Murray Wiki - User contributions [en]

Group Schedule, Fall 2023

2023-10-03T18:06:18Z

Zjuradoq:

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/myschedule.html|Richard's calendar]]
| width=50% |
* [[Group Schedule, Summer 2023]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits group meetings are in 111 Keck and NCS group meetings are in 110 Steele.

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

| width=25% |
=== Week 1: 25 Sep - 29 Sep ===
'''Biocircuits: Tue, 10a-12p'''
* Alex
'''NCS: <s>Tue, 3:30p-5p</s>'''
* No meeting this week

| width=25% |

=== Week 2: 2-6 Oct ===
'''Biocircuits: Mon, 10a-12p'''
* Manisha
'''NCS: Thu, 3:45p-5p'''
* Nikos

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=== Week 3: 9-13 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Synthetic Cell
'''NCS: Tue, 3:30p-5p'''
* T&E

| width=25% |

=== Week 4: 16-20 Oct ===
'''Biocircuits: <s>Tue</s> Mon, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Apurva

|- valign=top
| width=25% |

=== Week 5: 23-27 Oct ===
'''Biocircuits: <s>Tue, 10a-12p</s> Mon, 9a-11a '''
* Matt
'''NCS: <s>Wed, 3:45p</s> Tue, 3:30-5p'''
* Kellan

| width=25% |

=== Week 6: 30 Oct - 3 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Zoila
* Meeting might shift to Wed or Thu
'''NCS: Wed, 3:45p-5p'''
* TBD
* Meeting might shift to Tue or Thu

| width=25% |

=== Week 7: 6-10 Nov ===
'''Biocircuits: <s>Tue</s> Wed, 10a-12p'''
* Elin
* Meeting might shift to Wed
'''NCS: Wed, 3:45p-5p'''
* Josefine

| width=25% |

=== Week 8: 13-17 Nov ===
'''Biocircuits: Mon, 10a-12p'''
* Individual updates
'''NCS: Thu, 3:45p-5p'''
* T&E

|- valign=top
| width=25% |

=== Week 9: 20-26 Nov ===
* Thanksgiving week, no meetings

| width=25% |

=== Week 10: 27 Nov - 1 Dec ===
'''Biocircuits: <s>Tue</s> Wed, 10a-12p'''
* Yan
* Might shift to Wed
'''NCS: Wed, 3:45p-5p'''
* Kimia
'''Synthetic Cell: Thu, 10a-12p'''
* TBD

| width=25% |

=== Week 11: 4-8 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* TBD
'''NCS: Wed, 3:45p-5p'''
* Ioannis

| width=25% |

=== Week 12: 11-15 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* T&E
<hr>
* CDC'23 this week
|}

Paul Freemont, January 2023

2023-01-24T01:12:27Z

Zjuradoq: /* Tuesday */

Paul Freemont will visiting Caltech on 23-27 January. Sign up for times to meet with Paul here:
__NOTOC__

=== Monday ===
* 9:45 am: Richard Murray, 109 Steele Lab
* 10:15 am: Cell-free metabolism, 111 Keck (Ayush, Manisha, Yan, Zoila; Alex, Blade, Mark, Matt K, Zach)
* 12:15 pm: Lunch at the Ath with students/postdocs (Ayush, Manisha, Yan, Zoila)
* 1:30 pm: Open
* 2:00 pm: Gözde Demirer, 217 Spalding
* 3:00 pm: Open
* 5:30 pm: Done for the day

=== Tuesday ===
* 9 am: EBRC PI&E meeting (Zoom)
* 10 am: open
* 10:45 am: Active Matter, 111 Keck (Alex, Matt T (+n), Zach; Blade, Joe, Manisha, Mark, Matt K, Yan, Zoila)
* 12:30 pm: Lunch at the Ath with Richard, Elisa Franco
* 2:00 pm: Elisa Franco, 111 Steele Lab
* 2:45 pm: Zoila and Ayush, 111 Keck
* 3:30 pm: Synthetic cell #1, 111 Keck (Ayush, Alex, Blade, Manisha, Mark, Matt K, Steve, Yan, Zach, Zoila)
* 5:30 pm: Done for the day

=== Thursday ===
* 8:30 am: Richard, 109 Steele Lab
* 9:00 am: Schmidt Futures discussion
* 10:30 am: open
* 1:30 pm: Synthetic cell #2, 110 Steele [tentative] (Ayush, Blade, Manisha, Mark, Matt K, Steve, Yan, Zach, Zoila; Joe)
* 3:30 pm: Open
* 5:30 pm: Done for the day

=== Friday ===
* 8:00 am: Manisha candidacy
* 9:30 am: Richard Murray, 109 Steele Laboratory
* 10:00 am: Open
* 12:00 pm: Done for the day

Paul Freemont, January 2023

2023-01-23T22:56:11Z

Zjuradoq: /* Tuesday */

Paul Freemont will visiting Caltech on 23-27 January. Sign up for times to meet with Paul here:
__NOTOC__

=== Monday ===
* 9:45 am: Richard Murray, 109 Steele Lab
* 10:15 am: Cell-free metabolism, 111 Keck (Ayush, Manisha, Yan, Zoila; Alex, Blade, Mark, Matt K, Zach)
* 12:15 pm: Lunch at the Ath with students/postdocs (Ayush, Manisha, Yan, Zoila)
* 1:30 pm: Open
* 2:00 pm: Gözde Demirer, 217 Spalding
* 3:00 pm: Open
* 5:30 pm: Done for the day

=== Tuesday ===
* 9 am: EBRC PI&E meeting (Zoom)
* 10 am: open
* 10:45 am: Active Matter, 111 Keck (Alex, Matt T (+n), Zach; Blade, Joe, Manisha, Mark, Matt K, Yan, Zoila)
* 12:30 pm: Lunch at the Ath with Richard, Elisa Franco
* 2:00 pm: Elisa Franco, 111 Steele Lab
* 2:45 pm: Zoila and Ayush, TBD
* 3:30 pm: Synthetic cell #1, 111 Keck (Ayush, Alex, Blade, Manisha, Mark, Matt K, Steve, Yan, Zach, Zoila)
* 5:30 pm: Done for the day

=== Thursday ===
* 8:30 am: Richard, 109 Steele Lab
* 9:00 am: Schmidt Futures discussion
* 10:30 am: open
* 1:30 pm: Synthetic cell #2, 110 Steele [tentative] (Ayush, Blade, Manisha, Mark, Matt K, Steve, Yan, Zach, Zoila; Joe)
* 3:30 pm: Open
* 5:30 pm: Done for the day

=== Friday ===
* 8:00 am: Manisha candidacy
* 9:30 am: Richard Murray, 109 Steele Laboratory
* 10:00 am: Open
* 12:00 pm: Done for the day

Manos Alexis, Oct 2022

2022-10-21T16:50:12Z

Zjuradoq:

Manos Alexis, a PhD student at Cambridge interested in dynamical systems, control theory, synthetic biology and systems biology will visit our group the week of 24 Oct. You can sign up for a time to meet with him below:

=== 24 Oct (Mon) ===

* 9:00 am: Monica Nolasco, 107 Steele Lab
* 10:00 am: Richard Murray, 109 Steele Lab
* 10:45 am: Zoila Jurado, Red Door Cafe
* 11:30 am: Alex Johnson
* 12:00 pm: Lunch w/ soil syn bio students (tentative)
* 1:30 pm: John Marken
* 2:15 pm: open
* 3:00 pm: open
* 3:45 pm: open
* 4:30 pm: open

=== 25 Oct (Tue) ===

* 9:00 am: open
* 10:00 am: Biocircuits group meeting, 111 Keck
* 12:00 pm: Lunch w/ synthetic cell students (tentative)
* 1:30 pm: open
* 2:15 pm: open
* 3:00 pm: open
* 3:45 pm: open
* 4:30 pm: open

Manos Alexis, Oct 2022

2022-10-21T16:39:50Z

Zjuradoq:

Manos Alexis, a PhD student at Cambridge interested in dynamical systems, control theory, synthetic biology and systems biology will visit our group the week of 24 Oct. You can sign up for a time to meet with him below:

=== 24 Oct (Mon) ===

* 9:00 am: Monica Nolasco, 107 Steele Lab
* 10:00 am: Richard Murray, 109 Steele Lab
* 10:45 am: Zoila Jurado
* 11:30 am: Alex Johnson
* 12:00 pm: Lunch w/ soil syn bio students (tentative)
* 1:30 pm: John Marken
* 2:15 pm: open
* 3:00 pm: open
* 3:45 pm: open
* 4:30 pm: open

=== 25 Oct (Tue) ===

* 9:00 am: open
* 10:00 am: Biocircuits group meeting, 111 Keck
* 12:00 pm: Lunch w/ synthetic cell students (tentative)
* 1:30 pm: open
* 2:15 pm: open
* 3:00 pm: open
* 3:45 pm: open
* 4:30 pm: open

Nacho Gispert, 10 Aug 2022

2022-08-08T17:15:07Z

Zjuradoq:

Ignacio (Nacho) Gispert, a postdoc with Yuval Elani at Imperial will visit on 10 Aug 2022 (Wed).

Schedule:
* 9:15 am: Richard Murray, 109 Steele
* 10:00 am: Group meeting (Nacho + summer students + lab updates)
* 12:00 pm: Lunch with Manisha and Zoila
* 1:30 pm: Zoila
* 2:15 pm: open
* 3:00 pm: CDS Tea
* 3:45 pm: open
* 4:30 pm: open
* 5:30 pm: Richard, 109 Steele

Research interests: Nacho's research focuses on artificial/biological hybrid cells, specially on how to replicate cell characteristics and behavior in artificial cell-like entities.

Yan Zhang, 28 Mar 2022

2022-03-25T00:35:40Z

Zjuradoq:

Yan Zhang, a PhD student at Georgia Tech will visit on 28 Mar 2022.

Schedule:
* 8:30 am: Richard Murray, 109 Steele
* 9:00 am: Open
* 10:00 am: Group meeting presentation
* 12:00 pm: Lunch with Chelsea, Michaelle
* 1:15 pm: Open
* 2:00 pm: Meet with Ayush at Red Door
* 2:45 pm: Meet with Manisha (at Red Door?)
* 3:30 pm: Meet with Zoila (meet at Red Door -> walk to Lake)
* 4:15 pm: Open
* 5:00 pm: Richard Murray, 109 Steele

Research interests:
* Developed a new diagnostic platform interfacing cell-free biosensors with biphasic polymer systems for simultaneous detection of diverse classes of analytes that are robust to human biofluids and field-deployable.
* Integrated cell-free biosensors to a personal glucose monitor for rapid and reliable biomarker quantification at the point of need
* Designed, characterized, and optimized cell-free bacterial biosensors to detect micronutrient deficiencies, pathogenic bacterial infections, and heavy metal environment contaminants

David Garcia, 13 Feb 2020

2020-02-10T21:45:01Z

Zjuradoq: /* Schedule */

David Garcia, a PhD student working at Oak Ridge National Laboratory (ORNL) will visit Caltech on 13 Feb (Thu). If you would like to meet with him, sign up here (using your IMSS credentials).

=== Schedule ===
* 9:15 am: Richard (107 Steele Lab)
* 10:00 am: Seminar
* 11:00 am: Zoila
* 11:45 am: Lunch (Michaelle, Chelsea)
* 1:00 pm: Open
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Open
* 4:45 pm: Wrap up meet with Richard

=== Seminar ===

Cell-Free Enabled Bioproduction and Biological Discovery 
David Garcia, The University of Tennessee, Knoxville and Oak Ridge National Laboratory 

111 Keck or 114 Steele for Thu, 10a-11a

As our understanding of the microbial world has progressed, so too has the backlog of information and open questions generated from the thousands uncharacterized proteins and metabolites with potential applications as biofuels, therapeutics, and biomaterials. To address this problem, new tools need to be developed in order to rapidly test and take advantage of uncharacterized proteins and metabolites. Cell-free systems have developed into a high-throughput and scalable tool for synthetic biology and metabolic engineering with applications across multiple disciplines. The work presented in this talk leverages cell-free systems as a conduit for the exploration of protein function and metabolite production using two complementary approaches. The first elucidates interaction networks associated with secondary metabolite production using a computationally assisted pathway description pipeline that employs bioinformatic searches of genome databases, structural modeling, and ligand-docking simulations to predict the gene products most likely to be involved in a metabolic pathway. In vitro reconstructions of the pathway are then modularly assembled and chemically verified in Escherichia coli lysates in order to differentiate between active and inactive pathways. The second takes a systems and synthetic biology approach to engineer E. coli extracts capable of directing flux towards specific metabolites. Using growth and genome engineering-based methods, we produced cell-free proteomes capable of creating unconventional metabolic states with minimal impact on the cell in vivo. As a result of this work, we have significantly expanded our ability to use cell extracts outside of their native context to solve metabolic engineering problems and provide engineers new tools that can rapidly explore the functions of proteins and test novel metabolic pathways.

Group Schedule, Fall 2019

2019-10-04T18:13:14Z

Zjuradoq: /* Week 5: 28 Oct - 1 Nov */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Summer 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 314 Annenberg.

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

| width=25% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: Tue, <s>10a-12p</s> 9a-11a'''
* Ayush
* Cindy
* Note: meeting will probably shift to start at 9 am
'''NCS: Wed, 10a-11:30a, BBB 181'''
* Thomas Mohren (visitor)

| width=25% |

=== Week 2: 7-11 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Prithvi

| width=25% |

=== Week 3: 14-18 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Michaelle
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Sumanth

| width=25% |

=== Week 4: 21-27 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Meeting may shift to Mon, 3p-5p
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Karena
* Note: meeting may shift to 11a-12p

|- valign=top
| width=25% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Open
* William
'''NCS: Wed, 3:45p-5p'''
* Richard C

| width=25% |

=== Week 6: 4-8 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Tung

| width=25% |

=== Week 7: 11-15 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Chelsea
* Rory
'''NCS: Wed, 3:45p-5p'''
* Reza

| width=25% |

=== Week 8: 18-22 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Yuxiao
* Note: meeting may shift to Fri, 3p-4p

|- valign=top
| width=25% |

=== Week 9: 25-29 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Elin
* Rotation/UG

| width=25% |

=== Week 10: 2-6 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Apurva
* Note: meeting may shift to Mon, 4p-5p

| width=25% |

=== Week 11: 9-13 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* Rotation/UG
* Rotation/UG
'''NCS: Wed, 3:45p-5p'''
* Josefine

| width=25% |

=== Week 12: 16-20 Dec ===
* Winter recess

|}

Group Schedule, Fall 2019

2019-10-04T18:13:02Z

Zjuradoq: /* Week 3: 14-18 Oct */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Summer 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 314 Annenberg.

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

| width=25% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: Tue, <s>10a-12p</s> 9a-11a'''
* Ayush
* Cindy
* Note: meeting will probably shift to start at 9 am
'''NCS: Wed, 10a-11:30a, BBB 181'''
* Thomas Mohren (visitor)

| width=25% |

=== Week 2: 7-11 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Prithvi

| width=25% |

=== Week 3: 14-18 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Michaelle
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Sumanth

| width=25% |

=== Week 4: 21-27 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Meeting may shift to Mon, 3p-5p
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Karena
* Note: meeting may shift to 11a-12p

|- valign=top
| width=25% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Open
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Richard C

| width=25% |

=== Week 6: 4-8 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Tung

| width=25% |

=== Week 7: 11-15 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Chelsea
* Rory
'''NCS: Wed, 3:45p-5p'''
* Reza

| width=25% |

=== Week 8: 18-22 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Yuxiao
* Note: meeting may shift to Fri, 3p-4p

|- valign=top
| width=25% |

=== Week 9: 25-29 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Elin
* Rotation/UG

| width=25% |

=== Week 10: 2-6 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Apurva
* Note: meeting may shift to Mon, 4p-5p

| width=25% |

=== Week 11: 9-13 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* Rotation/UG
* Rotation/UG
'''NCS: Wed, 3:45p-5p'''
* Josefine

| width=25% |

=== Week 12: 16-20 Dec ===
* Winter recess

|}

Sara Molinari, 29 Jan 2019

2019-01-28T01:32:02Z

Zjuradoq: /* Schedule */

Sara Molinari will visit Caltech on 29-30 Jan 2019.

=== Schedule ===

{| width=100% border=1
|- valign=top
| width=50% |
29 Jan (Tue):
* 8:30 am: Richard, 109 Steele Lab
* 9:00 am: seminar
* 10:00 am: Andrey (meet after seminar)
* 10:45 am: Joe (Keck 238)
* 11:30 am: Zoila (Watson courtyard)
* 12:00 pm: Lunch with postdocs John McManus, Leo Green
* 1:00 pm: ELM discussion (Richard, James, Rory, ERDC?)
* 2:00 pm: Andy (meet at Richard's office)
* 2:45 pm: open
* 3:30 pm: open
* 4:15 pm: open
* 5:00 pm: done for the day
* 6:00 pm (or other): dinner with grad students (John Marken, Andy, Joe, Rory) (TBD)

| width=50% |
30 Jan (Wed):
* 9:00 am: Biocircuits group meeting
* 11:00 am: Hold: Niles?
* 11:45 am: open
* 12:30 pm: working lunch with James and Rory
* 1:45 pm: John Marken (103 Steele)
* 2:30 pm: Richard, 109 Steele Lab
* 3:00 pm: depart campus
|}

=== Talk ===

'''Engineering asymmetrical cell division into Escherichia coli'''

Sara Molinari, Rice University 
29 Jan (Tue) @ 9 am, 111 Keck

Multicellularity, in eukaryotic organisms, is ultimately responsible for most of the tissues features, such as controlling its shape and size, distributing biochemical, structural and reproductive tasks. Multicellularity is reached through asymmetrical cell division in which progenitor cells create a differentiated daughter cell while retaining their original phenotype. Here, we describe a synthetic genetic circuit for controlling asymmetrical cell division in Escherichia coli. Specifically, we engineered an inducible system that can bind and segregate plasmid DNA to a single position in the cell. Upon division, the co-localized plasmids are kept by one and only one of the daughter cells. The other daughter cell receives no plasmid DNA and is hence irreversibly differentiated from its sibling. In this way, we achieved asymmetric cell division though asymmetric plasmid partitioning. We used this system to achieve physical separation of genetically different cells. We also characterized an orthogonal inducible circuit that enables the simultaneous asymmetric partitioning of two plasmid species – resulting in pluripotent cells that have four distinct differentiated states. These results point the way towards engineering multicellular systems from prokaryotic hosts.