Programming Molecular Structure and Dynamics: Principles and Practice Using DNA

Seminar
Thursday, March 26, 2015
11:00 AM to 12:00 PM
POB 2.302
Free and open to the public

The goal of my research is to control the structure and dynamics of molecular systems at the nanoscale and to determine the fundamental limitations of this endeavor. A major unanswered challenge is to design molecular-scale systems with arbitrary structure and dynamics that consist of millions of simple interacting components and yet are robust to erroneous interactions, fluctuations in temperature, fluid flows and other uncontrolled factors. DNA is a versatile and programmable material that can meet these daunting criteria. The kinetics and thermodynamics of DNA are reasonably well-understood, and through straightforward Watson-Crick base-pairing interactions we can program this material to create complicated shapes and patterns, and to have intricate, even algorithmic, chemical dynamics, all at nanometer spatial resolution. The theory of computation will be a necessity to design and analyze the capabilities of such systems.

In this talk I will highlight some of my recent work on the theory and practice of programming molecules. Ongoing experimental work in the wet-lab includes building a DNA-based self-replicator capable of multiple generations of replication. Theoretical work involves developing a framework, or a complexity theory, for comparing self-assembly systems and knowing when one system is better than another.  The talk will show how computer science and biology can inspire our molecular designs, and how we can use mathematical and algorithmic tools to control a cacophony of interacting molecules by simply letting them interact in a hands-off self-assembling fashion.

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Speaker

Damien Woods

Damien Woods

Senior Research Fellow and Molecular Programming Fellow
California Institute of Technology

Damien Woods is a Senior Research Fellow and Molecular Programming Fellow at Caltech.  His PhD is from the National University of Ireland, Maynooth and he worked as a postdoctoral scholar in Ireland and Spain. His interests include molecular self-assembly, self-replication and molecular robotics as well as a variety of theoretical topics including the computational complexity of cellular automata, small universal Turing machines, Boolean circuits and optical computers. He uses the theory of computation to understand biological, chemical and physical mechanisms.

Ongoing work includes using simulation and intrinsic universality as tools to characterize the computational power of molecular self-assembly systems, and developing a theory of active rigid-body molecular robotics. In the wet-lab he is building a simple autonomous molecular self-replicator out of DNA. Work with former students and others answers known open questions and has developed new research directions. This includes showing that the simplest known general-purpose computers (such as Rule 110 and the smallest universal Turing machines) are time-efficient, developing the computational complexity theory of biologically-inspired membrane-bound computational devices, and exploring the computational power of optical computers.