Statistical Mechanics and Computation of DNA Self-Assembly

Session

Computation

3

27 May 2011, 09:00

Hotel Arkipelag, Mariehamn, Finland

260. Toward a Programmable Chemistry with Strand Displacement Cascades

Prof. David Soloveichik (University of Washington)

27/05/2011, 09:15

What challenges must be overcome before engineers can design molecules and their interactions with ease? The ideas of abstraction and modularity allowed the creation of software and hardware systems of extreme complexity consisting of millions of lines of code and hundreds of millions of transistors. Mimicking software and hardware engineering, an approach to the molecular challenge is...

261. The termination problem in self-assembly

Prof. Jarkko Kari (University of Turku)

27/05/2011, 10:30

We consider the algorithmic problem of determining if a given self-assembly system is terminating, that is, if an unbounded growth may happen or not. We prove that this question is undecidable even in the simple tiling model of self-assembly, by showing that no algorithm is able to determine if a given set of Wang tiles can form on the plane an infinite path where consecutive tiles match...

262. DNA codeword design: theory and application

Prof. Max Garzon (The University of Memphis)

27/05/2011, 11:15

Finding large sets of single DNA strands that do not crosshybridize to themselves or to their complements is an important problem in DNA computing, self-assembly, DNA memories and phylogenetic analyses, because of their error correction and prevention properties. The problem is in itself NP-complete, even in very simplified versions using any single reasonable measure that approximates...

263. On Recycling and its Limits in Strand Displacement Systems

Prof. Anne Condon (University of British Columbia)

27/05/2011, 14:30

We consider recycling, or reuse of molecules, in chemical reaction systems and their DNA strand displacement realizations. Recycling happens when a product of one reaction is a reactant in a later reaction. Recycling has the benefits of reducing consumption, or waste, of molecules and of avoiding fuel depletion. We will describe a binary counter that recycles molecules efficiently while...

264. Building a DNA brain

Dr Lulu Qian (Caltech)

27/05/2011, 15:15

Not long after Adleman showed that DNA can serve as a computing substrate, Baum proposed using DNA to build an associative memory larger than the brain. Attempts to bring these ideas to fruition have been hindered by requirements for enzymes or manual experimental steps. Here our interest is in DNA strand displacement circuits that can perform neural network computation autonomously. We...

265. A Design Framework for Carbon Nanotube Circuits Affixed on DNA Origami Tiles

Dr Eugen Czeizler (Aalto University)

27/05/2011, 16:30

Recent years have witnessed a burst of experimental activity concerning algorithmic self-assembly of nanostructures, motivated at least in part by the potential of this approach as a radically new manufacturing technology. Our specific interest is in the self-assembly of Carbon-Nanotube Field Effect Transistor (CNFET) circuits. In the present work, we propose a generic framework for the...