SURF 2008

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This page is intended for students interested in working on SURF projects in the Summer of 2008. It contains a list of project areas where I will be supervising projects this year. Students interested in writing proposals for SURF projects should contact me via e-mail to discuss what areas they are interested in and talk through possible SURF proposal topics. All applications should go through the normal SURF application process, described at

Project Areas

Autonomous Vehicles


Caltech participated in the 2007 DARPA Urban Challenge. We made it to the semi-finals, but failed to make it to the race this year. A detailed description of our system, including an analysis of the limitations of our system is available in the final report for our project [1]. The goal for this summer is to extend the capabilities of Alice so that it can drive on urban streets without accurate prior information about the location of the roads. This will require advances in a number of areas:

  • Detection and interpretation of road markings - we need to improve our line and curb detection algorithms and fuse this into a map of the road in front of us. Complicating factors include the presence of shadows, vehicles (moving or parked) and variations on road markings between different types of roads.
  • Dynamic planning algorithms - without prior information on road locations, we will have to do dynamical plan paths that depend on the real-time road information (which may be noisy)
  • Higher level logic for intersection handling and merging - our current logic handles intersections reasonably well, but needs improvement in handling merging into traffic (the test that we failed at the NQE)
  • Modeling and simulation environments - in order to effectively test our algorithms, we need to develop some good modeling infrastructure that allows different levels of simulations to be combined and integrated in an effective manner. Especially important is the inclusion of sensory-based simulations that can feed representative raw data into low level perceptors based on a simulated environment

This project can support 4-6 students who will work together as a team. There are currently 4 students who are working on proposals and an additional 6 have expressed interest in the general area of the project.


  1. J. W. Burdick et al., "Sensing, Navigation and Reasoning Technologies for the DARPA Urban Challenge. DARPA Final Report, 2007.
  2. L. B. Cremean et al., "Alice: An Information-Rich Autonomous Vehicle for High-Speed Desert Navigation". Journal of Field Robotics, 2006.
Titan SURF projects

The Jet Propulsion Laboratory (JPL) is working on a mission to Titan (one of Saturn's moon) that will involve flying a balloon in the atmosphere of the moon to take scientific readings of the ground. This project involves several faculty from Aeronautics, Mechanical Engineering and Control and Dynamical Systems. The projects in my group will focus on evaluating autonomous controls technology that can be used on a prototyped (to be developed as part of CS/EE/ME 75 in 2008-09). More information is available from the link above.

Synthetic Biology

Molecular Programming

A molecular program is a collection of molecules that may perform a computation, fabricate an object, or control a system of molecular sensors and actuators. The best examples are the biomolecular programs of life---from the low-level operating system controlling cell metabolism to the high-level code for development, the process by which a single cell becomes an entire organism. Life's biomolecular programs are intrinsically parallel, distributed, asynchronous, error-prone yet amazingly robust processes; this shows that issues central to computer science are intrinsic to molecular programs.

This project will explore the role of feedback in molecular programs and the design of specific feedback circuits using in vitro biochemistry. Possible project areas include the design of PID (or PI or PD) controllers using biopolyners (DNA and RNA). The projects should involve a combination of modeling, experiments and analysis.


  1. E. Franco, P.-O. Forsberg and R. M. Murray, Design, modeling and synthesis of an in vitro transcription rate regulatory circuit. Submitted, 2008 American Control Conference.
  2. Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree, Enzyme-Free Nucleic Acid Logic Circuits. Science, 2006.
Biological Circuit Design

Gene expression is often controlled by natural genetic regulatory networks that govern the rates at which genes are transcribed. Recent work has shown that synthetic versions of genetic networks can be designed and built in living cells. Applications for these synthetic regulatory networks include intracellular decision-making and computation. Our goal in working in this area is to design increasingly sophisticated synthetic devices based on engineering principles that can be adapted to the biological world. For instance, we would like to be able to realize a circuit exhibiting a hysteresis behavior, where one can actively engineer the hysteresis cycle thresholds, shape and limits guaranteeing robustness with respect to the variability of the employed biological parts. Cascade and parallel interconnections of existing circuits to get new function is another possible area for exploration.


  1. J. Ugander, M. J. Dunlop and R. M. Murray, Analysis of a Digital Clock for Molecular Computing. American Control Conference, 2007.
iGEM Competition

A team of 4-5 undergraduates will be assembled to work on a larger research challenge in Synthetic Biology. The goal of this research team will be to design, construct, and implement a synthetic biological system over the course of the summer. Team members will determine the group's entry, with guidance from a set of faculty and graduate student mentors. The overall research challenge will be broken up into smaller research projects that each team member will work on individually as appropriate. The design process will involve conceptual frameworks for engineering cellular function. The construction and characterization processes will involve significant molecular biology and biochemistry experimental techniques. Interested students should follow the link above for more information.

Additional Information

I can only take on a limited number of students in each project area. Unlike previous years, where we have preselected students to participate in writing a proposal, this year I will use the SURF proposal process to sort out the students that will be accepted into the program. This means that your SURF proposal will be compared against others in the same area and the only top proposals will be selected. To help avoid having a large number of proposals rejected, I will post information on this wiki page as students sign up for project areas, so that you know how many other proposals are being written.

Because there are quite a few students who have expressed interest in writing a proposal, it will not be possible for me to work closely with each of you in selecting a project area. Hence, you should do your homework and read about the project areas before contacting me about the possibility of doing a project. Sending me an e-mail expressing interest in a project area without having read some of the references that I have listed is not a good start! I will use this wiki page to post answers to questions and additional information about the projects, so that everyone has the same access to the information.

As a starting point to writing a proposal, I suggest that you consider putting together a GOTChA Chart. This is a simple planning tool that helps nail down the essence of a proposal and can then be used as an outline for the official SURF application.

Frequently Asked Questions