Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories

Simulating rare events using a weighted ensemble-based string method

(2013) Joshua L. Adelman et al.   JOURNAL OF CHEMICAL PHYSICS

Stochastic projective methods for simulating stiff chemical reacting systems

(2012) Haokai Lu et al.   COMPUTER PHYSICS COMMUNICATIONS

Rare switching events in non-stationary systems

(2012) Nils B. Becker et al.   JOURNAL OF CHEMICAL PHYSICS

An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates

(2012) Divesh Bhatt et al.   JOURNAL OF CHEMICAL PHYSICS

Non-stationary forward flux sampling

(2012) Nils B. Becker et al.   JOURNAL OF CHEMICAL PHYSICS

A Computational Model for Early Events in B Cell Antigen Receptor Signaling: Analysis of the Roles of Lyn and Fyn

(2012) D. Barua et al.   JOURNAL OF IMMUNOLOGY

AESS: Accelerated Exact Stochastic Simulation

(2011) David D. Jenkins et al.   COMPUTER PHYSICS COMMUNICATIONS

Automated estimation of rare event probabilities in biochemical systems

(2011) Bernie J. Daigle et al.   JOURNAL OF CHEMICAL PHYSICS

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events

(2011) Min K. Roh et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na+/Cl−, Methane/Benzene, and K+/18-Crown-6 Ether

(2011) Matthew C. Zwier et al.   Journal of Chemical Theory and Computation

Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range

(2011) T. M. Thomson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis and verification of the HMGB1 signaling pathway

(2010) Haijun Gong et al.   BMC BIOINFORMATICS

Reaching biological timescales with all-atom molecular dynamics simulations

(2010) Matthew C Zwier et al.   CURRENT OPINION IN PHARMACOLOGY

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm

(2010) Min K. Roh et al.   JOURNAL OF CHEMICAL PHYSICS

Steady-state simulations using weighted ensemble path sampling

(2010) Divesh Bhatt et al.   JOURNAL OF CHEMICAL PHYSICS

The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures

(2010) Bin W. Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response

(2010) Ofer Feinerman et al.   Molecular Systems Biology

Single-Molecule Approaches to Stochastic Gene Expression

(2009) Arjun Raj et al.   Annual Review of Biophysics

Aggregation of Membrane Proteins by Cytosolic Cross-Linkers: Theory and Simulation of the LAT-Grb2-SOS1 System

(2009) Ambarish Nag et al.   BIOPHYSICAL JOURNAL

An exact accelerated stochastic simulation algorithm

(2009) Eric Mjolsness et al.   JOURNAL OF CHEMICAL PHYSICS

Nonequilibrium umbrella sampling in spaces of many order parameters

(2009) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Refining the weighted stochastic simulation algorithm

(2009) Dan T. Gillespie et al.   JOURNAL OF CHEMICAL PHYSICS

D-leaping: Accelerating stochastic simulation algorithms for reactions with delays

(2009) Basil Bayati et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Accelerated stochastic simulation algorithm for coupled chemical reactions with delays

(2008) Wen Zhou et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

The stochastic nature of biochemical networks

(2008) Vahid Shahrezaei et al.   CURRENT OPINION IN BIOTECHNOLOGY

How noise statistics impact models of enzyme cycles

(2008) Aryeh Warmflash et al.   JOURNAL OF CHEMICAL PHYSICS

An efficient and exact stochastic simulation method to analyze rare events in biochemical systems

(2008) Hiroyuki Kuwahara et al.   JOURNAL OF CHEMICAL PHYSICS

Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlogl model revisited

(2008) M. Vellela et al.   Journal of the Royal Society Interface

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING