Open Access
Stochastic Models of Biological Processes.
Steven S. Andrews,Tuan A. Dinh,Adam P. Arkin +2 more
- pp 8730-8749
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The article was published on 2009-01-01 and is currently open access. It has received 47 citations till now. The article focuses on the topics: Stochastic modelling.read more
Citations
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Stochastic Processes in Physics and Chemistry
TL;DR: Van Kampen as mentioned in this paper provides an extensive graduate-level introduction which is clear, cautious, interesting and readable, and could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes.
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Detailed Simulations of Cell Biology with Smoldyn 2.1
TL;DR: This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient, and found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use.
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Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective
TL;DR: This work reviews not only the structural design and stochastic kinetics of individual single motors, but also their coordination, cooperation and competition as well as the assembly of multi-module motors in various intracellular kinetic processes.
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Fundamental limits on dynamic inference from single-cell snapshots.
TL;DR: A simple and asymptotically exact algorithm for inferring the unique dynamic solution under defined approximations and applying it to data from bone marrow stem cells and population balance analysis, which makes use of a method from spectral graph theory to solve a class of high-dimensional differential equations.
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Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface
TL;DR: This article presents several new features of Smoldyn, a spatial and stochastic biochemical simulator, which now supports two types of rule‐based modeling and includes new algorithms for simulating the diffusion of surface‐bound molecules and molecules with excluded volume.
References
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Journal ArticleDOI
Exact Stochastic Simulation of Coupled Chemical Reactions
TL;DR: In this article, a simulation algorithm for the stochastic formulation of chemical kinetics is proposed, which uses a rigorously derived Monte Carlo procedure to numerically simulate the time evolution of a given chemical system.
Journal ArticleDOI
The Chemical Basis of Morphogenesis
TL;DR: In this article, it is suggested that a system of chemical substances, called morphogens, reacting together and diffusing through a tissue, is adequate to account for the main phenomena of morphogenesis.
Book
Understanding Molecular Simulation: From Algorithms to Applications
Daan Frenkel,Berend Smit +1 more
TL;DR: In this paper, the physics behind molecular simulation for materials science is explained, and the implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.
Stochastic Processes in Physics and Chemistry
Abstract: Preface to the first edition. Preface to the second edition. Abbreviated references. I. Stochastic variables. II. Random events. III. Stochastic processes. IV. Markov processes. V. The master equation. VI. One-step processes. VII. Chemical reactions. VIII. The Fokker-Planck equation. IX. The Langevin approach. X. The expansion of the master equation. XI. The diffusion type. XII. First-passage problems. XIII. Unstable systems. XIV. Fluctuations in continuous systems. XV. The statistics of jump events. XVI. Stochastic differential equations. XVII. Stochastic behavior of quantum systems.
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Pattern formation outside of equilibrium
Michael Cross,P. C. Hohenberg +1 more
TL;DR: A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented in this article, with emphasis on comparisons between theory and quantitative experiments, and a classification of patterns in terms of the characteristic wave vector q 0 and frequency ω 0 of the instability.