |option=BE |completed=Mar 2021 |thesis=CaltechTHESIS:03262021-160841703}}<br /> {{PhD alum|Tung Phan |thesis=CaltechTHESIS:01132021-065636010}}<br /> &lt;/table&gt;<br /> | width=33% | <br /> &lt;table&gt;<br /> {{PhD alum|William Poole |option=CNS |completed=Aug 2021 |thesis=CaltechTHESIS:11102021-210013472}}<br /> {{PhD alum|Muruhan Rathinam | url=http:www.math.umbc.edu/~muruhan/ | thesis=CaltechETD:etd-01152008-082733}}<br /> {{PhD alum|Xinying (Cindy) Ren |option=CDS |completed=Jun 2021 |thesis=CaltechTHESIS:05262021-072231177}}<br /> {{PhD alum|Clancy Rowley* |url=http:weblamp.princeton.edu/cwrowley/}}<br /> {{PhD alum|Ben Shapiro |url=http:www.glue.umd.edu/~benshap/ |thesis=CaltechETD:etd-02272008-083040}}<br /> {{PhD alum|Ling Shi |url=http:www.cds.caltech.edu/~shiling/ |thesis=CaltechETD:etd-08272008-121822}}<br /> {{PhD alum|Andrey Shur |option=BE |completed=Dec 2021 |thesis=CaltechTHESIS:12212021-193826426}}<br /> {{PhD alum|Vipul Singhal |thesis=CaltechTHESIS:08262018-213846283}}<br /> {{PhD alum|Demetri Spanos |url=http:www.cds.caltech.edu/~demetri |thesis=CaltechETD:etd-06262006-171822}}<br /> {{PhD alum|Zachary Sun |option= |completed= |thesis=CaltechTHESIS:10012015-221355676/}}<br /> {{PhD alum|Sudipto Sur | url=http:alumnus.caltech.edu/~sur/ |thesis=CaltechETD:etd-01172008-092801}}<br /> {{PhD alum|Anandh Swaminathan |thesis=CaltechTHESIS:12132017-121914940}}<br /> {{PhD alum|Anu Thubagere* |option= |completed= |thesis=CaltechTHESIS:06082017-194534497}}<br /> {{PhD alum|Amber Thweatt#}}<br /> {{PhD alum|Jorge Tierno*}}<br /> {{PhD alum|Abhishek Tiwari |url=http:www.cds.caltech.edu/~atiwari/ |thesis=CaltechETD:etd-05202007-135411}}<br /> {{PhD alum|Pete Trautman |option= |completed= |thesis=CaltechTHESIS:05182013-191132413}}<br /> {{PhD alum|Stephanie Tsuei#}}<br /> {{PhD alum|David van Gogh#}}<br /> {{PhD alum|Tony Vanelli# |thesis=CaltechETD:etd-01162008-152619}}<br /> {{PhD alum|Ophelia Venturelli |thesis=CaltechTHESIS:06072013-095239958}}<br /> {{PhD alum|Yong Wang |url=http:www.mech.pku.edu.cn/robot/teacher/wangyong/ |thesis=CaltechETD:etd-06282005-103901}}<br /> {{PhD alum|Steve Waydo* |url=http:www.cds.caltech.edu/~waydo |thesis=CaltechETD:etd-11022007-104734}}<br /> {{PhD alum|Rory Williams |option= |completed=Dec 2021 |thesis=CaltechTHESIS:01042022-184525578}}<br /> {{PhD alum|Eric Wolff |option=CDS |completed= |thesis=CaltechTHESIS:02172014-121159358}}<br /> {{PhD alum|Nok Wongpiromsarn |url=http:robotics.caltech.edu/~nok |thesis=CaltechTHESIS:05272010-153304667}}<br /> {{PhD alum|Yong Wu |option= |completed= |thesis=CaltechTHESIS:08302017-121452132}}<br /> {{PhD alum|Huan (Mumu) Xu |url=http:www.aero.umd.edu/~mumu |thesis=CaltechTHESIS:05312013-103940337}}<br /> {{PhD alum|Enoch Yeung |option=CDS |completed=Jan 2016 |thesis=CaltechTHESIS:05272016-145559554}}<br /> {{PhD alum|Simon Yeung |url=http:www.linkedin.com/pub/3/a32/258 |thesis=CaltechETD:etd-02272008-083453}}<br /> &lt;/table&gt;<br /> |}<br /> &lt;font size=&quot;-2&quot;&gt;# Masters or Engineers degree &amp;nbsp;&amp;nbsp; * Co-advised student&lt;/font&gt;<br /> &lt;/blockquote&gt;<br /> <br /> ==== Former postdocs: ====<br /> * Kazu Echigo (2025) - CMS Postdoctoral Fellow<br /> * [[http:yzhang952.github.io|Yan Zhang]] (2022-24) - Presidential Postdoctoral Fellow<br /> * Inigo Incer (2022-24) - CMS Postdoctoral Fellow<br /> * Chelsea Hu (2018-22) - BE Postdoctoral Fellow<br /> * Ersin Das (2021-22) - CMS Postdoctoral Fellow<br /> <br /> &lt;blockquote&gt;<br /> {| width=100% border=0 cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=33% | <br /> &lt;table&gt;<br /> {{Postdoc alum|Raktim Bhattacharya|years=2002-04}}<br /> &lt;tr&gt;&lt;td&gt;[http://www.niu.edu/faculty/coller.shtml Brianno Coller] (1995-97) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Noel du Toit (2011)&lt;/td&gt;&lt;/tr&gt;<br /> {{Postdoc alum|Chuchu Fan|years=2019-20|title=CMS Postdoctoral Fellow}}<br /> &lt;tr&gt;&lt;td&gt;Samira Farahani (2014-15) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;David Garcia (2020-21) &lt;/td&gt;&lt;/tr&gt;<br /> {{Postdoc alum|Jin Ge|years=2016-18|title=CMS Postdoctoral Fellow}}<br /> &lt;tr&gt;&lt;td&gt;Leopold Green (2018-21) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Sofie Haesaert (2016-18) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Yutaka Hori (2013-16) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.ece.louisville.edu/~t0inan01/ Tamer Inanc] (2002-04)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Jongmin Kim (2010-14)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;/table&gt;<br /> | width=33% | <br /> &lt;table&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://soslab.ee.washington.edu/mw/index.php/User:Klavins Eric Klavins]* (2001-03)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://cc.ee.ntu.edu.tw/~fengli/ Feng-Li Lian] (2001-02)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Jun Liu (2011-2012)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Michaelle Mayalu (2017-22) &lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Catherine McGhan (2014-16)&lt;/td&gt;&lt;/tr&gt;<br /> {{Postdoc alum|John McManus*|years=2018-19|title=Visiting Postdoctoral Fellow}}<br /> &lt;tr&gt;&lt;td&gt;Yilin Mo (2013-15)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.aa.washington.edu/faculty/morgansen/ Kristi Morgansen] (1999-2001)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www-sop.inria.fr/icare/personnel/morin/morin-personnel.html Pascal Morin] (1996-97)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.ece.ucsb.edu/~ymostofi/ Yasamin Mostofi] (2004-06)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Reza Olfati-Saber (2001-04)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.cds.caltech.edu/~izi/ Yizhar Or] (2007-09)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;/table&gt;<br /> | width=33% | <br /> &lt;table&gt;<br /> &lt;tr&gt;&lt;td&gt;Necmiye Ozay (2010-13)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Pavithra Prabhakar (2011-12)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://cas.ensmp.fr/~petit/ Nicolas Petit] (2001-02)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Vasu Raman (2013-15)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.ee.kth.se/php/index.php?action=people&amp;cmd=extended&amp;peopleid=768 Henrik Sandberg] (2005-07)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Shaunak Sen (2011-12)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://me.nmsu.edu/~shashi/ B. N. Shashikanth*] (1998-2000)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Dan Siegal (2012-15)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[[http:www.its.caltech.edu/~astraw/|Andrew Straw*]] (2010)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Willem Sluis (1994-96)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;[http://www.cds.caltech.edu/~herb/ Herbert Streumper] (1997-99)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;tr&gt;&lt;td&gt;Ufuk Topcu (2008-12)&lt;/td&gt;&lt;/tr&gt;<br /> &lt;/table&gt;<br /> |}<br /> &lt;/blockquote&gt;<br /> '''Additional group alumni:''' &amp;nbsp; [[SURF alumni|SURF]] &amp;nbsp;&amp;nbsp; [[Undergraduate alumni|Undergrads]] &amp;nbsp;&amp;nbsp; [[Visitors]]<br /> <br /> == Teaching ==<br /> The list below is the courses that I have taught at Caltech (or at least most of them). The course links will take you to the (current) course homepage, where you can find the syllabus, handouts, and homework sets. The links for specific terms take you to the course homepage for that term. Links to [[Teaching Archive|older courses]] are available on a separate page.<br /> <br /> &lt;!--<br /> * BE/APh 162 - Physical Biology Laboratory ([http://www.rpgroup.caltech.edu/courses/aph162/2009/ Wi09])<br /> --&gt;<br /> * [[ACM/EE 116]] - Probability and Random Processes ([[ACM/EE_116,_Fall_2011|Fa11]])<br /> * [[BE 107]] - Exploring Biological Principles Through Bio-Inspired Design ([[BE 107, Spring 2015|Sp15]], [[BE 107, Spring 2016|Sp16]], [[BE 107, Spring 2019|Sp19]])<br /> * [[BE 150/Bi 250b]] - Systems Biology ([[Bi/BE_250c_Winter_2011|Wi11]], [[BE_150/Bi_250b_Winter_2012|Wi12]], [[BE_150/Bi_250b_Winter_2013|Wi13]], [[BE 150/Bi 250 Spring 2014|Sp14]])<br /> * [[BE/EE/MedE 189a]] - Design and Construction of Biodevices ([[BE/EE/MedE 189a, Fall 2024|Fa24]])<br /> * [[Bi/BE/CS 183]] - Introduction to Computational Biology and Bioinformatics ([[Bi/BE/CS 183, Winter 2024|Wi24]])<br /> * [[CS/EE/ME 75]] - Introduction to Multi-Disciplinary Systems Engineering (04-05, 06-07, 10-11, [[CS/EE/ME 75, 2015-16|15-16]])<br /> * [[CDS 90]] - Senior Thesis in Control and Dynamical Systems (2004-2014, 2020-2024)<br /> * [[CDS 101|CDS 101/110]] - Analysis and Design of Feedback Systems (Fa97, Fa01, [[http:www.cds.caltech.edu/~murray/courses/cds101/fa02|Fa02]], [[http:www.cds.caltech.edu/~murray/courses/cds101/fa03/|Fa03]], [[http:www.cds.caltech.edu/~murray/courses/cds101/fa04/|Fa04]], [[CDS 101/110a, Fall 2006|Fa06]], [[CDS 101/110a, Fall 2007|Fa07]], [[CDS 101/110a, Fall 2008|Fa08]], [[CDS 101/110a, Fall 2012|Fa12]], [[CDS 101/110, Fall 2015|Fa15]], [[CDS 110/ChE 130, Spring 2024|Sp24]])<br /> * [[CDS 112]] - Optimization-Based Control (Wi98, Wi02, Wi03, Wi04, [[CDS 110b, Winter 2006|Wi06]], [[CDS 110b, Winter 2007|Wi07]], [[CDS 110b, Winter 2008|Wi08]], [[CDS 112/Ae 103a, Winter 2022|Wi22]], [[CDS 112/Ae 103b, Winter 2023|Wi23]])<br /> * [[CDS 131]] - Linear Systems Theory ([[CDS 131, Fall 2018|Fa18]], [[CDS 131, Fall 2019|Fa19]], [[CDS 131, Fall 2020|Fa20]])<br /> * [[CDS 140]] - Differential Equations and Dynamical Systems ([[AM 101b/AM 125b/CDS 140a, Winter 2011|Wi11]], [[AM 101b/AM 125b/CDS 140a, Winter 2013|Wi13]], [[ACM 101b/AM 125b/CDS 140a, Winter 2014|Wi14]], [[CDS 140, Winter 2015|Wi15]])<br /> * [[CDS 240]] - Nonlinear Dynamical Systems ([[CDS 140b, Spring 2014|Sp14]], [[CDS 240, Spring 2016|Sp16]])<br /> * [[CDS 202]] - Geometry of Nonlinear Systems (Wi93, Wi94, [[http:www.cds.caltech.edu/~murray/courses/cds202/wi04/|Wi04]], [[CDS 202, Winter 2009|Wi09]], [[CDS 202, Spring 2013|Sp13]])<br /> * [[http:www.cds.caltech.edu/cs142|CS 142]] - Distributed Computing ([[CS 142, Fall 2017|Fa17]], [[CS 142, Fall 2019|Fa19]])<br /> * CS 143 - Communication Networks ([http://courses.cms.caltech.edu/cs143/ Fa18])<br /> * [[CMS 273]] - Frontiers in Computing and Mathematical Sciences ([[CMS 273, Winter 2019|Wi19]], [[CMS 273, Winter 2020|Wi20]], [[CMS 273, Winter 2021|Wi21]])<br /> * [[E/SEC 103]] - Management of Technology ([[E/SEC 103, Spring 2020|Sp20]], [[E/SEC 103, Spring 2023|Sp23]], [[E/SEC 103, Winter 2024|Wi24]], [[E/SEC 103, Winter 2025|Wi25]])<br /> * [[Courses#Older_courses_(not_on_this_wiki)|Older courses]] (not taught in the last 15 years)<br /> * [[:Category:Guest lectures|Guest lectures]] - some individual lectures I have given in various courses<br /> <br /> == Contact ==<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ==== Mailing Address ====<br /> Richard M. Murray&lt;br&gt;<br /> Control and Dynamical Systems 107-81&lt;br&gt;<br /> California Institute of Technology&lt;br&gt;<br /> 1200 E. California Blvd&lt;br&gt;<br /> Pasadena, CA 91125 USA<br /> | width=50% |<br /> <br /> ==== Contact information ====<br /> E-mail: murray@cds.caltech.edu &lt;br&gt;<br /> Office: 109 Steele Lab, (626) 395-6460 &lt;br&gt;<br /> Asst: Nuvia Alvarez, x2464 &lt;br&gt;<br /> Labs: 108, 116, 136 Keck<br /> |- valign=bottom<br /> |<br /> <br /> ==== Other links ====<br /> [http://www.caltech.edu Caltech]&lt;br&gt;<br /> [http://www.eas.caltech.edu Engineering and Applied Science]&lt;br&gt;<br /> [http://cms.caltech.edu Computing and Mathematical Sciences]&lt;br&gt;<br /> |<br /> [http://be.caltech.edu/ Bioengineering]&lt;br&gt;<br /> [http://www.cds.caltech.edu Control and Dynamical Systems]&lt;br&gt;<br /> [http://www.linkedin.com/in/murrayrm LinkedIn]<br /> |}</div> Murray https://murray.cds.caltech.edu/index.php?title=E/SEC_103,_Winter_2025&diff=27226 E/SEC 103, Winter 2025 2026-02-11T18:11:42Z <p>Murray: </p> <hr /> <div>{{Course<br /> |Course number=E/SEC 103<br /> |Course title=Management of Technology<br /> |Year=2025<br /> |Term=Winter<br /> |Lecture schedule=Mon/Wed, 1:30-2:55 pm<br /> |Instructors=Richard Murray (CDS/BE), Stu Feldman, Eric Schmidt<br /> |Instructor office hours=Wed, 3-3:45 pm, Annenberg lounge<br /> |TAs=Madison Dunitz, Liz Hughes<br /> |TA office hours=Fri, 1-2:30 pm<br /> }}<br /> &lt;!--<br /> This course is limited enrollment and auditors are not allowed. All students interested in participating must fill out a pre-enrollment survey to be considered for the course. Names for students selected for the course will be given to the Registrar to be enrolled as long as there are no time conflicts. A waiting list will be available in case any spaces open up.<br /> <br /> &lt;font color='red' size='+1'&gt;[[http:forms.gle/9UQMtB1MWb1gU8nw6|'''PRE-ENROLLEMENT SURVEY''']]&lt;/font&gt; (required for registration)<br /> * Surveys returned by 19 Nov (Tue) at 11:59 pm will be evaluated for pre-registration<br /> * Surveys may be returned until 26 Nov (Tue) at 11:59 pm for consideration if slots are available<br /> * Students who are placed on the waiting list will be notified by email<br /> --&gt;<br /> <br /> === Catalog Description ===<br /> <br /> This course is intended for students interested in learning how rapidly evolving technologies are harnessed to produce useful products or fertile new areas for research. Students will work learn about how technology and innovation leaders identify and shape emerging technologies and how technology can be harnessed and scaled to create new products and services. There will be a term project where students predict the future evolution of an exciting technology and explore the potential implications of that technology. The course is team-based and designed for students considering choosing an exciting research area, working in companies (any size, including start-ups), or eventually going to business school. Topics include technology as a growth agent, financial fundamentals, integration into other business processes, product development pipeline and portfolio management, learning curves, risk assessment, technology trend methodologies (scenarios, projections), motivation, rewards and recognition. Industries considered will include electronics (hardware and software), aerospace, medical, biotech, etc. Students will perform both primary and secondary research and present defensible projections based on their technology research.<br /> <br /> === Learning Objectives ===<br /> * Teach students how to identify and analyze new technology areas/trends and explore the potential new applications of those technologies with potential for large impact<br /> * Provide students with access to technology leaders in different fields who can provide new insights, ideas on how to manage technology, and help build students’ networks<br /> * Identify new areas of research for potential investment by funding agencies and philanthropic organizations, with anticipated roadmap/path to impact<br /> <br /> === Lecture Schedule ===<br /> <br /> {| class=&quot;mw-collapsible wikitable&quot; width=100% border=1 cellpadding=5<br /> |-<br /> | '''Week'''<br /> | '''Date'''<br /> | '''Topic'''<br /> | '''Lecturer(s)'''<br /> <br /> |- valign=top<br /> | rowspan=3 | W1<br /> | 6 Jan (Mon)<br /> | Class organization, project frameworks<br /> * {{E/SEC 103 pdf|wi2025|caltech/L1-1_intro-06Jan2025.pdf|Mon lecture slides}} (Caltech only)<br /> | RM, ST<br /> |- valign=top<br /> | 8 Jan (Wed)<br /> | &lt;s&gt;ES talk, veteran presentation&lt;/s&gt; [Class cancelled]<br /> | ES, SF, RM, ST<br /> |- valign=top<br /> | 10 Jan (Fri)<br /> | Project pitch workshop (1-2:30 pm, 213 ANB)<br /> | TAs<br /> <br /> |- valign=top<br /> | rowspan=2 | W2<br /> | 13 Jan (Mon)<br /> | Project pitches + What is Technology ([[http:link.springer.com/book/10.1007/978-3-030-88346-1|De Weck]], Ch 1)<br /> * Pitches: 1 slide, 2 min each (+ 2-3 min Q&amp;A)<br /> * {{E/SEC 103 pdf|wi2025|caltech/L2-1_technology-13Jan2025.pdf|Mon lecture slides}} (Caltech only)<br /> | MK, ST, RM<br /> <br /> |- valign=top<br /> | 15 Jan (Wed)<br /> | ES talk, veteran presentation [Rescheduled]<br /> * [[http:www.theatlantic.com/ideas/archive/2024/11/ai-genesis-excerpt-kissinger-schmidt-mundie/680619/|Genesis: Artificial Intelligence, Hope, and the Human Spirit]] (excerpt)<br /> * {{E/SEC 103 pdf|wi2025|caltech/L2-2_projects-15Jan2025.pdf|Wed lecture slides}}<br /> | ES, ST<br /> <br /> |- valign=top<br /> | rowspan=2 | W3<br /> | 20 Jan (Mon)<br /> | No class (Martin Luther King Day)<br /> | <br /> <br /> |- valign=top<br /> | 22 Jan (Wed)<br /> | Quantifying Technological Progress ([[#de_weck|De Weck]], Ch 4); Scaling Laws (ES notes), Zero to One [[#thiel|Thiel]], Ch 1-6 [skim]<br /> * {{E/SEC 103 pdf|wi2025|caltech/schmidt_scaling-feb2023.pdf|Scaling Laws paper}} (Caltech only)<br /> * {{E/SEC 103 pdf|wi2025|caltech/L3-2_metrics-22Jan2025.pdf|Wed lecture slides}} (Caltech only)<br /> &lt;!-- Technological Diffusion and Disruption ([[#de_weck|De Weck]], Ch 7; [[#thiel|Thiel]], Ch 1-6) --&gt;<br /> | RM<br /> <br /> |- valign=top<br /> | rowspan=2 | W4<br /> | 27 Jan (Mon)<br /> | Best practices for carrying out interviews ([[#fitzpatrick|Fitzpatrick]], Ch 3 and 8); Market Analysis ([[#de_weck|De Weck]], Ch 7))<br /> * {{E/SEC 103 pdf|wi2025|caltech//L4-1_interviews-27Jan2025.pdf|Mon lecture slides}} (Caltech only)<br /> | MD<br /> <br /> |- valign=top<br /> | 29 Jan (Wed)<br /> | [[http:en.wikipedia.org/wiki/Fermi_problem|Fermi Problems]]; project updates<br /> * {{E/SEC 103 pdf|wi2025|caltech/L4-2_fermi-29Jan2025.pdf|Wed lecture slides}} (Caltech only)<br /> | SF<br /> <br /> |- valign=top<br /> | rowspan=3 | W5<br /> | 3 Feb (Mon)<br /> | Techno-Economic Analysis; Systems Modeling and Technology Sensitivity Analysis ([[#de_weck|De Weck]], Ch 11)<br /> * Department of Energy Videos (or PDFs)<br /> ** [https://www.energy.gov/eere/iedo/life-cycle-assessment-and-techno-economic-analysis-training#TEA Introduction to Techno-Economic Analysis (TEA)]<br /> ** [https://www.energy.gov/eere/iedo/life-cycle-assessment-and-techno-economic-analysis-training#emc Estimating Manufacturing Costs for Pre-Commercial Technologies]<br /> ** Optional: [https://www.energy.gov/eere/iedo/life-cycle-assessment-and-techno-economic-analysis-training#functionalunit Defining Functional Units for Life Cycle Analysis (LCA) and TEA]<br /> ** Optional: [https://www.energy.gov/eere/iedo/life-cycle-assessment-and-techno-economic-analysis-training#techbenchmarking Technology Benchmarking for Comparative LCA and TEA]<br /> * {{E/SEC 103 pdf|wi2025|caltech/L5-1_sensitivity_TEA-03Feb2025.pdf|Mon lecture slides}} (Caltech only)<br /> | LH<br /> <br /> |- valign=top<br /> | 5 Feb (Wed)<br /> | Patents and Intellectual Property ([[#de_weck|De Weck]], Ch 5)<br /> * {{E/SEC 103 pdf|wi2025|caltech/L5-2_ip-05Feb2025.pdf|Wed lecture slides}} (Caltech only)<br /> | RM<br /> |- valign=top<br /> | 7 Feb (Fri)<br /> | Practice presentations (15 min + feedback; times TBD)<br /> | TAs<br /> |- valign=top<br /> | rowspan=2 | W6<br /> | 10 Feb (Mon)<br /> | Midterm presentations (1:30-3:30 pm)<br /> | SF, RM, ES*<br /> <br /> |- valign=top<br /> | 12 Feb (Wed)<br /> | Regulations + Midterm feedback<br /> * [https://regulatorystudies.columbian.gwu.edu/sites/g/files/zaxdzs4751/files/downloads/GW%20Reg%20Studies%20-%20Regulation%20A%20Primer%20-%20SDudley%20%26%20JBrito.pdf ''Regulation: A Primer''], Dudley and Brito, 2012. Chapters 1-3, 7 (skim).<br /> * {{E/SEC 103 pdf|wi2025|caltech/L6-2_regulations-12Feb2025.pdf|Wed lecture slides}} (Caltech only)<br /> &lt;!-- * {{E/SEC 103 pdf|wi2025|caltech/L6-2_midterm_feedback-12Feb2025_r.pdf|Wed lecture slides}} (Caltech only) --&gt;<br /> | RM<br /> <br /> |- valign=top<br /> | rowspan=2 | W7<br /> | 17 Feb (Mon)<br /> | No class (Presidents Day)<br /> | <br /> <br /> |- valign=top<br /> | 19 Feb (Wed)<br /> | External speaker (BG)<br /> &lt;!-- * {{E/SEC 103 pdf|wi2024|caltech/L10-1_gross-04Mar2024.pdf|Mon lecture slides}} (Caltech only) --&gt;<br /> | RM<br /> <br /> |- valign=top<br /> | rowspan=2 | W8<br /> | 24 Feb* (Mon)<br /> | External speaker (YY, CF)<br /> * {{E/SEC 103 pdf|wi2025|caltech/L8-1_yue_yisong-24Feb2025.pdf|YY slides}} (Caltech only)<br /> | TAs<br /> <br /> |- valign=top<br /> | 26&amp;nbsp;Feb*&amp;nbsp;(Wed)<br /> | No class<br /> | <br /> <br /> |- valign=top<br /> | rowspan=3 | W9<br /> | 3 Mar (Mon)<br /> | Project presentations to instructors (for feedback)<br /> | RM, ST<br /> <br /> |- valign=top<br /> | 5 Mar (Wed)<br /> | External Speaker (JS)<br /> * {{E/SEC 103 pdf|wi2025|caltech/L9-2_final_info-05Mar2025.pdf|Wed lecture slides}} (Caltech only)<br /> * {{E/SEC 103 pdf|wi2025|caltech/L9-2_schoenfeld_julie-05Mar2025.pdf|JS slides}} (Caltech only)<br /> | RM<br /> <br /> |- valign=top<br /> | 7 Mar (Fri)<br /> | Practice presentations (15 min + feedback; times TBD)<br /> | TAs<br /> <br /> |- valign=top<br /> | rowspan=2 | W10<br /> | 10 Mar (Mon)<br /> | No class (optional meetings with TAs)<br /> | TAs<br /> <br /> |- valign=top<br /> | 12 Mar (Wed)<br /> | Final presentations (1:30-3:30 pm)<br /> | SF, RM, ES<br /> <br /> |- valign=top<br /> | Finals<br /> | 19&amp;nbsp;Mar&amp;nbsp;(Wed)<br /> | Final report due<br /> | <br /> |}<br /> <br /> === Grading ===<br /> * 20% - Class participation: Based on participation in class, online, and team discussions<br /> * 20% - Midterm presentation: Team-based score content + presentation; individual score based 1-page write up<br /> * 30% - Final presentation: Team-based score content + presentation<br /> * 30% - Final writeup: Team-based report + 2-page individual writeup on your contributions + summary of contributions from teammates<br /> <br /> === Collaboration Policy ===<br /> <br /> This is a team-based class. Full collaboration is allowed and students are encouraged to discuss course materials, homework assignments, and projects with anyone that they choose. Course homework assignments are designed to be done as a group, but reports should reflect your individual understanding of the topic and/or your team's joint efforts, as appropriate.<br /> <br /> === Course Text and References ===<br /> <br /> # &lt;span id=&quot;de_weck&quot;&gt;&lt;b&gt;[De Weck]&lt;/b&gt;&lt;/span&gt; Olivier L. De Weck, Technology Roadmapping and Development: A Quantitative Approach to the Management of Technology. 1st edition, Springer, 2022. Available via [[http:link.springer.com/book/10.1007/978-3-030-88346-1|Springer Link]] (free Caltech download)<br /> # &lt;span id=&quot;fitzpatrick&quot;&gt;&lt;b&gt;[Fitzpatrick]&lt;/b&gt;&lt;/span&gt; Rob Fitzpatrick, The Mom Test: How to Talk to Customers and Learn if Your Business Is a Good Idea When Everyone Is Lying to You, https://www.momtestbook.com, 2013.<br /> # &lt;span id=&quot;thiel&quot;&gt;&lt;b&gt;[Thiel]&lt;/b&gt;&lt;/span&gt; Peter Thiel, Zero to One: Notes on Startups, or How to Build the Future. Crown Currency, 2014. Available from [[http:books.apple.com/us/book/zero-toone/id795977428|Apple]], [[http:www.amazon.com/Zero-One-Notes-Startups-Future/dp/0804139296|Amazon]], and other sellers.<br /> <br /> [[Category: Courses]]</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27225 Mengdi Wang, 11-12 Feb 2026 2026-02-11T14:21:30Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open (Annenberg 244)<br /> * 9:30 am: Yang Liu (Annenberg Treehouse lounge)<br /> * 10:00 am: Sam Looi (Annenberg Treehouse lounge)<br /> * 11:00 am: Chengrui Qu (Annenberg Treehouse lounge)<br /> * 11:30 am: Jiachen Yao (Annenberg Treehouse lounge)<br /> * 12:00 pm: Lunch with students (Ath, 5 + Mengdi): Chengrui Qu, Robert Joseph, Jiachen Yao, Xi Deng, Xinyi Li<br /> * 1:30 pm: Robert Joseph (meet at Ath, take to Aaron Ames when done)<br /> * 2:00 pm: Aaron Ames (Richard to pick up at ~2:45)<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Eric Mazumdar (Zoom)<br /> * 9:45 am: Soon-Jo Chung (235 Guggenheim)<br /> * 10:30 am: Jason Yang (will pick you up in Guggenheim and drop off with Georgia)<br /> * 11:15 am: Georgia Gkioxari<br /> * 12:00 pm: Lunch with Yisong Yue group (Yuan Sui coordinating; take to Chen when done)<br /> * 1:30 pm: Pietro Perona, Chen 3rd floor<br /> * 2:15 pm: Yisong Yue, ANB 3rd floor<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27224 Mengdi Wang, 11-12 Feb 2026 2026-02-11T02:27:19Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open (Annenberg 244)<br /> * 9:30 am: Yang Liu (Annenberg Treehouse lounge)<br /> * 10:00 am: Sam Looi (Annenberg Treehouse lounge)<br /> * 11:00 am: Chengrui Qu (Annenberg Treehouse lounge)<br /> * 11:30 am: Jiachen Yao (Annenberg Treehouse lounge)<br /> * 12:00 pm: Lunch with students (Ath, 5 + Mengdi): Chengrui Qu, Robert Joseph, Jiachen Yao, Open4, Open5<br /> * 1:30 pm: Robert Joseph (meet at Ath, take to Aaron Ames when done)<br /> * 2:00 pm: Aaron Ames (Richard to pick up at ~2:45)<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Eric Mazumdar (Zoom)<br /> * 9:45 am: Soon-Jo Chung (235 Guggenheim)<br /> * 10:30 am: Jason Yang (will pick you up in Guggenheim and drop off with Georgia)<br /> * 11:15 am: Georgia Gkioxari<br /> * 12:00 pm: Lunch with Yisong Yue group (Yuan Sui coordinating; take to Chen when done)<br /> * 1:30 pm: Pietro Perona, Chen 3rd floor<br /> * 2:15 pm: Yisong Yue, ANB 3rd floor<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27218 Mengdi Wang, 11-12 Feb 2026 2026-02-08T14:35:05Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open (Annenberg Treehouse lounge)<br /> * 9:30 am: Open (Annenberg Treehouse lounge)<br /> * 10:00 am: Open (Annenberg Treehouse lounge)<br /> * 11:00 am: Open (Annenberg Treehouse lounge)<br /> * 11:30 am: Jiachen Yao (Annenberg Treehouse lounge)<br /> * 12:00 pm: Lunch with students (Ath, 5 + Mengdi): Open1, Open2, Open3, Open4, Open5<br /> * 1:30 pm: Open (meet at Ath, take to Aaron Ames when done)<br /> * 2:00 pm: Aaron Ames (Richard to pick up at ~2:45)<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Eric Mazumdar (Zoom)<br /> * 9:45 am: Soon-Jo Chung (235 Guggenheim)<br /> * 10:30 am: Jason Yang (will pick you up in Guggenheim and drop off with Georgia)<br /> * 11:15 am: Georgia Gkioxari<br /> * 12:00 pm: Lunch with Yisong Yue group (Yuan Sui coordinating; take to Chen when done)<br /> * 1:30 pm: Pietro Perona, Chen 3rd floor<br /> * 2:15 pm: Yisong Yue, ANB 3rd floor<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27217 Mengdi Wang, 11-12 Feb 2026 2026-02-08T14:29:20Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open (Annenberg Treehouse lounge)<br /> * 9:30 am: Open (Annenberg Treehouse lounge)<br /> * 10:00 am: Open (Annenberg Treehouse lounge)<br /> * 11:00 am: Open (Annenberg Treehouse lounge)<br /> * 11:30 am: Jiachen Yao (Annenberg Treehouse lounge)<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:30 pm: Open (meet at Ath, take to Aaron Ames when done)<br /> * 2:00 pm: Aaron Ames (Richard to pick up at ~2:45)<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Eric Mazumdar (Zoom)<br /> * 9:45 am: Soon-Jo Chung (235 Guggenheim)<br /> * 10:30 am: Jason Yang (will pick you up in Guggenheim and drop off with Georgia)<br /> * 11:15 am: Georgia Gkioxari<br /> * 12:00 pm: Lunch with Yisong Yue group (Yuan Sui coordinating; take to Chen when done)<br /> * 1:30 pm: Pietro Perona, Chen 3rd floor<br /> * 2:15 pm: Yisong Yue, ANB 3rd floor<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27216 Mengdi Wang, 11-12 Feb 2026 2026-02-07T02:29:07Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Jiachen Yao<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Aaron Ames<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Eric Mazumdar (Zoom)<br /> * 9:45 am: Soon-Jo Chung (235 Guggenheim)<br /> * 10:30 am: Yuan Sui (will pick you up in Guggenheim)<br /> * 11:15 am: Georgia Gkioxari<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27211 Mengdi Wang, 11-12 Feb 2026 2026-02-05T19:29:30Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Jiachen Yao<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Aaron Ames<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Eric Mazumdar (Zoom)<br /> * 9:45 am: Soon-Jo Chung (235 Guggenheim)<br /> * 10:30 am: Yuan Sui (will pick you up in Guggenheim)<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27210 Mengdi Wang, 11-12 Feb 2026 2026-02-05T02:56:44Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Jiachen Yao<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Open<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Eric Mazumdar (Zoom)<br /> * 9:45 am: Soon-Jo Chung (235 Guggenheim)<br /> * 10:30 am: Yuan Sui (will pick you up in Guggenheim)<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27207 Mengdi Wang, 11-12 Feb 2026 2026-02-04T23:12:28Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Open<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Eric Mazumdar (Zoom)<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27206 Mengdi Wang, 11-12 Feb 2026 2026-02-04T03:30:10Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Open<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: Richard Murray, 109 Steele Lab (will pick up in Yisong's office)<br /> * 3:45 pm: Done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27205 Mengdi Wang, 11-12 Feb 2026 2026-02-04T03:23:42Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Open<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: done for the day<br /> <br /> &lt;hr&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;br&gt;<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;br&gt;<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27204 Mengdi Wang, 11-12 Feb 2026 2026-02-04T03:23:10Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Open<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: done for the day<br /> <br /> &lt;nowiki&gt;&lt;hr&gt;&lt;/nowiki&gt;<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang&lt;nowiki&gt;&lt;br&gt;&lt;/nowiki&gt;Princeton University<br /> <br /> 11 February (Wed), 3-4 pm&lt;nowiki&gt;&lt;br&gt;&lt;/nowiki&gt;213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27203 Mengdi Wang, 11-12 Feb 2026 2026-02-04T03:22:25Z <p>Murray: </p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> '''Wednesday, 11 Feb:'''<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Open<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> '''Thursday, 12 Feb:'''<br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: done for the day<br /> <br /> Seminar:<br /> <br /> '''From Genome to Theorem—and Back to the Lab: Can AI Co-Scientists Do Science?'''<br /> <br /> Professor Mengdi Wang<br /> Princeton University<br /> <br /> 11 February (Wed), 3-4 pm<br /> 213 Annenberg<br /> <br /> Large Language Models (LLMs) are increasingly used for scientific reasoning across mathematics, genomics, biology, and physics. This talk discusses recent advances in AI for science—including reasoning for math, physics and emerging science agents—while critically examining their limitations such as overestimated reasoning abilities. I then introduce LabOS, an AI-XR co-scientist that bridges computation and physical science by combining multimodal AI agents, extended-reality interfaces, and laboratory automation. By enabling AI systems to see experimental context, collaborate with humans, and assist in real-time execution, LabOS points toward a future where AI moves beyond analysis to active participation in scientific discovery.<br /> <br /> Mengdi Wang is an Associate professor at the Department of Electrical and Computer Engineering and Center for Statistics and Machine Learning at Princeton University. Mengdi received her PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology in 2013, where she was affiliated with the Laboratory for Information and Decision Systems. Mengdi received the Young Researcher Prize in Continuous Optimization of the Mathematical Optimization Society in 2016, an MIT Tech Review 35-Under-35 Innovation Award (China region) in 2018, and the American Automatic Control Council Donald P. Eckman Award in 2024.</div> Murray https://murray.cds.caltech.edu/index.php?title=Mengdi_Wang,_11-12_Feb_2026&diff=27202 Mengdi Wang, 11-12 Feb 2026 2026-02-04T03:21:11Z <p>Murray: Created page with &quot;Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her: Wednesday, 11 Feb: * 7:45 am: Richard Murray, Ath * 9:00 am: Open * 9:45 am: Open * 10:30 am: Open * 11:15 am: Open * 12:00 pm: Lunch with students (Ath) * 1:15 pm: Open * 2:00 pm: Open * 2:45 pm: Seminar setup * 3:00 pm: CDS tea * 3:30 pm: Seminar * 5:00 pm: Done for the day Thursday, 12 Feb: * 9:00 am: Open * 9:45 am: Open * 10:30 am: Open * 11:15 am: O...&quot;</p> <hr /> <div>Mengdi Wang from Princeton University will visit Caltech on 11-12 Feb 2026. Please sign up here to meet with her:<br /> <br /> Wednesday, 11 Feb:<br /> * 7:45 am: Richard Murray, Ath <br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with students (Ath)<br /> * 1:15 pm: Open<br /> * 2:00 pm: Open<br /> * 2:45 pm: Seminar setup<br /> * 3:00 pm: CDS tea<br /> * 3:30 pm: Seminar<br /> * 5:00 pm: Done for the day<br /> <br /> Thursday, 12 Feb:<br /> * 9:00 am: Open<br /> * 9:45 am: Open<br /> * 10:30 am: Open<br /> * 11:15 am: Open<br /> * 12:00 pm: Lunch with postdocs (S. Lake) <br /> * 1:30 pm: Pietro Perona, Chen<br /> * 2:15 pm: Yisong Yue, ANB<br /> * 3:00 pm: done for the day</div> Murray https://murray.cds.caltech.edu/index.php?title=Control_of_Functional_Bioenabled_Materials_using_Synthetic_Cells&diff=27198 Control of Functional Bioenabled Materials using Synthetic Cells 2026-01-11T16:31:03Z <p>Murray: </p> <hr /> <div>The goal of this project is to develop new approaches to design, implement, and control of functional bioenabled materials using synthetic cells. We will build on advances in synthetic biology and molecular sciences that have substantially advanced our ability to produce genetically-programmed synthetic cells from molecular components. These efforts provide techniques for the bottom-up construction of cell-like systems that can provide scientists with new insights into how natural cells work and harness the power of biology to create nanoscale, biomolecular materials.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Past participants:<br /> {{project past participants}}<br /> |<br /> Collaborators:<br /> {{project collaborators}}<br /> <br /> |}<br /> <br /> === Objectives ===<br /> [[Image:icb-synbiofilm.png|right|500px]]<br /> The long-term objective of this project is to understand the state-of-the-art and evaluate the possibility of using externally stimulated, biological circuits to control the functionality of bioenabled materials.<br /> Specific objectives for the first two years of the project are to:<br /> * Identify and develop one or more different technical approaches that allow control of functional biomaterials using synthetic cells via changes in the external environment (chemical, electrical, or mechanical).<br /> * Demonstrate the viability of these approaches through the creation of small material samples for experimental testing and characterization.<br /> * Evaluate the overall feasibility of the proposed techniques for Army-relevant applications and identify future activities to overcome the primary technical hurdles that are identified.<br /> Additional objectives for a third year of optional funding are to:<br /> * Further experimental testing and characterization to determine what approaches are more practical to lead towards innovative material properties.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> {{Project<br /> |Title=Control of Functional Bioenabled Materials using Synthetic Cells<br /> |Agency=ARO/ICB<br /> |Grant number=W911NF-19-D-90001<br /> |Start date=1 Aug 2023<br /> |End date=31 Jul 2025<br /> |Support summary=2 graduate students<br /> |Reporting requirements=Annual reports<br /> |Project ID=ICB Synthetic Biofilms<br /> |ack=This research is supported by the Institute for Collaborative Biotechnologies through contract W911NF-19-D-90001 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=RMM_research_meetings,_Jan_2026&diff=27184 RMM research meetings, Jan 2026 2025-12-31T16:11:08Z <p>Murray: Created page with &quot;Please sign up for a slot below on both Mon and Tue (we&#039;ll meet on Mon unless I get called in for jury duty): 12 Jan (Mon): * 9:00 am: Open * 11:00 am: Open * 1:00 pm: Open * 2:00 pm: Open * 3:00 pm: Open * 4:00 pm: Open&quot;</p> <hr /> <div>Please sign up for a slot below on both Mon and Tue (we'll meet on Mon unless I get called in for jury duty):<br /> <br /> 12 Jan (Mon):<br /> * 9:00 am: Open<br /> * 11:00 am: Open<br /> * 1:00 pm: Open<br /> * 2:00 pm: Open<br /> * 3:00 pm: Open<br /> * 4:00 pm: Open</div> Murray https://murray.cds.caltech.edu/index.php?title=Actuation_of_Synthetic_Cells_Via_Proto-Flagellar_Motors&diff=27183 Actuation of Synthetic Cells Via Proto-Flagellar Motors 2025-12-07T06:25:55Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This project focuses on the development of functioning molecular motors for micron-scale synthetic cells, demonstrating mechanisms for motility in (synthetic) cellular systems. Recent advances in the fields of synthetic biology and molecular sciences have substantially advanced the ability to produce genetically-programmed synthetic cells and multicellular machines from molecular components. These efforts provide techniques for the bottom-up construction of cell-like systems that can provide scientists with new insights into how natural cells work, harness the power of biology to create nanoscale, biomolecular machines, and provide an exciting pathway for exploration of the Rules of Life. This project considers the &quot;actuation&quot; subsystem of a synthetic cell, with the goal of allowing expression of membrane-integrated actuation complexes that can serve as a starting point to modulate the motility of the cell. The project engages undergraduate students from the Summer Undergraduate Research Fellowship (SURF) program at California Institute of Technology and establishes collaborations between the US Build-A-Cell consortium and Imperial College, London, that includes personnel exchanges to build stronger international ties.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> | Collaborators:<br /> * Yuval Elani (Imperial College)<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:cellsys-actuation.png|right|400px]]<br /> Our work is split into 4 high-level objectives:<br /> # Construct vesicle systems capable of reconstituting functioning proto-flagella for motility of synthetic cells;<br /> # Controllably engineer new vesicle systems capable of integrating protein complexes expressed in a transcription-translation system into lipid bilayer systems;<br /> # Demonstrate control over motility using the technology from (i) and (ii) to provide internal expression of the actuation complexes and their inducible regulators;<br /> # Provide opportunities for participation in synthetic cell collaboration networks (such as Build- A-Cell), undergraduate research projects, and international collaborations as integrated parts of the research activities.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=Actuation of Synthetic Cells Via Proto-Flagellar Motors<br /> |Agency=NSF<br /> |Grant number=MCB-2039277<br /> |Start date=15 Aug 2020<br /> |End date=31 Jul 2022<br /> |Support summary=1 graduate student, 1 undergraduate<br /> |Reporting requirements=Annual reports<br /> |Project ID=NSF EAGER<br /> |ack=Research supported by the National Science Foundation award number 2039277.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=An_Open_Synthetic_Biology_Toolkit_for_Engineering_Reliable_Genetic_Circuits_in_Microbes_in_Soil&diff=27182 An Open Synthetic Biology Toolkit for Engineering Reliable Genetic Circuits in Microbes in Soil 2025-12-07T06:25:31Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This goal of this project is to demonstrate the feasibility of an “open source” toolkit for soil synthetic biology, with the goal of bootstrapping a larger effort that would enable the use of engineered microbes to understand and modulate the complex dynamics of the rhizosphere. We will identify and characterize genetically tractable microbes capable of long-term persistence; create a toolbox of genetic parts for gene circuits and pathways in soil conditions; and design, build, and test a stimulus-response circuit operating in soil. Long-term applications include engineering microbial communities to optimize nutrient uptake and improve survival against environmental hazards such as drought, toxins, or pathogens.<br /> <br /> {| cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> | Collaborators:<br /> * Carnegie Institution for Science, Department of Plant Biology<br /> * Army Corps of Engineers, Cold Region Research and Engineering Laboratory<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:RSI-soil_syn_bio.png|right|400px]]<br /> The extensive progress that synthetic biology has made in the past 20 years on engineering microbes to perform complex tasks such as logical computation, non-native metabolic pathways, and autonomous control functions makes the field well-poised to address the sustainability challenges facing our society today, e.g. by increasing crop yield by providing plants with the ability to dynamically respond to conditions like drought or disease. However, soil synthetic biology presents a unique set of challenges that have yet to be addressed substantially by the field. An engineered microbial system must be able to persist and maintain its function within a predictable range in the soil over months- or even years-long timescales. As the developments in synthetic biology have thus far been implemented primarily in E. coli cells in exponential-phase growth in laboratory conditions, it is unlikely that they can be directly applied in situ to a soil-based application.<br /> Our project will address this need for a well-characterized toolkit of strains and genetic parts with which to build biological circuits that can function reliably in long-term soil environments. Our specific objectives are to:<br /> * Identify &amp; characterize genetically-tractable microbes capable of long-term soil persistence<br /> * Create a toolbox of genetic parts for building gene circuits for long-term soil deployment<br /> * Design, build, and test a stimulus-response circuit with predictable function in soil<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=An open synthetic biology toolkit for engineering reliable genetic circuits in microbes in soil<br /> |Agency=Resnick Sustainability Institute<br /> |Grant number=N/A<br /> |Start date=1 Jul 2020<br /> |End date=30 Jun 2022<br /> |Support summary=1 graduate student for 1 year<br /> |Reporting requirements=Biannual progress reports<br /> |Project ID=RSI Soil Syn Bio<br /> |ack=This work was supported by the Resnick Sustainability Institute.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=An_Open_Synthetic_Biology_Toolkit_for_Engineering_Reliable_Genetic_Circuits_in_Microbes_in_Soil&diff=27181 An Open Synthetic Biology Toolkit for Engineering Reliable Genetic Circuits in Microbes in Soil 2025-12-07T06:25:16Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This goal of this project is to demonstrate the feasibility of an “open source” toolkit for soil synthetic biology, with the goal of bootstrapping a larger effort that would enable the use of engineered microbes to understand and modulate the complex dynamics of the rhizosphere. We will identify and characterize genetically tractable microbes capable of long-term persistence; create a toolbox of genetic parts for gene circuits and pathways in soil conditions; and design, build, and test a stimulus-response circuit operating in soil. Long-term applications include engineering microbial communities to optimize nutrient uptake and improve survival against environmental hazards such as drought, toxins, or pathogens.<br /> <br /> {| cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> |<br /> Collaborators:<br /> * Carnegie Institution for Science, Department of Plant Biology<br /> * Army Corps of Engineers, Cold Region Research and Engineering Laboratory<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:RSI-soil_syn_bio.png|right|400px]]<br /> The extensive progress that synthetic biology has made in the past 20 years on engineering microbes to perform complex tasks such as logical computation, non-native metabolic pathways, and autonomous control functions makes the field well-poised to address the sustainability challenges facing our society today, e.g. by increasing crop yield by providing plants with the ability to dynamically respond to conditions like drought or disease. However, soil synthetic biology presents a unique set of challenges that have yet to be addressed substantially by the field. An engineered microbial system must be able to persist and maintain its function within a predictable range in the soil over months- or even years-long timescales. As the developments in synthetic biology have thus far been implemented primarily in E. coli cells in exponential-phase growth in laboratory conditions, it is unlikely that they can be directly applied in situ to a soil-based application.<br /> Our project will address this need for a well-characterized toolkit of strains and genetic parts with which to build biological circuits that can function reliably in long-term soil environments. Our specific objectives are to:<br /> * Identify &amp; characterize genetically-tractable microbes capable of long-term soil persistence<br /> * Create a toolbox of genetic parts for building gene circuits for long-term soil deployment<br /> * Design, build, and test a stimulus-response circuit with predictable function in soil<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=An open synthetic biology toolkit for engineering reliable genetic circuits in microbes in soil<br /> |Agency=Resnick Sustainability Institute<br /> |Grant number=N/A<br /> |Start date=1 Jul 2020<br /> |End date=30 Jun 2022<br /> |Support summary=1 graduate student for 1 year<br /> |Reporting requirements=Biannual progress reports<br /> |Project ID=RSI Soil Syn Bio<br /> |ack=This work was supported by the Resnick Sustainability Institute.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=An_Open_Synthetic_Biology_Toolkit_for_Engineering_Reliable_Genetic_Circuits_in_Microbes_in_Soil&diff=27180 An Open Synthetic Biology Toolkit for Engineering Reliable Genetic Circuits in Microbes in Soil 2025-12-07T06:25:06Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This goal of this project is to demonstrate the feasibility of an “open source” toolkit for soil synthetic biology, with the goal of bootstrapping a larger effort that would enable the use of engineered microbes to understand and modulate the complex dynamics of the rhizosphere. We will identify and characterize genetically tractable microbes capable of long-term persistence; create a toolbox of genetic parts for gene circuits and pathways in soil conditions; and design, build, and test a stimulus-response circuit operating in soil. Long-term applications include engineering microbial communities to optimize nutrient uptake and improve survival against environmental hazards such as drought, toxins, or pathogens.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> |<br /> Collaborators:<br /> * Carnegie Institution for Science, Department of Plant Biology<br /> * Army Corps of Engineers, Cold Region Research and Engineering Laboratory<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:RSI-soil_syn_bio.png|right|400px]]<br /> The extensive progress that synthetic biology has made in the past 20 years on engineering microbes to perform complex tasks such as logical computation, non-native metabolic pathways, and autonomous control functions makes the field well-poised to address the sustainability challenges facing our society today, e.g. by increasing crop yield by providing plants with the ability to dynamically respond to conditions like drought or disease. However, soil synthetic biology presents a unique set of challenges that have yet to be addressed substantially by the field. An engineered microbial system must be able to persist and maintain its function within a predictable range in the soil over months- or even years-long timescales. As the developments in synthetic biology have thus far been implemented primarily in E. coli cells in exponential-phase growth in laboratory conditions, it is unlikely that they can be directly applied in situ to a soil-based application.<br /> Our project will address this need for a well-characterized toolkit of strains and genetic parts with which to build biological circuits that can function reliably in long-term soil environments. Our specific objectives are to:<br /> * Identify &amp; characterize genetically-tractable microbes capable of long-term soil persistence<br /> * Create a toolbox of genetic parts for building gene circuits for long-term soil deployment<br /> * Design, build, and test a stimulus-response circuit with predictable function in soil<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=An open synthetic biology toolkit for engineering reliable genetic circuits in microbes in soil<br /> |Agency=Resnick Sustainability Institute<br /> |Grant number=N/A<br /> |Start date=1 Jul 2020<br /> |End date=30 Jun 2022<br /> |Support summary=1 graduate student for 1 year<br /> |Reporting requirements=Biannual progress reports<br /> |Project ID=RSI Soil Syn Bio<br /> |ack=This work was supported by the Resnick Sustainability Institute.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Assurance_for_Learning_Enabled_Systems&diff=27179 Assurance for Learning Enabled Systems 2025-12-07T06:24:44Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This project will extend previous work in automatic synthesis methods for planning and model-predictive control to address<br /> (1) real-time synthesis through efficient and incremental constraint-solving, and (2) risk-awareness by explicitly modeling uncertainty in perception and dynamics modeling. ALES includes a risk-aware planning and real-time synthesis engine to generate plans, protocols and control that are correct-by-construction. We plan to use a special class of stochastic predicates called chance constraints to express confidence in the learned component or its individual outputs. We specify the semantics of the temporal evolution of this logical model based on an underlying learning algorithm. <br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> * Yuxiao Chen (postdoc)<br /> | Collaborators:<br /> * Susmit Jha (SRI)<br /> * Chuchu Fan (MIT)<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:assured-autonomy.png|right|400px]]<br /> SRI and Caltech shall develop algorithms for correct-by-construction synthesis from high- level contracts, and planning in presence of uncertainty. Caltech's primary objectives are to support the following milestones:<br /> * Year 1: Develop algorithms for correct-by-construction synthesis with probabilistic notion of safety<br /> * Year 2: Extend the approaches to incorporate risk measures such as Conditional Value-at-Risk.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:NCS projects]]<br /> {{Project<br /> |Title=Assurance for Learning Enabled Systems<br /> |Agency=DARPA<br /> |Grant number=FA8750-19-C-0089<br /> |Start date=1 September 2019<br /> |End date=30 Jun 2021<br /> |Support summary=1 postdoc, 0.5 graduate student<br /> |Reporting requirements=Monthly updates<br /> |Project ID=DARPA ALES<br /> |ack=The project or effort depicted was or is sponsored by the Defense Advanced Research Projects Agency (Agreement FA8750-19-C-0089). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Biomolecular_Breadboards_for_Prototyping_and_Debugging_Synthetic_Biocircuits&diff=27178 Biomolecular Breadboards for Prototyping and Debugging Synthetic Biocircuits 2025-12-07T06:24:15Z <p>Murray: </p> <hr /> <div>{{righttoc}} This is a joint project between Richard Murray (Caltech), Vincent Noireaux (U. Minnesota) and Paul Rothemund (Caltech), funded by the DARPA Living Foundries program. The information on this page focuses primarily on the work involving my research group. Additional information about this project is available on our [[http:www.openwetware.org/wiki/Biomolecular_Breadboards_for_Prototyping_and_Debugging_Synthetic_Biocircuits|OpenWetWare web pages]]. <br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | width=50% | Project participants:<br /> * {{Zachary Sun}}<br /> * {{Clarmyra Hayes}}<br /> * {{Sean Sanchez}}<br /> * {{Yong Wu}}<br /> * {{Vipul Singhal}}<br /> * {{Enoch Yeung}}<br /> * {{Jongmin Kim}}*<br /> * {{Joe Meyerowitz}}*<br /> * {{Dan Siegal-Gaskins}}*<br /> * {{Anu Thubagere}}*<br /> * Gita Mahmoudabadi (PhD student, BE)*<br /> * Zoltan Tuza (visiting student, Hungary)<br /> | Collaborators<br /> * [[http:sites.google.com/site/abatelab/home|Adam Abate]] (UCSF)<br /> * [[http:www.dna.caltech.edu/~pwkr/|Paul Rothemund]] (Caltech)<br /> * [[http:www.physics.umn.edu/people/noireaux.html|Vincent Noireaux]] (U. Minnesota)<br /> |}<br /> &lt;nowiki&gt;* Partially supported&lt;/nowiki&gt;<br /> <br /> == Objectives ==<br /> <br /> {| style=&quot;float: right&quot;<br /> |-<br /> | [[Image:breadboards-process.png|400px]]<br /> |-<br /> | align=center | Overview of the cell-free expression breadboard process.<br /> |}<br /> The goal of this project is to build a set of “biomolecular breadboards” to create a systematic, engineering-oriented approach to synthesizing biomolecular circuits that involves developing, modeling, and debugging a sequence of prototype devices, each at increasing levels of complexity and each allowing the incorporation of increasingly realistic operating environments for either ''in vitro'' or ''in vivo'' applications. We are <br /> adapting an existing cell-free toolbox developed at U. Minnesota to create a set of prototyping environments for testing biological circuits. A sequence of increasingly complex environments, ending in prokaryotic cells, will be used to demonstrate the ability to prototype circuits that function in vivo, with iteration in in vitro assays and models to streamline development of predictable, in vivo functionality.<br /> <br /> '''Phase I''' (complete)<br /> * Post protocols for producing basic cell-free breadboard on public web site along with summary of costs. Provide sequences for positive controls.<br /> * Demonstrate the use of cell-free breadboard on 2 existing circuits (chosen from negatively autoregulated gene, simple genetic switch, oscillator, feedforward loop) and document time required to implement a simple circuit and perform design iterations.<br /> * Post complete documentation of a transcription-translation cell-free platform that includes a set of transcriptional repression units (non-degradable and degradable versions), the working principles of the toolbox (procedures and protocols), and validated models for the repressors based on in vitro and in vivo characterization.<br /> * Demonstrate the design of a simple circuit (3–6 unique promoters) that consists of a new set of genetic elements, documenting the interactions, conditions, and compensation mechanisms required to obtain a working circuit in E. coli. Investigators shall provide an analysis of the design cycle times compared to iGEM standard assembly protocol and Gibson- based protocol (using in vivo testing and debugging). Target 3 day prototyping cycle time and 1 month from design to implementation, with the ability to test 25 circuit variants simultaneously.<br /> <br /> '''Phase II'''<br /> * Train interested researchers in the use of the cell-free breadboard system, including a design project that demonstrates the design, modeling, implementation and debugging of a simple circuit <br /> * Demonstrate the ability to use a combination of modeling combined with a sequence of in vitro design cycles to get a novel circuit (4–8 unique promoters) working in E. coli.<br /> * Demonstrate the ability to get a modest complexity circuit (8–16 unique promoters, based on composing simpler circuits) working in E. coli. Target 1 day prototyping cycle time and 1 week from design to implementation, with the ability to test 100 circuit variants simultaneously.<br /> * Develop, document and dessiminate a set of protocols and technologies enabling the use of digital microfluidics (droplets) to carry out TX-TL reactions for prototyping and debugging of biological circuits.<br /> * Demonstrate the ability to create and screen circuit combinations using high throughput ($10^6$ droplets/day) microfluidics, demonstrating 2-4X improvement in pathway yield.<br /> <br /> == References ==<br /> {{project paper list}}<br /> * [http://www.cds.caltech.edu/~murray/talks/breadboard_denver-11Jun14.pdf DARPA Living Foundries program review presentation], 11 Feb 2014<br /> * [http://www.cds.caltech.edu/~murray/papers/tskm13-cdc.html An &lt;i&gt;In Silico&lt;/i&gt; Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System], Zoltan A. Tuza, Vipul Singhal, Jongmin Kim, Richard M. Murray. Submitted, 2013 Conference on Decision and Control (CDC).<br /> * {{snm13-acc}}<br /> * {{sun+13-jove}}<br /> * [http://www.openwetware.org/wiki/Biomolecular_Breadboards OpenWetWare Biomolecular Breadboards project page]<br /> * [http://www.cds.caltech.edu/~murray/talks/breadboard_kickoff-12Jul12.pdf DARPA Living Foundries kickoff presentation], 12 Jul 2012<br /> <br /> {{grant info|<br /> | agency = DARPA<br /> | pm = Alicia Jackson<br /> | ack = Research supported by the Defense Advanced Research<br /> Projects Agency (DARPA/MTO) Living Foundries program, contract number HR0011-12-C-0065. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing official policies, either expressly or implied, of the Defense Advanced Research Projects Agency or the U.S. Government.<br /> | grantno = HR0011-12-C-0065<br /> | start = 21 May 2012<br /> | end = 2 Nov 2014<br /> | support = 2 graduate students/postdocs, technician + supplies<br /> | reports= quarterly reports<br /> }}<br /> [[Category:Completed projects]]</div> Murray https://murray.cds.caltech.edu/index.php?title=Biomolecular_Feedback_Circuits_for_Modular,_Robust_and_Rapid_Response&diff=27177 Biomolecular Feedback Circuits for Modular, Robust and Rapid Response 2025-12-07T06:23:43Z <p>Murray: </p> <hr /> <div>{{righttoc}} This is a joint project with [http://www.mayo.caltech.edu/ Steve Mayo], funded by the [http://www.icb.ucsb.edu/ ARO Institute for Collaborative Biotechnologies].<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | width=50% | Project participants:<br /> * {{Victoria Hsiao}}<br /> * {{Dan Siegal-Gaskins}}*<br /> * {{Sean Sanchez}}*<br /> * {{Emzo de los Santos}}<br /> * Paul Nguyen (undergrad)<br /> * {{Shaunak Sen}}<br /> * Nikki Thadani (undergrad)<br /> | Collaborators<br /> * Steve Mayo (Bi)<br /> |}<br /> &lt;nowiki&gt;* partial funding&lt;/nowiki&gt;<br /> <br /> == Objectives ==<br /> {| style=&quot;float: right&quot; width=40% border=1 cellpadding=5<br /> |-<br /> | [[Image:biomolecular-twoloop.png|360px]]&lt;br&gt;<br /> Block diagram of the proposed control architecture. The (slow) transcriptional regulation is used to maintain an appro- priate concentration of protein whose activity can be modulated via a conformation change. An allosteric regulation mechanism is then used to produce an active protein (or protein complex) at a much faster timescale. The protein must both have the desired function (e.g., fluorescence) and allow a mechanism to compare its concentration to that of a reference species (inducer). <br /> |}<br /> We are working to develop a new class of feedback circuits that makes use of synthetic biological components to implement rapid response to input signals in a more robust and modular fashion. Our approach is to make use of biological processes that operate on timescales of seconds to minutes, primarily through feedback mechanisms using allosteric and covalent modifications that affect protein function. We are exploring the use of the modularity of protein domains to design circuit elements that can be reused more easily than existing components, and we will test our circuits across a variety of cellular contexts to assess robustness as a fundamental property of the design.<br /> <br /> Specific objectives for this project include:<br /> * Exploration of RNA-based mechanisms for regulating protein expression<br /> * Develop and characterize a set of programmable covalent modifications that modulate protein activity<br /> * Design, synthesize and test a circuit that uses multiple, heterogeneous feedback mechanisms for regulation of gene activity<br /> <br /> == References ==<br /> {{project paper list}}<br /> * [http://www.cds.caltech.edu/~murray/papers/2012q_dhm13-acc.html Design and Implementation of a Biomolecular Circuit for Tracking Protein Concentration], Emmanuel L. C. de los Santos, Victoria Hsiao and Richard M. Murray. 2013 American Control Conference (ACC).<br /> * {{sm12-cdc}}<br /> * [http://openwetware.org/wiki/CAGEN:_Robust_Gene_Response_Challenge CAGEN Robust Gene Response Challenge]<br /> <br /> {{grant info|<br /> | ack = This research is supported by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office. The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> | agency = Army Research Office<br /> | grantno = W911NF-09-0001<br /> | start = 15 Dec 2008<br /> | end = 14 Dec 2013<br /> | support = 1-2 graduate students + supplies<br /> | reports = Annual reports due in June<br /> }}<br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]</div> Murray https://murray.cds.caltech.edu/index.php?title=CAGEN:_Critical_Assessment_of_Genetically_Engineered_Networks&diff=27176 CAGEN: Critical Assessment of Genetically Engineered Networks 2025-12-07T06:23:12Z <p>Murray: </p> <hr /> <div>The Critical Assessment for Genetically Engineered Networks (CAGEN) is a competition intended to drive new approaches to designing robust, synthetic biological circuits. The competition involves teams of established researchers designing circuits that implement a given function and the assessment of their circuit's performance across a set of multiple operating environments. More information is available on the [[http:www.openwetware.org/wiki/CAGEN|CAGEN web site]] (on OpenWetWare). __NOTOC__<br /> <br /> Project participants:<br /> * {{Clarmyra Hayes}}<br /> * {{Shaunak Sen}}<br /> <br /> == Project Overview ==<br /> We propose to develop and prototype a new competition designed to<br /> improve the robustness and performance of human-designed biological<br /> circuits and devices operating in cells. The Competitive Assessment for<br /> Genetically Engineered Networks (CAGEN, pronounced &quot;cajun&quot;) will<br /> bring together leading research groups in biological circuit design<br /> to compete to demonstrate their abilities at designing circuits that<br /> perform in a prescribed manner in a variety of cellular contexts.<br /> Each year, a steering committee will propose a challenge problem that<br /> involves the design of an increasingly complex set of biological<br /> functions in a range of environments. Teams must submit their<br /> sequences, plasmid DNA implementing their circuit and data characterizing<br /> the performance of their system against a specified test suite. The<br /> top 3-5 designs will be submitted to the NSF BIOFAB (run by Adam<br /> Arkin and Drew Endy) for final characterization, and the winner will<br /> be selected based on a set of quantifiable metrics.<br /> <br /> As part of this proposal, we plan to implement one iteration of the<br /> competition, including selecting the challenge problem, implementing a<br /> set of reference test protocols, announcing and publicizing the<br /> competition, implementing the selection process and choosing a winner.<br /> If successful, we believe that the competition can be proposed for<br /> continued funding from other sources and that over the medium term<br /> (5-10 years) CAGEN could lead toward a more robust set of biological<br /> design methods that allow human-designed circuits and devices to<br /> perform at levels closer to their biological<br /> counterparts.<br /> <br /> == Publications ==<br /> * {{sm12-cdc}}<br /> <br /> [[Category:Completed projects]]<br /> {{#set: agency=NAKFI | end date = 2012}}</div> Murray https://murray.cds.caltech.edu/index.php?title=Cell-Free_Expression_of_Membrane_Proteins_with_Applications_to_Drug_Discovery&diff=27175 Cell-Free Expression of Membrane Proteins with Applications to Drug Discovery 2025-12-07T06:22:51Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> The goal of this project is to demonstrate the ability to express functionally-active, membrane- bound proteins in a cell-free transcription-translation (TX-TL) system that has been developed at Caltech. We will make use of a novel nanodisc structure that emulates the cell membrane and has been successfully tested at Amgen. The TX-TL breadboard has been demonstrated to enable rap- id, cost-effective, and high-throughput exploration of complex biomolecular circuits (Niederholtmeyer et al. 2015), metabolic engineering pathways (Wu et al. 2015), and engineered enzyme variants (de los Santos et al. 2015). We believe that given these three applications, the TX-TL breadboard can also enable expression and assay of functionally-active, membrane-bound proteins. Building on a recently established collaboration between Caltech and Amgen, we propose to demonstrate the utility of this approach for automation-enabled drug discovery.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> * Abel Chiao*<br /> * Zach Sun<br /> | Collaborators:<br /> * Ching Chen (Amgen)<br /> |}<br /> <br /> == Objectives ==<br /> High-level cell expression of membrane proteins is often difficult or self-prohibited due to cell toxicity. Purification and reconstitution of membrane-bound proteins has also proven to be very challenging compared to non-membrane bound analogues. The direct cell-free expression of challenging membrane-bound proteins provides an attractive alternative to overcome these difficulties. This project aims to achieve high-level expression and display of membrane proteins by integration of two technologies: (1), cell-free expression, and (2), assembly of membrane proteins into nanodiscs. The successful implementation of the combined technologies will produce and display membrane proteins in nanodiscs with defined size and lipid components. Together, it will enable us to develop robust and reliable measurements of kinetic and equilibrium binding for membrane proteins.<br /> <br /> == References ==<br /> {{project paper list}}<br /> <br /> {{grant info|<br /> | agency = Amgen<br /> | grantno = AMGEN.CBEARMM<br /> | pm = Ching Chen<br /> | ack = Research supported through an Amgen Chem-Bio-Engineering Award (CBEA).<br /> | start = 1 Nov 2015<br /> | end = 31 Dec 2016<br /> | support = ~1 graduate student, technician support + supplies<br /> | reports = Presentation at semi-annual research review + short written summary of research (annually).<br /> | width=50%<br /> | ID = Amgen TX-TL<br /> }}<br /> [[Category:Completed projects]]</div> Murray https://murray.cds.caltech.edu/index.php?title=Control_Design_for_Cyberphysical_Systems_Using_Slow_Computing&diff=27174 Control Design for Cyberphysical Systems Using Slow Computing 2025-12-07T06:22:11Z <p>Murray: </p> <hr /> <div>[[Image:slowncs-arch.png|right|400px]]<br /> This project seeks to develop new, systematic methods for the design of<br /> control systems that can work in the presence of slow computing<br /> elements. The development of such an architecture has the<br /> possibility of providing new ways of integrating control into systems<br /> where large amounts of fast computation are not easily available,<br /> either due to limitations on power, physical size or choice of computing<br /> substrate. This project is supported by the National Science Foundation (NSF), award number 0931746.<br /> <br /> Project participants:<br /> * {{Andrea Censi}}<br /> * {{Shuo Han}}<br /> * Javad Lavaei<br /> * Somayeh Sojoudi<br /> * Andrew Straw<br /> <br /> == Objectives ==<br /> * Develop an ''architecture'' for control using slow computing<br /> * Develop new theory and and tools for design of controller for cyberphysical systems that scale to slow computing<br /> * Demonstrations of the methodology on university scale experiments in micro-vehicles.<br /> <br /> == Publications ==<br /> * [http://www.cds.caltech.edu/~murray/papers/2011j_chm12-icra.html Fault detection and isolation from uninterpreted data in robotic sensorimotor cascades], Andrea Censi, Magnus Håkansson and Richard M. Murray. Submitted, 2012 International Conference on Robotics and Automation (ICRA).<br /> * [http://www.cds.caltech.edu/~murray/papers/2011i_cm12-icra.html Learning diffeomorphism models of robotic sensorimotor cascades], Andrea Censi and Richard M. Murray. Submitted, 2012 International Conference on Robotics and Automation.<br /> * [http://www.cds.caltech.edu/~murray/papers/2011f_cm11-iros.html A group-theoretic approach to formalizing bootstrapping problems], Andrea Censi and Richard M. Murray. 2011 International Conference on Intelligent Robots and Systems (IROS).<br /> * [http://www.cds.caltech.edu/~murray/papers/2011d_cm11-icdl.html Uncertain semantics, representation nuisances, and necessary invariance properties of bootstrapping agents], A. Censi and R. M. Murray. IEEE International Conference on Development and Learning and Epigenetic Robotics (ICDL/EpiRob), 2011.<br /> * [http://www.cds.caltech.edu/~murray/papers/2010o_cm11-icra.html Bootstrapping bilinear models of robotic sensorimotor cascades], Andrea Censi and Richard M. Murray. 2011 International Conference on Robotics and Automation (ICRA).<br /> * {{hcsm10-iros}}<br /> * {{lsm10-acc}}<br /> * {{chfm09-cdc}}<br /> * {{hcsm09-icra}}<br /> <br /> == Additional Information ==<br /> * [http://www.cds.caltech.edu/~murray/proposals/nsf09-cps.pdf Project proposal (Feb 2009)]<br /> <br /> [[Category:Completed projects]]<br /> {{#set: agency=NSF | end date = 2013}}</div> Murray https://murray.cds.caltech.edu/index.php?title=Deciphering_the_Rules_of_Nucleus_Architecture_with_Synthetic_Cells_and_Organelles&diff=27173 Deciphering the Rules of Nucleus Architecture with Synthetic Cells and Organelles 2025-12-07T06:21:42Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> The goal of this project is to decipher the fundamental principles for compartmentalization in cells by building and modeling synthetic cells and organelles from the bottom-up. Working with Imperial College London, we are developing new synthetic biology, microfluidics, biomembrane engineering, and mathematical modelling platform technologies. These are being used to make and model synthetic nuclei that will be used to address fundamental questions relating to its central role in all eukaryotes, by taking an &quot;understanding by building&quot; approach. This research aims to establish a new framework for understanding cell biology fundamentals, that can be used in future studies by us and others. By the end of the project, we will have developed a technological toolkit to probe the principles underpinning compartmentalization in cells, and use these to answer key unanswered biological questions that are uniquely placed to be addressed using our approach.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> | Collaborators:<br /> {{project collaborators}}<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:bbsrc-synnucleus.png|right|240px]]<br /> Caltech's activities in this collabrative proposal with Imperial College London are focused on the following objectives:<br /> * Development of model-based analysis, design and systems optimization for synthetic organelles. This work will leverage prior work in open-source software tools for modeling of biomolecular systems and will result in extended modeling and analysis tools that will be made available for distribution both to the project and the public.<br /> * Systematic exploration of the effects of compartmentalization on coupled biochemical processes, using the experimental platforms developed at Imperial to validate and build on modeling predictions.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=Deciphering the Rules of Nucleus Architecture with Synthetic Cells and Organelles<br /> |Agency=NSF<br /> |Grant number=MCB-2152267<br /> |Start date=15 Oct 2021<br /> |End date=30 Sep 2024<br /> |Support summary=2 graduate students<br /> |Reporting requirements=Annual report<br /> |Project ID=BBSRC SynNucleus<br /> |ack=Research supported by the National Science Foundation award number 2152267.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Design_of_Digitally_Controlled_Bacterial_Circuits_for_Bioenabled_Materials&diff=27172 Design of Digitally Controlled Bacterial Circuits for Bioenabled Materials 2025-12-07T06:21:12Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This proposal seeks to understand if bacteria can be designed to perform on demand when inside of a composite material. Bacteria provide a rich source that can be exploited to develop novel and cost-effective adaptive systems that could be superior to traditional materials. Critical to this concept is the ability to control bacterial activity inside materials. To explore this, we will test the hypothesis that if bacteria can be designed to respond to weak currents and survive in UV-activated polymers, then combining those bacteria with nanomaterials in a UV-activated polymer will create a material where the activity of embedded bacteria can be controlled using a computer interface. The hypothesis will be tested by engineering circuits in bacteria that are responsive to oxidation/reduction at the surface of nanowires. We will then use scalable assembly processes to combine bacteria and nanowires in mixed UV-activated polymers to create rigid/soft composite material. Composite bacterial nanowire materials will be interfaced with computer controllers to examine manipulation of bacterial activity in the composite materials.<br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> | Collaborators:<br /> * UCSB<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:arl20-elm.png|right|400px]]<br /> The work taking place at Caltech is focused on amplification of redox signal via long-distance, pulsatile cell-cell signaling. Cells embedded in a solid media will have diffusion-limited access to molecules oxidized or reduced at the electrode surface. To achieve uniform response to electrical signals, cells nearer to the electrode must communicate with distant cells. We will augment the redox-sensitive cells with a long-distance signaling circuit, previously studied by our lab, to promote a uniform bacterial reaction to electrical input.<br /> <br /> Specific objectives under this task:<br /> * Modify the synthetic SoxR/S regulon such that the output protein is Cmi, the signal synthaseproteinoftheP.aeruginosaCm quorumsensingsystem.<br /> * Demonstrate that the redox-sensitive cells can initiate a traveling pulse of cell-cell signaling activity that moves through cells embedded in a hydrogel to increase the population of cells activated in response to electrical input.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=Design of Digitally Controlled Bacterial Circuits for Bioenabled Materials<br /> |Agency=Army Research Lab/Institute for Collaborative Biotechnologies<br /> |Grant number=W911NF-19-D-0001/KK1956 (Task 6)<br /> |Start date=1 Oct 2019<br /> |End date=30 Sep 2021<br /> |Support summary=1 graduate student<br /> |Reporting requirements=Annual report<br /> |Project ID=ICB Materials<br /> |ack=This research is supported by the Institute for Collaborative Biotechnologies through contract W911NF-19-D-0001 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Developing_Standardized_Cell-Free_Platforms_for_Rapid_Prototyping_of_Synthetic_Biology_Circuits_and_Pathways&diff=27171 Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways 2025-12-07T06:20:44Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> The goal of this project is to further advance standardized cell-free systems from engineered ''E. coli'' and other organisms for use in prototyping synthetic circuit and pathway designs. Such standardized systems will both explore the boundaries of cell-free prototyping and characterization, and enable more detailed understanding of key mechanisms, accelerating the usage and broader utility of cell-free systems in industry and academia. The long term vision for this project is to establish cell-free systems as a platform for implementation of synthetic biological circuits, pathways, and systems, where modular and complex biomolecular systems can be engineered in a systematic fashion. This project seeks to overcome some of the current limitations of cell-free systems through a combination of experimental characterization and computational modeling.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> | Collaborators:<br /> * Paul Freemont (Imperial College London)<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:nsf19-cellfree.png|right|600px]]<br /> The main objectives of this project are:<br /> * Development of well-understood, standardized TX-TL reaction systems that are suitable for prototyping circuits and pathways for a variety of cells<br /> * Characterization and modeling of complex synthetic biology components, circuits, and pathways using TX-TL that enable forward engineering<br /> * Development of new biochemical indicator components for use in TX-TL systems to achieve better understanding and more predictive models<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways<br /> |Agency=NSF<br /> |Grant number=CBET-1903477<br /> |Start date=1 Jul 2019<br /> |End date=30 Jun 2023<br /> |Support summary=1 graduate student<br /> |Reporting requirements=Annual reports<br /> |Project ID=NSF Cell Free<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Distributed_Sense_and_Control_Systems&diff=27170 Distributed Sense and Control Systems 2025-12-07T06:20:22Z <p>Murray: </p> <hr /> <div>[[Image:musyc-logo.gif|right]]<br /> This is a large consortium project led by UC Berkeley as part of the [http://www.musyc.org/ Multiscale Systems Center (MuSyC)]. This page primarily describes the work done in Richard Murray's group. __NOTOC__<br /> <br /> Project participants:<br /> * {{Mumu Xu}}<br /> * {{Necmiye Ozay}}<br /> * {{Clemens Wiltsche}}<br /> <br /> Substantial research challenges exist in the design and verification of large-scale, complex, distributed sensing, actuation and control systems. Three topics of particular interest are the design in information flows, cooperative behavior between distributed agents, and verification of distributed, asynchronous control systems. Each of these topics relates to a difficult aspect in the proper operation of large-scale distributed system in which the temporal scales of the underlying dynamics of the systems, the rate of communications between agents, and the latency in computation and multi-threaded execution cannot be separated. The additional need to be able to rapidly design, implement and commission such systems requires new techniques in modeling, analysis, design and verification.<br /> <br /> To approach the interlinked challenges of information flow, cooperative behavior and verification, we plan to combine tools and recent advances from control theory, networked systems and computer science. The primary tools that we expect to build on are graph theory, partial order theory, temporal logic, graph grammars, formal methods and optimization-based control. This combination of tools allows us to model and analyze complex, protocol-based control systems by using temporal logic to specify desired behavior, graph theory (in particular the graph Laplacian and other associated matrices) to model and design the information flow, graph grammars to design cooperative behavior, lattice theory and Lyapunov theory to understand convergence properties via invariant sets, and model-checking and receding horizon control to design systems whose asynchronous execution sequences satisfy a given specification. Previous results in each of these areas has demonstrated the efficacy of modeling and analysis of distributed, asynchronous sensing, actuation and control systems; future work will focus on advances required to support large-scale systems and modularity.<br /> <br /> == Objectives ==<br /> * Develop algorithms, protocols and verification tools for distributed control that are aimed at optimized resource allocation between multiple agents in a decentralized and scaleable manner. <br /> * Extend existing work in gossip algorithms, load balancing and consensus protocols to allow more sophisticated scheduling of shared resources in a dynamic environment with model-based predictions of future demand/availability. <br /> * Application areas that will be used as drivers for the theoretical advancements include (1) power management networks in handheld devices, vehicles, buildings, manufacturing plants and geographic regions; (2) aircraft avionics and (3) cooperative control of multi-vehicle systems. <br /> <br /> == Publications ==<br /> * {{lotm12-acc}}<br /> * {{notm12-acc}}<br /> * {{tolm12-hscc}}<br /> * {{otm11-cdc}}<br /> * {{otwm11-iccps}}<br /> * {{Won+11-hscc}}<br /> * {{wtm11-infotech}}<br /> * {{Xu+11-allerton}}<br /> * {{cltx10-cdc}}<br /> <br /> [[Category:Completed projects]]<br /> {{#set: agency=DARPA FCRP | end date = 2013}}</div> Murray https://murray.cds.caltech.edu/index.php?title=Engineering_Durable_Cell-Free_Biological_Capabilities_for_Advanced_Sensing_and_Prototyping&diff=27169 Engineering Durable Cell-Free Biological Capabilities for Advanced Sensing and Prototyping 2025-12-07T06:20:01Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> The goal of this project is to systematically expand the operating range and utility of cell-free systems sourced from new diverse organisms. These next-generation cell free systems will enable new capabilities for prototyping and implementing durable synthetic circuit designs. Such standardized systems will not only explore the boundaries of cell-free prototyping and characterization but will also enable proper comparisons of data measured by multiple groups, thereby accelerating the usage and<br /> broader utility of cell-free systems in industry and academia. <br /> <br /> Project participants:<br /> {{project past participants}}<br /> <br /> === Objectives ===<br /> [[Image:arl19-cellfree.png|right|500px]]<br /> The two primary focus areas for this project are to (1) increase the number of organisms and portable parts available for synthetic biologists for design, prototyping, and implementation of cell-free biomolecular circuits and pathways in a rapid, systematic, and predictable way and (2) improve the durability, sensitivity, and robustness of cell-free detection systems. <br /> The specific objectives for the project are:<br /> # Develop high-throughput, cell-free methods for measuring and modeling key parameters of transcriptional and translational processes of biological parts in a diverse set of organisms.<br /> # Perform a demonstration of the utility of these models by moving parts and circuits from one organism to another with a repeatable and predictable outcome.<br /> # Demonstrate expanded capabilities for detection and diagnostics of chemical and biological signals in simulated or real field operating conditions, with the goal of increasing sensitivity, specificity, and output signal strength of cell-free biological detectors.<br /> # Distribute the tools and techniques to the synthetic biology community for broader use.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=Engineering Durable Cell-Free Biological Capabilities for Advanced Sensing and Prototyping<br /> |Agency=Army Research Office<br /> |Grant number=W911NF-19-D-0001<br /> |Start date=14 Feb 2019<br /> |End date=13 Feb 2021<br /> |Support summary=1 graduate student<br /> |Reporting requirements=Annual reports<br /> |Project ID=ARL cellfree<br /> |ack=This research is supported by the Institute for Collaborative Biotechnologies through contract W911NF-19-D-0001 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Engineering_Reliable_Genetic_Circuits_for_Characterization_and_Remediation_of_Soil_Ecologies&diff=27168 Engineering Reliable Genetic Circuits for Characterization and Remediation of Soil Ecologies 2025-12-07T06:19:37Z <p>Murray: </p> <hr /> <div>The goal of this project is to develop genetic circuits that can be implemented in engineered microbes operating in (laboratory-based) soil environments that are able to sense and manipulate the concentration of small molecules present in the soil. We plan to use phosphorous as our initial molecule of interest, as a model for other chemical species present in soils. {{righttoc}} <br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> | Collaborators:<br /> * [[Dianne Newman]]<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:icb-soil-syn-bio.png|right|200px]]<br /> <br /> '''Use of engineered microorganisms for sensing and characterizing rhizosphere properties'''<br /> <br /> ​A key element of characterization and remediation of soil ecologies will be developing and understanding of the biology and chemistry of soil ecosystems. Culture and sequencing can provide a broad outline of what is in the rhizosphere. In situ hybridization can contribute to provide some spatial information for specific species and the genes they are expressing. However, much of what we want to know involves understanding the roles of particular genes, and the levels of nutrients and metabolites in specific species in specific microenvironments. While many compounds are found in soils, one of the most important is phosphate, a vital macronutrient. Recently, we have discovered that diverse soil bacteria produce redox-active antibiotics (e.g. phenazines) in response to phosphorus limitations; phenazines help make phosphorus more bioavailable by catalyzing the reductive dissolution of minerals to which phosphorus is adsorbed. Because phenazines biosynthesis is genetically tractable and phenazines can be electrochemically detected, there is an exciting opportunity to build on these discoveries using synthetic biology to detect phosphorus concentration as an exemplar for ​in situ​ detection of other chemical species. Species-specific transgenesis and the creation of reporters and biosensors will contribute to this goal, more broadly showcasing how synthetic biology can be applied to sense compounds of interest in soils.<br /> <br /> '''Use of engineered microorganisms to detect, respond, and manipulate rhizosphere conditions'''<br /> <br /> ​In addition to characterization, we ultimately want to be able to perturb the rhizosphere to enhance desired characteristics such as soil material properties or to remediate spills that may have been affected by toxins. Engineered microorganisms provide a mechanism for detecting local environmental conditions and then responding to these conditions by synthesizing and exporting small molecules or proteins that modulate the biological and chemical state of the soil. This work will involve introduction of novel extant wildtype members of other species into environments, and characterization of their fate and influence on other species. It will also involve genetic modification, creation of circuits, and engineering of cooperative and competitive interactions that function in the soil environment. In particular, we plan to demonstrate the ability to sense and respond to the presence of phosphorus, again as an exemplar of manipulation of compounds of interest in soils.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=Engineering Reliable Genetic Circuits for Characterization and Remediation of Soil Ecologies<br /> |Agency=Army Research Office<br /> |Grant number=W911NF-19-D-0001<br /> |Start date=15 Oct 2021<br /> |End date=14 Oct 2023<br /> |Support summary=2 graduate students, part-time technician<br /> |Reporting requirements=Annual reports<br /> |Project ID=ICB Soil Syn Bio<br /> |ack=This research is supported by the Institute for Collaborative Biotechnologies through contract W911NF-19-D-0001 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Engineering_Reliable_Genetic_Circuits_for_Characterization_and_Remediation_of_Soil_Ecologies&diff=27167 Engineering Reliable Genetic Circuits for Characterization and Remediation of Soil Ecologies 2025-12-07T06:19:08Z <p>Murray: </p> <hr /> <div>The goal of this project is to develop genetic circuits that can be implemented in engineered microbes operating in (laboratory-based) soil environments that are able to sense and manipulate the concentration of small molecules present in the soil. We plan to use phosphorous as our initial molecule of interest, as a model for other chemical species present in soils. {{righttoc}} <br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> | Collaborators:<br /> * Dianne Newman<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:icb-soil-syn-bio.png|right|200px]]<br /> <br /> '''Use of engineered microorganisms for sensing and characterizing rhizosphere properties'''<br /> <br /> ​A key element of characterization and remediation of soil ecologies will be developing and understanding of the biology and chemistry of soil ecosystems. Culture and sequencing can provide a broad outline of what is in the rhizosphere. In situ hybridization can contribute to provide some spatial information for specific species and the genes they are expressing. However, much of what we want to know involves understanding the roles of particular genes, and the levels of nutrients and metabolites in specific species in specific microenvironments. While many compounds are found in soils, one of the most important is phosphate, a vital macronutrient. Recently, we have discovered that diverse soil bacteria produce redox-active antibiotics (e.g. phenazines) in response to phosphorus limitations; phenazines help make phosphorus more bioavailable by catalyzing the reductive dissolution of minerals to which phosphorus is adsorbed. Because phenazines biosynthesis is genetically tractable and phenazines can be electrochemically detected, there is an exciting opportunity to build on these discoveries using synthetic biology to detect phosphorus concentration as an exemplar for ​in situ​ detection of other chemical species. Species-specific transgenesis and the creation of reporters and biosensors will contribute to this goal, more broadly showcasing how synthetic biology can be applied to sense compounds of interest in soils.<br /> <br /> '''Use of engineered microorganisms to detect, respond, and manipulate rhizosphere conditions'''<br /> <br /> ​In addition to characterization, we ultimately want to be able to perturb the rhizosphere to enhance desired characteristics such as soil material properties or to remediate spills that may have been affected by toxins. Engineered microorganisms provide a mechanism for detecting local environmental conditions and then responding to these conditions by synthesizing and exporting small molecules or proteins that modulate the biological and chemical state of the soil. This work will involve introduction of novel extant wildtype members of other species into environments, and characterization of their fate and influence on other species. It will also involve genetic modification, creation of circuits, and engineering of cooperative and competitive interactions that function in the soil environment. In particular, we plan to demonstrate the ability to sense and respond to the presence of phosphorus, again as an exemplar of manipulation of compounds of interest in soils.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=Engineering Reliable Genetic Circuits for Characterization and Remediation of Soil Ecologies<br /> |Agency=Army Research Office<br /> |Grant number=W911NF-19-D-0001<br /> |Start date=15 Oct 2021<br /> |End date=14 Oct 2023<br /> |Support summary=2 graduate students, part-time technician<br /> |Reporting requirements=Annual reports<br /> |Project ID=ICB Soil Syn Bio<br /> |ack=This research is supported by the Institute for Collaborative Biotechnologies through contract W911NF-19-D-0001 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Field-Programmable,_Recombinase-Based_Biomolecular_Circuits&diff=27166 Field-Programmable, Recombinase-Based Biomolecular Circuits 2025-12-07T06:18:41Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This project funded by the [http://www.icb.ucsb.edu/ Army's Institute for Collaborative Biotechnologies], an Army University Affiliated Research Center (UARC)<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | <br /> Project participants:<br /> {{project past participants}}<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:aicb19-fieldprogrammable.png|right|400px]]<br /> This project explores the use of recombinases -- integrases, excisionases, and other methods of manipulating DNA -- as platform for engineering biomolecular circuits. Our high-level goal is to develop a design-oriented framework for recombinase-based, genetically-encoded circuits that can be used for detection, diagnostics, and logging of environmental signals and events. <br /> The specific objectives this project are to:<br /> * Develop circuit components, mathematical models, experimental protocols, and system characterization methods that enable recombinase-based circuits to be designed and utilized in a systematic fashion. <br /> * Implement a set of biological “event detectors” in both cell-free and cell-based assays, and demonstrate their utility in applications that combine digital, analog, and stochastic operations. <br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{Project<br /> |Title=Field-Programmable, Recombinase-Based Biomolecular Circuits<br /> |Agency=Army Research Office<br /> |Grant number=W911NF-19-2-0026<br /> |Start date=1 Dec 2018<br /> |End date=30 Nov 2021<br /> |Support summary=1 graduate student, part-time technician<br /> |Reporting requirements=Annual reports<br /> |Project ID=AICB MRSB<br /> |ack=This research is supported by the Institute for Collaborative Biotechnologies through cooperative agreement W911NF-19-2-0026 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Formal_Methods_for_V%26V_and_T%26E_of_Autonomous_Systems&diff=27165 Formal Methods for V&V and T&E of Autonomous Systems 2025-12-07T06:18:27Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> The goal of this project to advance the mathematical and algorithmic foundations of test and evaluation by com- bining advances in formal methods for specification and verification of reactive, distributed systems with algorithmic design of multi-agent test scenarios, and algorithmic evaluation of test results. Building on previous results in synthesis of formal contracts for performance of agents and subsystems, development of barrier certificate methods for provably safe performance of nonlinear control systems, and experience in the development of operational autonomous systems we are creating a mathematical framework for specifying the desired characteristics of multi-agent systems involving cooperative, adversarial, and adaptive interactions, develop algorithms for verification and validation (V&amp;V) as well as test and evaluation (T&amp;E) of the specifications, and per- form proof-of-concept demonstrations that demonstrate the use of formal methods for V&amp;V and T&amp;E of autonomous systems. If successful, our results will provide more systematic methods for describing the desired properties of military systems in complex environments; new algorithms for verification of system-level designs against those properties, synthesis of test plans, and analysis of test results; de- sign rules that allow adaptation and machine learning to be integrated without compromising system safety and performance specifications; and demonstration of the envisioned techniques in a multi-agent, free-flight arena that will provide experimental validation of the results.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> * Prithvi Akella (PhD student, ME)<br /> | Collaborators:<br /> * Aaron Ames (ME/CDS)<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:afosr-testandeval.png|right|240px]]<br /> The output of the project will be a set of tools (theory and algorithms) that address these challenges by demonstrating the use of formal techniques for specification, design, verification, and testing of autonomous systems operating in heterogeneous, multi-agent, adversarial environments. More specifically, we aim to accomplish the following specific objectives:<br /> * Create a mathematical framework for specification of desired characteristics of multi-agent autonomous and semi-autonomous systems that account for cooperative, adversarial, and adaptive interactions between agents.<br /> * Develop algorithms and software toolboxes for creation of layered models that are suitable for al- gorithmic verification of performance that incorporate existing test data as well as generate test plans and performance monitors for using in operational test and evaluation.<br /> * Demonstrate key concepts on a proof-of-concept experimental testbed that demonstrates the integration of test data with formal methods for specification and verification of autonomous and semi-autonomous system performance.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> {{Project<br /> |Title=Formal Methods for V&amp;V and T&amp;E of Autonomous Systems<br /> |Agency=AFOSR<br /> |Grant number=FA9550-19-1-0302<br /> |Start date=1 July 2019<br /> |End date=30 Apr 2023<br /> |Support summary=1.5 postdocs, 2 graduate students<br /> |Reporting requirements=Annual program review + report<br /> |Project ID=AFOSR T&amp;E<br /> |ack=Research supported by the AFOSR Test and Evaluation program, grant FA9550-19-1-0302.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=Genetic_Circuits_for_Multi-Cellular_Machines&diff=27164 Genetic Circuits for Multi-Cellular Machines 2025-12-07T06:17:44Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> The use of microbial consortia for implementing synthetic circuits and biosynthesis pathways has a number of advantages over design using single strains, including separation and specialization of func- tion, reduction of loading on individual cells, and reuse of limited molecular and genetic components. However, differences in growth rate between different organisms in the consortium and the effects of mutation on community function can interfere with consortium function. We propose an experimental framework for distributing circuit and pathway functionality across a collection of cells, and regulating the effects of differential growth rate and mutation in microbial consortia.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | Project participants:<br /> {{project past participants}}<br /> | Collaborators:<br /> * Jim Sumner, ARL/SEDD<br /> |}<br /> <br /> === Objectives ===<br /> [[Image:icb-microbial.png|right|400px]]<br /> Year 1: In the first year of the project we will develop the basic components that are required to implement genetic circuits for multi-cellular machines:<br /> * Demonstrate 2-strain synchronization to cell-cell signaling pulse, triggered by external “stress” event (temperature, pH, etc).<br /> * Demonstrate the ability to utilize integrase-mediated recombination to &quot;differentiate&quot; bacteria by simultaneously activating circuit/pathway expression and ceasing plasmid replication.<br /> * Model and experimentally validate the dynamics of 2-4 species communities exchanging metabolites and responding to cell-cell signaling, both in well-mixed and spatially structured conditions.<br /> <br /> Year 2: In the second year of the project, we will integrate the individual signaling and regulation func- tions and demonstrate the ability to implement multi-cellular machines capable of implementing distributed circuits and pathways:<br /> * Combine metabolic cross-feeding community structures with cell-signaling circuits and growth control circuits, and demonstrate the ability to maintain stable community structures that respond to environmental inputs/stress factors.<br /> * Utilize engineered consortia with differentiation/conditional plasmid replication as chassis for multi-step complex biosynthesis of compounds of Army interest (e.g., terpenoids, flavonoids, alkaloids, or polyketides). Compare yield, robustness, and duration of production with/without differentiation and metabolic cross-feeding structures.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> {{Project<br /> |Title=Genetic Circuits for Multi-Cellular Machines<br /> |Agency=Army Research Lab/Institute for Collaborative Biotechnologies<br /> |Grant number=W911NF-09-D-0001<br /> |Start date=1 Jan 2018<br /> |End date=31 Dec 2020<br /> |Support summary=2 graduate students<br /> |Reporting requirements=Annual reports<br /> |Project ID=ICB Microbial<br /> |ack=This research is supported by the Institute for Collaborative Biotechnologies through grant W911NF-09-D-0001 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray https://murray.cds.caltech.edu/index.php?title=ICyPhy:_Industrial_Cyber-Physical_Systems&diff=27163 ICyPhy: Industrial Cyber-Physical Systems 2025-12-07T06:17:08Z <p>Murray: </p> <hr /> <div>&lt;!-- [[Image:icyphy-logo.gif|right]] --&gt;<br /> The Industrial Cyberphysical Systems Center ([http://icyphy.org iCyPhy]) is a university-industrial consortium including Caltech, IBM, UC Berkeley and United Techologies Corporation (UTC). This page primarily describes the work done in Richard Murray's group. __NOTOC__<br /> <br /> Project participants:<br /> * Benson Christalin<br /> * Michele Colledanchise (KTH)<br /> * Quentin Maillet<br /> * {{Necmiye Ozay}}<br /> * {{Mumu Xu}}<br /> * Yllin Mo (Jul 2013)<br /> <br /> Cyber-Physical Systems (CPS) are integrations of computation, networking, and physical processes. Embedded computers and networks monitor and control the physical processes, with feedback loops where physical processes affect computations and vice versa. The economic and societal potential of such systems is vastly greater than what has been realized, and major investments are being made worldwide to develop the technology. The technology builds on the older (but still very young) discipline of embedded systems, computers and software embedded in devices whose principle mission is not computation, such as cars, toys, medical devices, and scientifi c instruments. CPS integrates the dynamics of the physical processes with those of the software and networking, providing abstractions and modeling, design, and analysis techniques for the integrated whole.<br /> <br /> Caltech portion of the project is focused on developing new tools for modeling, specification and synthesis of control laws and control protocols for cyber- physical systems, replacing current techniques that rely on text-based requirements and manual design, followed by time-consuming, difficult, and costly V&amp;V and redesign. We will demonstrate new algorithms for automated synthesis of decision-making logic in representative application areas, including aircraft, vehicle management systems, building management systems, mixed-domain, software-controlled cyber-physical systems.<br /> <br /> == Objectives ==<br /> * Extend temporal logic planning (TuLiP) toolbox to allow conversion from multiple specification and modeling language formats, use of alternative model-checking and synthesis tools, and output in SysML, SIMULINK and other standard formats.<br /> * Extend and integrate preliminary work that includes use of cost/reward functions, probabilistic guarantees and &quot;on the fly&quot; synthesis into TuLiP, test these methods on representative problems of interest to sponsoring industries, and evaluate applicability and gaps.<br /> <br /> == Publications ==<br /> {{project paper list}}<br /> * {{mxom13-cdc}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:NCS projects]]<br /> {{#set: agency=IBM, UTC | start date = 1 Jan 2013 | end date = 31 Dec 2015}}</div> Murray https://murray.cds.caltech.edu/index.php?title=Improvement_of_E._coli_transcription-translation_(TX-TL)_system&diff=27162 Improvement of E. coli transcription-translation (TX-TL) system 2025-12-07T06:16:48Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This project is focuses on the improving methods of production of cell-free transcription-translation (TX-TL) systems. It is funded by the Caltech Grubstake program, which is aimed at transitioning Caltech research to commercial implementation.<br /> <br /> {| width=80%<br /> |- valign=top<br /> | width=50% | Project participants:<br /> {{project past participants}}<br /> * Tiffany Zhou (undergraduate)<br /> * {{Zachary Sun}}<br /> * {{Abel Chiao}}<br /> | width=50% | Collaborators:<br /> * Synvitrobio, Inc.<br /> |}<br /> <br /> == Overview ==<br /> {| style=&quot;float: right&quot;<br /> |-<br /> | [[Image:breadboards-process.png|400px]]<br /> |-<br /> | align=center | Overview of the cell-free expression breadboard process.<br /> |}<br /> In vitro ''E. coli'' lysate systems have been used for more than a half-century to probe biological phenomena. However, the advancement of molecular and synthetic biology tools has resulted in increased alternative applications. In particular, in vitro systems emulate a simplistic cellular environment for rapid biological circuit prototyping. In vitro systems can also produce large amounts of protein in a controlled manner. Despite recent application advancements, there has not been commiserate research into lysate protocols. As a result, lysate development has been costly and not tuned to the specific application. We have developed a novel in vitro transcription-translation system, or TX-TL, which has shown high demand from collaborators outstripping supply. We believe that that we can increase applicability and decrease production costs by 2-5X, enabling viable commercialization of the TX-TL system.<br /> <br /> Project aims:<br /> * Optimize preparation methods for TX-TL to meet application needs. Current preparation methods to make extract for circuit prototyping are low-yield (18 mL per batch). However, alternative preparation methods exist (45 mL per batch) which are significantly less labor-intensive, but are not optimized for circuit prototyping. Research on preparation methods will be conducted to increase yields but match cellular conditions more precisely.<br /> <br /> * Reduce costs of production of TX-TL by 2-5X. Current costs, including labor, are $0.03/µL. However, with preparation modifications as well as adjustments of reaction formulas we believe we can decrease this cost. In particular, labor constitutes 60% of the cost, but the current TX-TL protocol is relatively inefficient. <br /> <br /> == Publications ==<br /> {{project paper list}}<br /> <br /> {{grant info|<br /> | agency = Caltech Grubstake<br /> | grantno = <br /> | start = 30 March 2015<br /> | end = 31 Aug 2016<br /> | support = ~1 technician + supplies<br /> | reports= final report due at end of project<br /> | ID = Caltech Grubstake<br /> }}<br /> [[Category:Completed projects]]</div> Murray https://murray.cds.caltech.edu/index.php?title=Model-guided_Discovery_and_Optimization_of_Cell-based_Sensors&diff=27161 Model-guided Discovery and Optimization of Cell-based Sensors 2025-12-07T06:15:57Z <p>Murray: </p> <hr /> <div>{{righttoc}} This is a MURI project led by Chris Voigt at MIT and involving Domitilla Del Vecchio (MIT), Michael Laub (MIT), Vincent Noireaux (UMN), Eduardo Sontag (Rutgers), Howard Salis (Penn State) and Jeff Tabor (Rice). The information on this page focuses primarily on the work involving my research group.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | width=33% |<br /> Project participants:<br /> {{project past participants}}<br /> |<br /> {| width=100% cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=50% |<br /> Collaborators:<br /> * Chris Voigt (MIT) <br /> * Domitilla Del Vecchio (MIT)<br /> * Michael Laub (MIT)<br /> * Vincent Noireaux (UMN)<br /> | width=50% |<br /> &amp;nbsp;<br /> * Eduardo Sontag (Rutgers)<br /> * Howard Salis (Penn State)<br /> * Jeff Tabor (Rice)<br /> |}<br /> |}<br /> <br /> == Objectives ==<br /> [[Image:muri11-synbio.png|right|400px]]<br /> We are applying tools from synthetic biology to construct high-performance and robust sensors that respond to non-natural signals. Our collaborators are focused on the design of sensors for the non-visible light spectrum (UV and IR) and magnetic fields, including the use of discovery methods to build first-generation genetic sensors. In practice, while these synthetic sensors are responsive under lab conditions, they lack the performance, reliability, and environmental robustness necessary for in-field applications. To this end, we are applying tools from control theory and a new concept for the ''in vitro'' characterization of genetic devices (“breadboarding”) to develop parts and design principles that make the sensors robust to environment, genetic context, and host.<br /> <br /> * Task 3.1: Analyze the robustness of alternative sensors designs that incorporate positive and negative feedback loops<br /> * Task 3.2: Quantify the impact of feedback loop timescales on sensor robustness<br /> * Task 3.3: Determine the design principles for robustness of of phosphorelay circuits to changes in the concentration of ATP and AcetylBP.<br /> <br /> == References ==<br /> {{project paper list}}<br /> * [[http:www.cds.caltech.edu/~murray/papers/guo+14-wqbio.html|Implementation And Simulation Of Phosphorylation-Based Insulator In Transcription-Translation Platform]], Shaobin Guo, Enoch Yeung, Kayzad Soli Nilgiriwala, Domitilla Del Vecchio, Richard M. Murray. Submitted, 2014 Winter q-bio Conference (5 Nov 2013).<br /> * [[http:www.cds.caltech.edu/~murray/papers/2013l_ygm14-wqbio.html|System identification of phosophorylation based insulator in a cell-free in vitro transcription-translation system]], Enoch Yeung, Shaobin Guo, Richard M. Murray. Submitted, 2014 Winter q-bio Conference (5 Nov 2013).<br /> <br /> {{grant info|<br /> | agency = Office of Naval Research<br /> | grantno = N00014-13-1-0074<br /> | start = 1 Feb 2013<br /> | end = 30 Jan 2018<br /> | support = ~2 graduate students + supplies<br /> | reports= annual reports due in June<br /> | ID = ONR MURI<br /> }}<br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]</div> Murray https://murray.cds.caltech.edu/index.php?title=Model-guided_Discovery_and_Optimization_of_Cell-based_Sensors&diff=27160 Model-guided Discovery and Optimization of Cell-based Sensors 2025-12-07T06:15:42Z <p>Murray: </p> <hr /> <div>{{righttoc}} This is a MURI project led by Chris Voigt at MIT and involving Domitilla Del Vecchio (MIT), Michael Laub (MIT), Vincent Noireaux (UMN), Eduardo Sontag (Rutgers), Howard Salis (Penn State) and Jeff Tabor (Rice). The information on this page focuses primarily on the work involving my research group.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | width=33%<br /> Project participants:<br /> {{project past participants}}<br /> |<br /> {| width=100% cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=50% |<br /> Collaborators:<br /> * Chris Voigt (MIT) <br /> * Domitilla Del Vecchio (MIT)<br /> * Michael Laub (MIT)<br /> * Vincent Noireaux (UMN)<br /> | width=50% |<br /> &amp;nbsp;<br /> * Eduardo Sontag (Rutgers)<br /> * Howard Salis (Penn State)<br /> * Jeff Tabor (Rice)<br /> |}<br /> |}<br /> <br /> == Objectives ==<br /> [[Image:muri11-synbio.png|right|400px]]<br /> We are applying tools from synthetic biology to construct high-performance and robust sensors that respond to non-natural signals. Our collaborators are focused on the design of sensors for the non-visible light spectrum (UV and IR) and magnetic fields, including the use of discovery methods to build first-generation genetic sensors. In practice, while these synthetic sensors are responsive under lab conditions, they lack the performance, reliability, and environmental robustness necessary for in-field applications. To this end, we are applying tools from control theory and a new concept for the ''in vitro'' characterization of genetic devices (“breadboarding”) to develop parts and design principles that make the sensors robust to environment, genetic context, and host.<br /> <br /> * Task 3.1: Analyze the robustness of alternative sensors designs that incorporate positive and negative feedback loops<br /> * Task 3.2: Quantify the impact of feedback loop timescales on sensor robustness<br /> * Task 3.3: Determine the design principles for robustness of of phosphorelay circuits to changes in the concentration of ATP and AcetylBP.<br /> <br /> == References ==<br /> {{project paper list}}<br /> * [[http:www.cds.caltech.edu/~murray/papers/guo+14-wqbio.html|Implementation And Simulation Of Phosphorylation-Based Insulator In Transcription-Translation Platform]], Shaobin Guo, Enoch Yeung, Kayzad Soli Nilgiriwala, Domitilla Del Vecchio, Richard M. Murray. Submitted, 2014 Winter q-bio Conference (5 Nov 2013).<br /> * [[http:www.cds.caltech.edu/~murray/papers/2013l_ygm14-wqbio.html|System identification of phosophorylation based insulator in a cell-free in vitro transcription-translation system]], Enoch Yeung, Shaobin Guo, Richard M. Murray. Submitted, 2014 Winter q-bio Conference (5 Nov 2013).<br /> <br /> {{grant info|<br /> | agency = Office of Naval Research<br /> | grantno = N00014-13-1-0074<br /> | start = 1 Feb 2013<br /> | end = 30 Jan 2018<br /> | support = ~2 graduate students + supplies<br /> | reports= annual reports due in June<br /> | ID = ONR MURI<br /> }}<br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]</div> Murray https://murray.cds.caltech.edu/index.php?title=Model-guided_Discovery_and_Optimization_of_Cell-based_Sensors&diff=27159 Model-guided Discovery and Optimization of Cell-based Sensors 2025-12-07T06:15:03Z <p>Murray: </p> <hr /> <div>{{righttoc}} This is a MURI project led by Chris Voigt at MIT and involving Domitilla Del Vecchio (MIT), Michael Laub (MIT), Vincent Noireaux (UMN), Eduardo Sontag (Rutgers), Howard Salis (Penn State) and Jeff Tabor (Rice). The information on this page focuses primarily on the work involving my research group.<br /> <br /> {| cellpadding=0 cellspacing=0 width=80%<br /> |- valign=top<br /> | <br /> Project participants:<br /> {{project past participants}}<br /> |<br /> {| width=100% cellpadding=0 cellspacing=0<br /> |- valign=top<br /> | width=50% |<br /> Collaborators:<br /> * Chris Voigt (MIT) <br /> * Domitilla Del Vecchio (MIT)<br /> * Michael Laub (MIT)<br /> * Vincent Noireaux (UMN)<br /> | width=50% |<br /> &amp;nbsp;<br /> * Eduardo Sontag (Rutgers)<br /> * Howard Salis (Penn State)<br /> * Jeff Tabor (Rice)<br /> |}<br /> |}<br /> <br /> == Objectives ==<br /> [[Image:muri11-synbio.png|right|400px]]<br /> We are applying tools from synthetic biology to construct high-performance and robust sensors that respond to non-natural signals. Our collaborators are focused on the design of sensors for the non-visible light spectrum (UV and IR) and magnetic fields, including the use of discovery methods to build first-generation genetic sensors. In practice, while these synthetic sensors are responsive under lab conditions, they lack the performance, reliability, and environmental robustness necessary for in-field applications. To this end, we are applying tools from control theory and a new concept for the ''in vitro'' characterization of genetic devices (“breadboarding”) to develop parts and design principles that make the sensors robust to environment, genetic context, and host.<br /> <br /> * Task 3.1: Analyze the robustness of alternative sensors designs that incorporate positive and negative feedback loops<br /> * Task 3.2: Quantify the impact of feedback loop timescales on sensor robustness<br /> * Task 3.3: Determine the design principles for robustness of of phosphorelay circuits to changes in the concentration of ATP and AcetylBP.<br /> <br /> == References ==<br /> {{project paper list}}<br /> * [[http:www.cds.caltech.edu/~murray/papers/guo+14-wqbio.html|Implementation And Simulation Of Phosphorylation-Based Insulator In Transcription-Translation Platform]], Shaobin Guo, Enoch Yeung, Kayzad Soli Nilgiriwala, Domitilla Del Vecchio, Richard M. Murray. Submitted, 2014 Winter q-bio Conference (5 Nov 2013).<br /> * [[http:www.cds.caltech.edu/~murray/papers/2013l_ygm14-wqbio.html|System identification of phosophorylation based insulator in a cell-free in vitro transcription-translation system]], Enoch Yeung, Shaobin Guo, Richard M. Murray. Submitted, 2014 Winter q-bio Conference (5 Nov 2013).<br /> <br /> {{grant info|<br /> | agency = Office of Naval Research<br /> | grantno = N00014-13-1-0074<br /> | start = 1 Feb 2013<br /> | end = 30 Jan 2018<br /> | support = ~2 graduate students + supplies<br /> | reports= annual reports due in June<br /> | ID = ONR MURI<br /> }}<br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]</div> Murray https://murray.cds.caltech.edu/index.php?title=Molecular_Programming_Architectures,_Abstractions,_Algorithms,_and_Applications&diff=27158 Molecular Programming Architectures, Abstractions, Algorithms, and Applications 2025-12-07T06:14:42Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> This is a joint project between Caltech, Harvard, U. Washington and UCSF. This page primarily describes the work done in Richard Murray's group; see the [[http:molecular-programming.org|MPP homepage]] for a description of the complete project.<br /> <br /> {| width=80%<br /> |- valign=top<br /> | width=50% | Project participants:<br /> {{project past participants}}<br /> * {{Jongmin Kim}}<br /> | width=50% | Collaborators<br /> {{project collaborators}}<br /> |}<br /> <br /> == Overview ==<br /> [[Image:nsf13-mpp.png|right|400px]]<br /> Molecular programming involves the specification of structures, circuits, and behaviors both within living and non-living systems—systems in which computing and decision-making will carried out by chemical processes themselves. Our work focuses on the development of ''in vitro'' circuits that demonstrate the principles of feedback in biomolecular systems and the application of cell-free assays as a &quot;biomolecular breadboard&quot; for molecular programming.<br /> <br /> == Publications ==<br /> {{project paper list}}<br /> <br /> &lt;br clear=both&gt;&lt;hr&gt;<br /> {{grant info|<br /> | agency = NSF<br /> | grantno = 1317694<br /> | start = 1 Oct 2013<br /> | end = 30 Sep 2018<br /> | support = shared students/postdocs + supplies<br /> | reports = annually in September<br /> | ack = Research supported by the National Science Foundation award number 1317694.<br /> | ID = NSF MPP2<br /> }}<br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]</div> Murray https://murray.cds.caltech.edu/index.php?title=Molecular_Programming_Project&diff=27157 Molecular Programming Project 2025-12-07T06:14:25Z <p>Murray: </p> <hr /> <div>This is a joint project with Erik Winfree (PI), Shuki Bruck, Eric Klavins (UW), Niles Pierce and Paul Rothemund, funded by the NSF Expeditions program. This page primarily describes the work done in Richard Murray's group; see the [[http:molecular-programming.org|MPP homepage]] for a description of the complete project.<br /> <br /> {| <br /> |- valign=top<br /> | Project participants:<br /> * {{Dan Siegal (-Gaskins)}}<br /> * {{Anu Thubagere}}<br /> * {{Sean Sanchez}}*<br /> &lt;br&gt;<br /> __TOC__<br /> |<br /> * {{Dionysios Barmpoutis}}<br /> * {{Fei Chen}}<br /> * Nadine Dabby (PhD student, CNS)<br /> * Mattius Falk (SURF)<br /> * Juan Flores-Quijano (SURF)<br /> * {{Elisa Franco}}<br /> * Giulia Giordano (SURF)<br /> * Aurelija Grigonyte (SURF)<br /> * Shaunak Kar (SURF)<br /> | &amp;nbsp;<br /> * Ishan Kheterpal (SURF)<br /> * {{Jongmin Kim}}<br /> * Patrik Lundin (SURF)<br /> * Monica Li (SURF)<br /> * Andrew Ng (SURF)<br /> * Arjun Ravikumar (SURF)<br /> * Rohit Sharma (SURF)<br /> * {{Christopher Sturk}}<br /> |}<br /> <br /> == Objectives ==<br /> {| style=&quot;float: right&quot; width=40% border=1<br /> |-<br /> | [[Image:rate-regulator.png|320px]]&lt;br&gt;<br /> Schematic for a positive rate regulator (a) and a negative rate regulator (b). The negative rate regulator on the right works by creating two transcripts that are complementary to teach other and also contain sequences complementary to an activator strand for the &quot;genelets&quot; T1:A1 and T2:A2. If one of the templates produces excess transcripts compared to the other, the excess strands will strip off the activators, downregulating the appropriate genelet. The positive rate regulator works in a similar fashion, except the outputs from the genelets cross upregulate.<br /> |}<br /> The long term goal of the Molecular Programming Project is to establish a fundamental approach to the design of complex molecular and chemical systems based on the principles of computer science. The focus of our study, molecular programs, are collections of molecules that may perform a computation, fabricate an object, or control a system of molecular sensors and actuators. This project aims to develop tools and theories for molecular programming--such as programming languages and compilers--that will enable systematic design and implementation in the laboratory.<br /> <br /> Current work includes:<br /> * Developing ''in vitro'' transcriptional circuits capable of equalizing the rates of production of transcripts (Franco, Chen)<br /> * Modeling and analyzing the role of crosstalk in biological circuits (Barmpoutis)<br /> * Modeling, characterization and interconnection of transcriptional oscillators (Franco, Winfree)<br /> <br /> == Publications ==<br /> ==== Journal ====<br /> * {{fra+11-pnas}}<br /> ==== Conference ====<br /> * {{gfm13-acc}}<br /> * {{yeu+12-cdc}}<br /> * {{km11-biocas}}<br /> * {{sfm10-cdc}}<br /> * {{fdm09-cdc}}<br /> * {{fm08-cdc}}<br /> <br /> [[Category:Completed projects]]<br /> [[Category:Biocircuits projects]]<br /> {{#set: agency=NSF | end date = 2014}}<br /> {{#set: ID=NSF MPP}}</div> Murray https://murray.cds.caltech.edu/index.php?title=Multi-Layer,_Composable_and_Programmable_Biomolecular_Circuits_for_Microbial_Consortia&diff=27156 Multi-Layer, Composable and Programmable Biomolecular Circuits for Microbial Consortia 2025-12-07T06:13:33Z <p>Murray: </p> <hr /> <div>{{righttoc}} <br /> The long-term goal of this project is to create the mathematical, experimental, and application framework for recombinase-based biomolecular circuits, with a new focus on distributed operations in microbial consortia. Initial work has demonstrated the construction of a synthetic plasmid conjugation system that can pass plasmids to defined recipient strains within a population. In this project, we will build on those results and use plasmid conjugation as a means to implement multi-strain engineered microbial consortia with dynamic properties that are relevant for a range of modular, composable and programmable biological behaviors, including event logging, materials synthesis, programmable biofilms, and engineered living materials.<br /> <br /> Project participants:<br /> {{project past participants}}<br /> <br /> === Objectives ===<br /> [[Image:icb-multilayer.png|right|240px]]<br /> Our objective for this project is to demonstrate that by decoupling transfer blocking from plasmid cleavage, we can engineer programmable behavior that operates at the population-level layer. Then, by encoding variants of a given transcriptional circuit on different plasmid types, we will demonstrate the composability of circuit dynamics across multiple layers. Finally, we will construct strain-level circuit elements and compose them with circuit elements at the transcriptional and plasmid layers to demonstrate how multilayer systems lead to multiplicative scaling in the number of system configurations.<br /> <br /> === References ===<br /> {{project paper list}}<br /> <br /> [[Category:Completed projects]]<br /> {{Project<br /> |Title=Multi-Layer, Composable and Programmable Biomolecular Circuits for Microbial Consortia<br /> |Agency=Army Research Office<br /> |Grant number=W911NF-19-2-0026<br /> |Start date=1 Dec 2021<br /> |End date=30 Nov 2023<br /> |Support summary=1 graduate student, part-time technician<br /> |Reporting requirements=Annual reports<br /> |Project ID=ICB multilayer<br /> |ack=This research is supported by the Institute for Collaborative Biotechnologies through cooperative agreement W911NF-19-2-0026 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.<br /> }}</div> Murray