Simulation tools for particle-based reaction-diffusion dynamics in continuous space

Explicit Spatiotemporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes

(2014) Johannes Schöneberg et al.   BIOPHYSICAL JOURNAL

Diffusion of finite-size particles in two-dimensional channels with random wall configurations

(2014) Maximilian Bauer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How Molecular Motors Work in the Crowded Environment of Living Cells: Coexistence and Efficiency of Normal and Anomalous Transport

(2014) Igor Goychuk et al.   PLoS One

Effect of crowding by Dextrans in enzymatic reactions

(2013) Isabel Pastor et al.   BIOPHYSICAL CHEMISTRY

Anomalous versus Slowed-Down Brownian Diffusion in the Ligand-Binding Equilibrium

(2013) Hédi Soula et al.   BIOPHYSICAL JOURNAL

Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime

(2013) Bertrand R. Caré et al.   PHYSICAL REVIEW E

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

(2013) Johannes Schöneberg et al.   PLoS One

Implications of macromolecular crowding for protein–protein association kinetics in the cytoplasm of living cells

(2013) Marcin Tabaka et al.   Soft Matter

Generalized Facilitated Diffusion Model for DNA-Binding Proteins with Search and Recognition States

(2012) Maximilian Bauer et al.   BIOPHYSICAL JOURNAL

Membrane Clustering and the Role of Rebinding in Biochemical Signaling

(2012) Andrew Mugler et al.   BIOPHYSICAL JOURNAL

Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers

(2012) Xavier Periole et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2012) Michael Klann et al.   PLoS One

Exploring Weak, Transient Protein–Protein Interactions in Crowded In Vivo Environments by In-Cell Nuclear Magnetic Resonance Spectroscopy

(2011) Qinghua Wang et al.   BIOCHEMISTRY

Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants

(2011) Michael T Klann et al.   BMC Systems Biology

Impact of receptor clustering on ligand binding

(2011) Bertrand R Caré et al.   BMC Systems Biology

Rhodopsin is spatially heterogeneously distributed in rod outer segment disk membranes

(2011) Nikolay Buzhynskyy et al.   JOURNAL OF MOLECULAR RECOGNITION

Clusters of Proteins in Biomembranes: Insights into the Roles of Interaction Potential Shapes and of Protein Diversity

(2011) Nicolas Meilhac et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rule-based spatial modeling with diffusing, geometrically constrained molecules

(2010) Gerd Gruenert et al.   BMC BIOINFORMATICS

An alternative scenario for the formation of specialized protein nano-domains (cluster phases) in biomembranes

(2010) N. Destainville   EPL

A Metabolic Model of Human Erythrocytes: Practical Application of the E-Cell Simulation Environment

(2010) Ayako Yachie-Kinoshita et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

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

(2010) Michael J. Byrne et al.   NEUROINFORMATICS

Syntaxin clusters assemble reversibly at sites of secretory granules in live cells

(2010) S. Barg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single secretory granules of live cells recruit syntaxin-1 and synaptosomal associated protein 25 (SNAP-25) in large copy numbers

(2010) M. K. Knowles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatio-temporal correlations can drastically change the response of a MAPK pathway

(2010) K. Takahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

(2010) T. Ando et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying the Effects of Elastic Collisions and Non-Covalent Binding on Glutamate Receptor Trafficking in the Post-Synaptic Density

(2010) Fidel Santamaria et al.   PLoS Computational Biology

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

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

Detailed Simulations of Cell Biology with Smoldyn 2.1

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

Common Crowding Agents Have Only a Small Effect on Protein-Protein Interactions

(2009) Yael Phillip et al.   BIOPHYSICAL JOURNAL

Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy

(2009) Derek Greenfield et al.   PLOS BIOLOGY

Crowding Effects on Diffusion in Solutions and Cells

(2008) James A. Dix et al.   Annual Review of Biophysics

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

(2008) Douglas Ridgway et al.   BIOPHYSICAL JOURNAL

Myosin Vb Mobilizes Recycling Endosomes and AMPA Receptors for Postsynaptic Plasticity

(2008) Zhiping Wang et al.   CELL

Mesoscopic Monte Carlo Simulations of Stochastic Encounters between Photoactivated Rhodopsin and Transducin in Disc Membranes

(2008) Daniele Dell'Orco et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation

(2008) A. B. Lindner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Biological Interpretation of Transient Anomalous Subdiffusion. II. Reaction Kinetics

(2007) Michael J. Saxton   BIOPHYSICAL JOURNAL