Murray Wiki - User contributions [en]

March 2013 meeting schedule

2013-03-04T03:56:36Z

Ckempes: /* 7 Mar (Thu) */

The list below has times that I am available to meet between 4 March and 13 March. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). Please only sign up for one time slot. __NOTOC__

{| width=100% border=1
|- valign=top
| width=30% |
==== 6 Mar (Wed) ====
{{agenda begin}}
{{agenda item|8:45-9:45|Ophelia}}
{{agenda item||}}
{{agenda item|1:15-2:00|Stephanie}}
{{agenda item||}}
{{agenda item|5:00-5:45|Shuo}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Jongmin}}
{{agenda item|6:45-7:30|Zoltan}}
{{agenda end}}
| width=30% |

==== 7 Mar (Thu) ====
{{agenda begin}}
{{agenda item|2:00-3:30|DARPA breadboards}}
{{agenda item|4:00-4:15|UG advisee}}
{{agenda item|4:15-5:00|Open}}
{{agenda item|5:00-5:45|Chris Kempes}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Anandh}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
| width=30% |

==== 8 Mar (Fri) ====
{{agenda begin}}
{{agenda item|8:45-9:30|Enoch}}
{{agenda item||}}
{{agenda item|11:00-11:45|ALL telecon (Enoch, Joe M)}}
{{agenda item||}}
{{agenda item|12:00-1:15|NCS group meeting}}
{{agenda item|1:15-2:00|Nadine (might get shortened)}}
{{agenda item||}}
{{agenda item|5:00-5:45|Eric}}
{{agenda item|5:45-6:30|Scott Livingston}}
{{agenda end}}

|- valign=top
|

==== 10 Mar (Sun) ====
{{agenda begin}}
{{agenda item|2:30-2:45|UG advisee}}
{{agenda item|2:45-3:00|UG advisee}}
{{agenda item|3:00-4:00|dan}}
{{agenda item|4:00-5:00|Open}}
{{agenda item|5:00-6:00|Open}}
{{agenda item|6:00-6:15|UG advisee}}
{{agenda item|6:15-6:30|UG advisee}}
{{agenda end}}
|

==== 11 Mar (Mon) ====
{{agenda begin}}
{{agenda item|3:30-4:15|Mumu}}
{{agenda item|4:15-5:00|Shaobin}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Marcella}}
{{agenda item|6:00-6:45|Victoria}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|

==== 12 Mar (Tue) ====
{{agenda begin}}
{{agenda item|11:00-11:45|Emzo}}
{{agenda item||}}
{{agenda item|1:00-3:00|Biocircuits meeting}}
{{agenda item||}}
{{agenda item|3:30-4:15|Nathan Belliveau}}
{{agenda item|4:15-5:00|Vipul}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Open}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|}

SURF 2013: The connection between biological structure and function in dynamic environments

2013-01-16T21:59:49Z

Ckempes: Created page with "'''2013 SURF project description''' * Mentor: Richard Murray * Co-mentor: Chris Kempes The connection between biological structure and function is one of the o..."

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Chris Kempes

The connection between biological structure and function is one of the oldest interests in science. Recently there has been renewed interest in focusing on biological structure as a central property of organisms. We are offering two potential SURF projects focusing on biological structure as it relates to either 1.) organized communities of bacteria or 2.) the structure of forest ecosystems and the Earth’s climate.

1.) Recently it has been shown that communities of bacteria that group together increase their overall chances of survival [1]. These communities can often produce remarkably complex structures composed of billions of cells. In this project we will investigate the cellular behaviors responsible for these structures through simulations and comparisons with existing empirical data.

2.) Recently we have produced a model which connects generalized tree structure with local resources and simple physical principles to successfully predict maximum tree height across the United States [2]. This SURF project will expand our model to predict many forest features, such as the total leaf cover, and to link our simulation with the Earth’s climate system to test the feedback that vegetation has on climate change.

----

==== References ====

# Xavier, Joao B., and Kevin R. Foster. "Cooperation and conflict in microbial biofilms." Proceedings of the National Academy of Sciences 104.3 (2007): 876-881.
# Kempes, Christopher P., et al. "Predicting maximum tree heights and other traits from allometric scaling and resource limitations." PLoS One 6.6 (2011): e20551.

SURF 2013

2013-01-16T21:57:46Z

Ckempes:

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2013. It contains a list of project areas where I will be supervising projects this year along with information about how to apply for a SURF project in my group.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 11 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student or part of one of our CDS exchange programs (Lund, KTH), I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 12 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on 22 Feb 2013.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 18 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
| {{SURF entry|2013|The costs and benefits of various designs of biochemical 'decision engines'}}
| [[Molecular Programming Project|MPP]]
| Dan Siegal-Gaskins
|
|-
| {{SURF entry|2013|Robot Motion Planning with Complex Tasks}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| Eric Wolff
|
|-
| {{SURF entry|2013|Experiments with dynamic obstacles and correct-by-construction controllers}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| [http://scottman.net Scott C. Livingston]
|
|-
| {{SURF entry|2013|Synthetic logic circuits using RNA aptamers}}
| [[Molecular Programming Project|MPP]]
| Jongmin Kim
|
|-
| {{SURF entry|2013|Role of Delays in Biological Processes}}
| [[Molecular Programming Project|MPP]]
| Marcella Gomez
|
|-
| {{SURF entry|2013|Designing phosphorylation sensitive protein domains for use in synthetic circuits}}
| [[Molecular Programming Project|MPP]]
| Emzo de los Santos
|
|-
| {{SURF entry|2013|Synthetic biological circuit design implementing protein degradation in-vitro}}
| [[Molecular Programming Project|MPP]]
| [http://www.its.caltech.edu/~zsun Zach Sun]
|
|-
|{{SURF entry|2013|Understanding the Effect of Compositional Context on Biocircuit Performance}}
| [[Molecular Programming Project|MPP]]
| [http://www.cds.caltech.edu/~eyeung Enoch Yeung]
|
|-
|{{SURF entry|2013|Investigating physical methods of protecting linear DNA fragments in cell-free expression systems}}
| [[Molecular Programming Project|MPP]]
| Anu Thubagere
|
|-
| {{SURF entry|2013|The connection between biological structure and function in dynamic environments}}
|
| Chris Kempes
|
|}

SURF 2013

2013-01-16T21:57:33Z

Ckempes:

SURF 2013

2013-01-16T21:57:07Z

Ckempes:

Group Schedule, Spring 2012

2012-04-02T21:38:47Z

Ckempes: /* Week 6: 7 May - 11 May */

Group Schedule, Winter 2012

2011-12-13T02:02:46Z

Ckempes:

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


==== Directions: ====
* '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.
* '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once
* '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates
* '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)


<center>
'''Please sign up for at least one presentation in the first six weeks of the term.'''
</center>

Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed
 

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 11 Jan (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 2-4 pm'''
* Research presentation (30-40 min)
* Dan (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Enoch (10-15 min)
* Lab updates
'''Group meeting: 25 Jan (Wed), 12-1:15'''
* Necmiye
'''Robotics: 25 Jan (Wed), 4-6 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Research Presentation (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Chris Kempes
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Research presentation (30-40 min)
* Marcella (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Open (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Dec 2011 meetings

2011-12-07T03:53:16Z

Ckempes: /* 15 Dec (Thu) */

The list below has times that I am available to meet on 15-21 Dec. __NOTOC__
* Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and see if you can switch).
* To maximize the chance I get to meet with everyone, '''please sign up for times on 19-22 Dec if you are around that week'''

 
<table width=100% border=1>
<tr valign=top><td width=20%>
==== 15 Dec (Thu) ====
{{agenda begin}}
{{agenda begin}}
{{agenda item|10:00a|Enoch}}
{{agenda item|11:00a|Victoria}}
{{agenda item||}}
{{agenda item|4:30p|Shaunak}}
{{agenda item|5:30p|Hamed}}
{{agenda item|6:30p|Chris Kempes}}
{{agenda end}}
</td><td width=20%>

==== 16 Dec (Fri) ====
{{agenda begin}}
{{agenda item|10:00a|Open}}
{{agenda item|11:00a|Open}}
{{agenda item||}}
{{agenda item|2:30p|Shuo}}
{{agenda item|3:30p|Jongmin/Shaunak}}
{{agenda item|4:30p|Dominic}}
{{agenda item|5:30p|Andrea}}
{{agenda end}}
</td><td width=20%>

==== 19 Dec (Mon) ====
{{agenda begin}}
{{agenda item|12:30p|Mumu}}
{{agenda item|1:30p|Lab inspection}}
{{agenda item||}}
{{agenda item|5:00p|Ophelia}}
{{agenda end}}
</td><td width=20%>

==== 20 Dec (Tue) ====
{{agenda begin}}
{{agenda item|10:00a| Scott Livingston}}
{{agenda item|11:00a|Open}}
{{agenda item||}}
{{agenda item|2:00p|Open}}
{{agenda item|3:00p|Open}}
{{agenda item|4:00p|Open}}
{{agenda end}}
</td><td width=20%>

==== 21 Dec (Wed) ====
{{agenda begin}}
{{agenda item|11:30a|Open}}
{{agenda item||}}
{{agenda item|2:00p|Open}}
{{agenda item|4:00p|Open}}
{{agenda item|5:00p|Open}}
{{agenda end}}
</td></tr>
</table>