CS/ICES/Chemistry Colloquia - Professor Erik Winfree/California Institute of Technology, "Computational Tools for Molecular Programming: Design, Simulation, and Analysis," ACES 2.302

Contact Name: 
Jenna Whitney
May 8, 2012 10:00am - 11:00am

There is a sign-up schedule for this event that can be found at


Type o

f Talk: CS/ICES/Chemistry Colloquia

Speaker/Affiliation: Professor Eri

k Winfree/California Institute of Technology

Talk Audience: UTCS facul

ty, graduate students, undergraduate students and outside interested part


Date/Time: Tuesday, May 8, 2012, 10:00 am

Location: ACES 2


Host: Peter Stone

Talk Title: Computational Tools for Molecu

lar Programming: Design, Simulation, and Analysis

Talk Abstract:

Inspired by the information processing core of biological organisms and its
ability to fabricate intricate machinery from the molecular scale up to th

e macroscopic scale, research in synthetic biology,
molecular programmi

ng, and nucleic acid nanotechnology aims to create information-based chemi

cal systems that carry out human-defined molecular programs that input, ou

tput, and manipulate molecules and molecular structures. For chemistry to
become the next information technology substrate, we will need improved t

ools for designing, simulating, and analyzing complex molecular circuits

and systems. Using DNA nanotechnology as a model system, I will discuss ho

w programming languages can be devised for specifying molecular systems at

a high level, how compilers can translate such specifications into concret

e molecular implementations, how both high-level and low-level specificati

ons can be simulated and verified according to behavioral logic and the und

erlying biophysics of molecular interactions, and how Bayesian analysis te

chniques can be used to understand and predict the behavior of experimental
systems that, at this point, still inevitably contain many ill-character

ized components and interactions."

Speaker Bio:
Professor Winfree''s
research involves theoretical and experimental aspects of molecular progra

mming. Models of computation are developed that incorporate essential featu

res of molecular folding, molecular self-assembly, biochemical circuits,
and molecular robotics. These models are studied to determine their expres

siveness for programming behaviors such as memory, behavior, and morphoge

nesis. Methods for compiling abstract molecular programs into actual molec

ules are developed and tested in the laboratory.

Degrees and Appointme

B.S., University of Chicago, 1991 Ph.D., Caltech, 1998. Assistant
Professor, 1999-2006 Associate Professor of Computer Science and Computat

ion and Neural Systems, 2006-07 Associate Professor, 2007-10 Professor,


List of Research Areas
molecular programming, DNA nanotechno

logy, DNA Computing, nucleic acid systems, biophysics, complexity theor

y, programming languages and compilers, evolutionary systems