A New Coarse-Grained Model for E. coli Cytoplasm: Accurate Calculation of the Diffusion Coefficient of Proteins and Observation of Anomalous Diffusion

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

(2014) Fabio Sterpone et al.   CHEMICAL SOCIETY REVIEWS

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

(2013) Tadashi Ando et al.   JOURNAL OF CHEMICAL PHYSICS

Reaching new levels of realism in modeling biological macromolecules in cellular environments

(2013) Michael Feig et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

A Minimalist Model of Protein Diffusion and Interactions: The Green Fluorescent Protein within the Cytoplasm

(2013) Fabio Trovato et al.   MACROMOLECULES

Single-particle tracking data reveal anticorrelated fractional Brownian motion in crowded fluids

(2013) Matthias Weiss   PHYSICAL REVIEW E

A Physics-Based Approach of Coarse-Graining the Cytoplasm of Escherichia coli (CGCYTO)

(2012) Qian Wang et al.   BIOPHYSICAL JOURNAL

Spatial Simulations in Systems Biology: From Molecules to Cells

(2012) Michael Klann et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations

(2012) Alexander V. Predeus et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions

(2012) Paolo Mereghetti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Subdiffusive motion of a polymer composed of subdiffusive monomers

(2010) Stephanie C. Weber et al.   PHYSICAL REVIEW E

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

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

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

Elucidating the Origin of Anomalous Diffusion in Crowded Fluids

(2009) Jedrzej Szymanski et al.   PHYSICAL REVIEW LETTERS

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

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

Protein folding in confined and crowded environments

(2007) Huan-Xiang Zhou   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS