SURF 2013

This page is intended for students working on SURF projects in the Summer of 2013. Mainly for me to keep track of everything that is going on.

Students

Student	Mini-group	Co-mentor(s)	Project
Bern, James	NCS	Eric	Robot Motion Planning with Complex Tasks
Falt, Mattias	NCS	Marcella	The role of delays in biological systems
Grigonyte, Aurelija	Biocricuits	Emzo	Characterizing gene expression for different extracts
Li, Monica	Biocircuits	Anu	Investigating physical methods of protecting linear DNA fragments in cell free expression systems
Mickelin, Oscar	NCS	Necmiye	Synthesis of correct-by-construction control protocols for air management systems of aircraft
Ng, Andrew	Biocircuits	Enoch	Understanding and Quantifying the Effect of Compositional Context on Biocircuit Performance
Quijano, Juan	Biocircuits	Jongmin	Synthetic logic circuits using RNA aptamers
Sharma, Rohit	Biocircuits	Zach	Synthetic biological circuit design implementing protein degradation in-vitro
Zheng, Chris	NCS	Scott	Experiments with dynamic obstacles and correct-by-construction controllers
Zhou, Tiffany	Biocircuits	Dan	The costs and benefits of various designs of biochemical 'decision engines'

Meetings on 18-24 June

Tue (18 Jun) SURF orientation

Wed (19 Jun) 10:00 - Meeting with co-mentors, 114 Steele Lab Biocircuits: lab orientation/cleanup 12:00 - SURF seminar 1:30 - Caltech safety briefing (mandatory) 2:30-5:00 - TX-TL course (biocircuits)

Thu (20 Jun) 10:00-5:00 - TX-TL course (biocircuits)

Fri (21 Jun) 10:00-5:00 - TX-TL course (biocircuits) 10:00-11:30 - Lab orientation/cleanup (NCS) 12 Steele (NCS SURFs, co-mentors, Andrea)

Mon (24 Jun) 10:00-12:00 - SURF group meeting with Richard and co-mentors, 114 Steele 1 chart overviews (5 min each)

Original project descriptions

This section 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.

1. 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.
2. 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
3. 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.
4. 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.
5. All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on 22 Feb 2013.
6. 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

Title	Grant/Project	Co-Mentors	Comments
The costs and benefits of various designs of biochemical 'decision engines'	MPP	Dan Siegal-Gaskins
Robot Motion Planning with Complex Tasks	Boeing	Eric Wolff
Experiments with dynamic obstacles and correct-by-construction controllers	Boeing	Scott C. Livingston
Synthetic logic circuits using RNA aptamers	MPP	Jongmin Kim
Role of Delays in Biological Processes	MPP	Marcella Gomez
Designing phosphorylation sensitive protein domains for use in synthetic circuits	MPP	Emzo de los Santos
Synthetic biological circuit design implementing protein degradation in-vitro	MPP	Zach Sun
Understanding the Effect of Compositional Context on Biocircuit Performance	MPP	Enoch Yeung
Investigating physical methods of protecting linear DNA fragments in cell-free expression systems	MPP	Anu Thubagere
The connection between biological structure and function in dynamic environments		Chris Kempes