Hybrid spatial Gillespie and particle tracking simulation

Membrane Clustering and the Role of Rebinding in Biochemical Signaling

(2012) Andrew Mugler et al.   BIOPHYSICAL JOURNAL

Computational modeling of cellular signaling processes embedded into dynamic spatial contexts

(2012) Bastian R Angermann et al.   NATURE METHODS

Spatial Modeling of Vesicle Transport and the Cytoskeleton: The Challenge of Hitting the Right Road

(2012) Michael Klann et al.   PLoS One

A Computational Analysis of the Dynamic Roles of Talin, Dok1, and PIPKI for Integrin Activation

(2011) Florian Geier et al.   PLoS One

Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

(2011) Jana Lipková et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Signalling ballet in space and time

(2010) Boris N. Kholodenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology

(2010) Michael J. Byrne et al.   NEUROINFORMATICS

Stochastic Simulation of Signal Transduction: Impact of the Cellular Architecture on Diffusion

(2009) Michael T. Klann et al.   BIOPHYSICAL JOURNAL

A diffusional bimolecular propensity function

(2009) Daniel T. Gillespie   JOURNAL OF CHEMICAL PHYSICS

Effect of excluded volume on 2D discrete stochastic chemical kinetics

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

Coupled Stochastic Spatial and Non-Spatial Simulations of ErbB1 Signaling Pathways Demonstrate the Importance of Spatial Organization in Signal Transduction

(2009) Michelle N. Costa et al.   PLoS One

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

(2008) Douglas Ridgway et al.   BIOPHYSICAL JOURNAL

Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network

(2008) Marco J. Morelli et al.   JOURNAL OF CHEMICAL PHYSICS

Stochastic simulation of chemical reactions in spatially complex media

(2007) Dan V. Nicolau et al.   COMPUTERS & MATHEMATICS WITH APPLICATIONS