A framework for discrete stochastic simulation on 3D moving boundary domains

Geometry-induced protein pattern formation

(2016) Dominik Thalmeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME

(2016) Brian Drawert et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Reaction rates for mesoscopic reaction-diffusion kinetics

(2015) Stefan Hellander et al.   PHYSICAL REVIEW E

Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries

(2015) Atiyo Ghosh et al.   PLoS One

Discrete and continuous models for tissue growth and shrinkage

(2014) Christian A. Yates   JOURNAL OF THEORETICAL BIOLOGY

Spatial Stochastic Dynamics Enable Robust Cell Polarization

(2013) Michael J. Lawson et al.   PLoS Computational Biology

GDI-Mediated Cell Polarization in Yeast Provides Precise Spatial and Temporal Control of Cdc42 Signaling

(2013) Ben Klünder et al.   PLoS Computational Biology

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

(2012) Brian Drawert et al.   BMC Systems Biology

Going from microscopic to macroscopic on nonuniform growing domains

(2012) Christian A. Yates et al.   PHYSICAL REVIEW E

Reaction-diffusion master equation in the microscopic limit

(2012) Stefan Hellander et al.   PHYSICAL REVIEW E

Noise filtering tradeoffs in spatial gradient sensing and cell polarization response

(2011) Ching-Shan Chou et al.   BMC Systems Biology

Flexible single molecule simulation of reaction–diffusion processes

(2011) Stefan Hellander et al.   JOURNAL OF COMPUTATIONAL PHYSICS

A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules

(2011) Alexandra Jilkine et al.   PLoS Computational Biology

DOLFIN

(2010) Anders Logg et al.   ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE

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

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

Detailed Simulations of Cell Biology with Smoldyn 2.1

(2010) Steven S. Andrews et al.   PLoS Computational Biology

From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains

(2009) Ruth E. Baker et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes

(2009) Stefan Engblom et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity

(2008) Andrew B. Goryachev et al.   FEBS LETTERS

Robust Spatial Sensing of Mating Pheromone Gradients by Yeast Cells

(2008) Travis I. Moore et al.   PLoS One

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