Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model

(2016) Sepideh Dolatshahi et al.   Molecular BioSystems

Identification of Metabolic Pathway Systems

(2016) Sepideh Dolatshahi et al.   Frontiers in Genetics

Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly

(2015) Tyler M. Earnest et al.   BIOPHYSICAL JOURNAL

Are protein-protein interfaces special regions on a protein’s surface?

(2015) Sam Tonddast-Navaei et al.   JOURNAL OF CHEMICAL PHYSICS

Toward an Accurate Modeling of Hydrodynamic Effects on the Translational and Rotational Dynamics of Biomolecules in Many-Body Systems

(2015) Maciej Długosz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effects of confinement on models of intracellular macromolecular dynamics

(2015) Edmond Chow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes

(2015) Hanae Shimo et al.   PLoS Computational Biology

Whole Cell Modeling: From Single Cells to Colonies

(2014) John A. Cole et al.   ISRAEL JOURNAL OF CHEMISTRY

Computationally efficient algorithms for incorporation of hydrodynamic and excluded volume interactions in Brownian dynamics simulations: A comparative study of the Krylov subspace and Chebyshev based techniques

(2014) Amir Saadat et al.   JOURNAL OF CHEMICAL PHYSICS

Synthetic biology: How best to build a cell

(2014)   NATURE

A brief history of synthetic biology

(2014) D. Ewen Cameron et al.   NATURE REVIEWS MICROBIOLOGY

Towards a Computational Model of a Methane Producing Archaeum

(2014) Joseph R. Peterson et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models

(2014) Tadashi Ando et al.   PLoS Computational Biology

What is the total number of protein molecules per cell volume? A call to rethink some published values

(2013) Ron Milo   BIOESSAYS

On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation

(2013) Tadashi Ando et al.   BIOPHYSICAL JOURNAL

Function and design of the Nox1 system in vascular smooth muscle cells

(2013) Weiwei Yin et al.   BMC Systems Biology

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

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

Effects of Macromolecular Crowding on Burst Phase Kinetics of Cytochrome c Folding

(2012) Eefei Chen et al.   BIOCHEMISTRY

Estimation of dynamic flux profiles from metabolic time series data

(2012) I-Chun Chou et al.   BMC Systems Biology

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

(2012) Tadashi Ando et al.   JOURNAL OF CHEMICAL PHYSICS

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

Are Hydrodynamic Interactions Important in the Kinetics of Hydrophobic Collapse?

(2012) Jingyuan Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics in dense hard-sphere colloidal suspensions

(2012) Davide Orsi et al.   PHYSICAL REVIEW E

Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes

(2011) Joseph A. Morrone et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein self-diffusion in crowded solutions

(2011) F. Roosen-Runge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics

(2011) Qian Wang et al.   PLoS Computational Biology

Mobility of Cytoplasmic, Membrane, and DNA-Binding Proteins in Escherichia coli

(2010) Mohit Kumar et al.   BIOPHYSICAL JOURNAL

Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

(2010) Paolo Mereghetti et al.   BIOPHYSICAL JOURNAL

Size Dependence of Protein Diffusion in the Cytoplasm of Escherichia coli

(2010) A. Nenninger et al.   JOURNAL OF BACTERIOLOGY

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

Automated piecewise power-law modeling of biological systems

(2010) Anna Machina et al.   JOURNAL OF BIOTECHNOLOGY

Hydrodynamic effects in proteins

(2010) Piotr Szymczak et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Origins of the anomalous stress behavior in charged colloidal suspensions under shear

(2010) Amit Kumar 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

Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected

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

Improving the yeast two-hybrid system with permutated fusions proteins: the Varicella Zoster Virus interactome

(2010) Thorsten Stellberger et al.   Proteome Science

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

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

Macromolecular Crowding Modulates Folding Mechanism of α / β Protein Apoflavodoxin

(2009) Dirar Homouz et al.   BIOPHYSICAL JOURNAL

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou 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