Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units

(2012) Ivan Komarov et al.   PLoS One

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Decision Making in Living Cells: Lessons from a Simple System

(2011) Ido Golding   Annual Review of Biophysics

StochKit2: software for discrete stochastic simulation of biochemical systems with events

(2011) K. R. Sanft et al.   BIOINFORMATICS

Central dogma at the single-molecule level in living cells

(2011) Gene-Wei Li et al.   NATURE

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

(2011) Elijah Roberts et al.   PLoS Computational Biology

Accelerating reaction–diffusion simulations with general-purpose graphics processing units

(2010) Matthias Vigelius et al.   BIOINFORMATICS

The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation

(2010) Brian Drawert et al.   JOURNAL OF CHEMICAL PHYSICS

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Stochastic reaction-diffusion kinetics in the microscopic limit

(2010) D. Fange et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

Efficient stochastic simulation of reaction–diffusion processes via direct compilation

(2009) Mieszko Lis et al.   BIOINFORMATICS

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

(2009) Hong Li et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems

(2009) Sotiria Lampoudi et al.   JOURNAL OF CHEMICAL PHYSICS

An adaptive algorithm for simulation of stochastic reaction–diffusion processes

(2009) Lars Ferm et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Visual proteomics of the human pathogen Leptospira interrogans

(2009) Martin Beck et al.   NATURE METHODS

Reaction-diffusion master equation, diffusion-limited reactions, and singular potentials

(2009) Samuel A. Isaacson et al.   PHYSICAL REVIEW E

Universal architecture of bacterial chemoreceptor arrays

(2009) A. Briegel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

The Reaction-Diffusion Master Equation as an Asymptotic Approximation of Diffusion to a Small Target

(2009) Samuel A. Isaacson   SIAM JOURNAL ON APPLIED MATHEMATICS

Coarse-Grained Molecular Simulation of Diffusion and Reaction Kinetics in a Crowded Virtual Cytoplasm

(2008) Douglas Ridgway et al.   BIOPHYSICAL JOURNAL

Virtual Cell modelling and simulation software environment

(2008) I.I. Moraru et al.   IET Systems Biology

Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon

(2008) Luis R Comolli et al.   ISME Journal