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pro vyhledávání: '"Winfree, Erik"'
Autor:
Winfree, Erik, Qian, Lulu
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-assembled DNA origami tile arrays. Here, we formulate an abstract model
Externí odkaz:
http://arxiv.org/abs/2301.01929
Publikováno v:
Nature 625, 500-507, 2024
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also arise within
Externí odkaz:
http://arxiv.org/abs/2207.06399
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 the principles that allow for life's existence are far from being proven
Externí odkaz:
http://arxiv.org/abs/2205.06313
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 time (MFPT) of its CTMC. However, a typical issue in CTMCs is that the
Externí odkaz:
http://arxiv.org/abs/2101.03657
Publikováno v:
In Computational Biology and Chemistry June 2023 104
Stochastic Chemical Reaction Networks for Robustly Approximating Arbitrary Probability Distributions
Publikováno v:
Theoretical Computer Science, 2019
We show that discrete distributions on the $d$-dimensional non-negative integer lattice can be approximated arbitrarily well via the marginals of stationary distributions for various classes of stochastic chemical reaction networks. We begin by provi
Externí odkaz:
http://arxiv.org/abs/1810.02854
Autor:
Poole, William, Ortiz-Muñoz, Andrés, Behera, Abhishek, Jones, Nick S., Ouldridge, Thomas E., Winfree, Erik, Gopalkrishnan, Manoj
Publikováno v:
DNA Computing and Molecular Programming (DNA 23), R. Brijder and L. Qian (Eds.): LNCS 10467, pp. 210-231, 2017
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 chemical reaction networks sample? We begin tackling these questions by show
Externí odkaz:
http://arxiv.org/abs/1707.06221
Publikováno v:
Journal of the Royal Society Interface, 17: 20190866 (2020)
DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages by formali
Externí odkaz:
http://arxiv.org/abs/1505.03738
Akademický článek
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Publikováno v:
Theoretical Computer Science, Volume 765, 18 April 2019, Pages 67-96
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves multiple
Externí odkaz:
http://arxiv.org/abs/1411.0782