(Q51916299)

17 April 2018

title

Variable-free exploration of stochastic models: a gene regulatory network example. (English)

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17 April 2018

author name string

Radek Erban

1

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Thomas A Frewen

2

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Xiao Wang

3

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Timothy C Elston

4

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Ronald Coifman

5

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Boaz Nadler

6

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Ioannis G Kevrekidis

7

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language of work or name

English

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publication date

1 April 2007

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17 April 2018

Journal of Chemical Physics

published in

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volume

126

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issue

15

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page(s)

155103

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Exact stochastic simulation of coupled chemical reactions

cites work

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Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks

21 January 2018

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Approximate accelerated stochastic simulation of chemically reacting systems

21 January 2018

1 reference

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation

21 January 2018

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Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions

21 January 2018

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The slow-scale stochastic simulation algorithm.

21 January 2018

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Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates.

21 January 2018

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Binomial distribution based tau-leap accelerated stochastic simulation.

21 January 2018

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Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps.

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Geometric diffusions as a tool for harmonic analysis and structure definition of data: multiscale methods

21 January 2018

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Apparent hysteresis in a driven system with self-organized drag

21 January 2018

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Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes.

21 January 2018

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Construction of a genetic toggle switch in Escherichia coli

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Engineered gene circuits.

21 January 2018

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Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations

21 January 2018

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Coarse-grained kinetic computations for rare events: application to micelle formation.

21 January 2018

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21 January 2018

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Learning eigenfunctions links spectral embedding and kernel PCA.

21 January 2018

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Optimization by Simulated Annealing

21 January 2018

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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

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A global geometric framework for nonlinear dimensionality reduction

21 January 2018

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Nonlinear dimensionality reduction by locally linear embedding

21 January 2018

1 reference

Hessian eigenmaps: locally linear embedding techniques for high-dimensional data

21 January 2018

1 reference

Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm

21 January 2018

1 reference

Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method

21 January 2018

1 reference

Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations

21 January 2018

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21 January 2018

Identifiers

DOI

10.1063/1.2718529

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17 April 2018

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17 April 2018