Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size

(2015) Jaeoh Shin et al.   Soft Matter

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability

(2014) Stephan Hamperl et al.   DNA REPAIR

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS

(2014) C. A. Brackley et al.   JOURNAL OF CHEMICAL PHYSICS

Effects of supercoiling on enhancer–promoter contacts

(2014) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Ring Polymers in the Melt State: The Physics of Crumpling

(2014) Angelo Rosa et al.   PHYSICAL REVIEW LETTERS

Quantitation of interactions between two DNA loops demonstrates loop domain insulation inE. colicells

(2014) David G. Priest et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells

(2013) Jay K. Fisher et al.   CELL

Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes

(2013) Julien Dorier et al.   NUCLEIC ACIDS RESEARCH

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Fluids of semiflexible ring polymers: effective potentials and clustering

(2012) Marco Bernabei et al.   Soft Matter

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

(2011) Jonathan D. Halverson et al.   JOURNAL OF CHEMICAL PHYSICS

Conformation of Ring Polymers in 2D Constrained Environments

(2011) G. Witz et al.   PHYSICAL REVIEW LETTERS

Chromosome dynamics, molecular crowding, and diffusion in the interphase cell nucleus: a Monte Carlo lattice simulation study

(2010) Christian C. Fritsch et al.   CHROMOSOME RESEARCH

Excluded Volume Effects on Semiflexible Ring Polymers

(2010) Fabian Drube et al.   NANO LETTERS

Entropy as the driver of chromosome segregation

(2010) Suckjoon Jun et al.   NATURE REVIEWS MICROBIOLOGY

Dimension of ring polymers in bulk studied by Monte-Carlo simulation and self-consistent theory

(2009) Jiro Suzuki et al.   JOURNAL OF CHEMICAL PHYSICS

Interplay of DNA supercoiling and catenation during the segregation of sister duplexes

(2009) M. L. Martinez-Robles et al.   NUCLEIC ACIDS RESEARCH

Topological origins of chromosomal territories

(2009) Julien Dorier et al.   NUCLEIC ACIDS RESEARCH

Polymer induced condensation of DNA supercoils

(2008) José Ésio Bessa Ramos et al.   JOURNAL OF CHEMICAL PHYSICS

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Effect of Knotting on the Shape of Polymers

(2008) Eric J. Rawdon et al.   MACROMOLECULES