DNA as a universal substrate for chemical kinetics

D Soloveichik, G Seelig… - Proceedings of the …, 2010 - National Acad Sciences
Molecular programming aims to systematically engineer molecular and chemical systems of
autonomous function and ever-increasing complexity. A key goal is to develop embedded …

Markovian dynamics on complex reaction networks

J Goutsias, G Jenkinson - Physics reports, 2013 - Elsevier
Complex networks, comprised of individual elements that interact with each other through
reaction channels, are ubiquitous across many scientific and engineering disciplines …

Programmable chemical controllers made from DNA

YJ Chen, N Dalchau, N Srinivas, A Phillips… - Nature …, 2013 - nature.com
Biological organisms use complex molecular networks to navigate their environment and
regulate their internal state. The development of synthetic systems with similar capabilities …

Thermal logic gates: computation with phonons

L Wang, B Li - Physical review letters, 2007 - APS
Logic gates are basic digital elements for computers. We build up thermal logic gates that
can perform similar operations as their electronic counterparts. The thermal logic gates are …

[PDF][PDF] The program-size complexity of self-assembled squares

PWK Rothemund, E Winfree - Proceedings of the thirty-second annual …, 2000 - dl.acm.org
Molecular self-assembly gives rise to a great diversity of complex forms, from crystals and
DNA helices to microtubules and holoenzymes. We study a formal model of …

Nonequilibrium thermodynamics of chemical reaction networks: Wisdom from stochastic thermodynamics

R Rao, M Esposito - Physical Review X, 2016 - APS
We build a rigorous nonequilibrium thermodynamic description for open chemical reaction
networks of elementary reactions. Their dynamics is described by deterministic rate …

A simple DNA gate motif for synthesizing large-scale circuits

L Qian, E Winfree - Journal of the Royal Society Interface, 2011 - royalsocietypublishing.org
The prospects of programming molecular systems to perform complex autonomous tasks
have motivated research into the design of synthetic biochemical circuits. Of particular …

An RNA-based theory of natural universal computation

H Akhlaghpour - Journal of Theoretical Biology, 2022 - Elsevier
Life is confronted with computation problems in a variety of domains including animal
behavior, single-cell behavior, and embryonic development. Yet we currently do not know of …

Computation with finite stochastic chemical reaction networks

D Soloveichik, M Cook, E Winfree, J Bruck - natural computing, 2008 - Springer
A highly desired part of the synthetic biology toolbox is an embedded chemical
microcontroller, capable of autonomously following a logic program specified by a set of …

Energetic costs of cellular computation

P Mehta, DJ Schwab - … of the National Academy of Sciences, 2012 - National Acad Sciences
Cells often perform computations in order to respond to environmental cues. A simple
example is the classic problem, first considered by Berg and Purcell, of determining the …