258 citations · 625 across the 13 of their papers we have counts for
13 papers
Two-dimensional tile displacement can simulate cellular automata
Erik Winfree, Lulu Qian
Tile displacement is a newly-recognized mechanism in DNA nanotechnology that exploits principles analogous to toehold-mediated strand displacement but within the context of self-as…
Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly
Constantine Glen Evans, Jackson O'Brien, Erik Winfree +1
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensiona…
Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines
William Poole, Thomas Ouldridge, Manoj Gopalkrishnan +1
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but th…
The pathway elaboration method for mean first passage time estimation in large continuous-time Markov chains with applications to nucleic acid kinetics
Sedigheh Zolaktaf, Frits Dannenberg, Mark Schmidt +2
For predicting the kinetics of nucleic acid reactions, continuous-time Markov chains (CTMCs) are widely used. The rate of a reaction can be obtained through the mean first passage…
Stochastic Chemical Reaction Networks for Robustly Approximating Arbitrary Probability Distributions
Daniele Cappelletti, Andrés Ortiz-Muñoz, David Anderson +1
We show that discrete distributions on the -dimensional non-negative integer lattice can be approximated arbitrarily well via the marginals of stationary distributions for vario…
Chemical Boltzmann Machines
William Poole, Andrés Ortiz-Muñoz, Abhishek Behera +4
How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemic…