A single nucleotide resolution model for large-scale simulations of double stranded DNA

Stochastic Model of Supercoiling-Dependent Transcription

(2016) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

DNA denaturation bubbles: Free-energy landscape and nucleation/closure rates

(2015) François Sicard et al.   JOURNAL OF CHEMICAL PHYSICS

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

(2015) Benedict E. K. Snodin et al.   JOURNAL OF CHEMICAL PHYSICS

Topological patterns in two-dimensional gel electrophoresis of DNA knots

(2015) Davide Michieletto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

(2015) Christian Matek et al.   Scientific Reports

Pack, unpack, bend, twist, pull, push: the physical side of gene expression

(2014) Christophe Lavelle   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein–DNA binding site

(2014) Ilda D'Annessa et al.   NUCLEIC ACIDS RESEARCH

DNA supercoiling: A regulatory signal for the   repressor

(2014) Y. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Threading Dynamics of Ring Polymers in a Gel

(2014) Davide Michieletto et al.   ACS Macro Letters

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

(2013) Daniel M. Hinckley et al.   JOURNAL OF CHEMICAL PHYSICS

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Developments in understanding and controlling self assembly of DNA-functionalized colloids

(2013) Lorenzo Di Michele et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

(2013) C. A. Brackley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

(2011) Juan J. de Pablo   Annual Review of Physical Chemistry

Supramolecular DNA assembly

(2011) Christopher K. McLaughlin et al.   CHEMICAL SOCIETY REVIEWS

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments

(2010) Jan Lipfert et al.   NATURE METHODS

Supercoiling Induces Denaturation Bubbles in Circular DNA

(2010) Jae-Hyung Jeon et al.   PHYSICAL REVIEW LETTERS

Entropic organization of interphase chromosomes

(2009) Peter R. Cook et al.   JOURNAL OF CELL BIOLOGY

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

(2009) Eva Fadrná et al.   Journal of Chemical Theory and Computation

Towards self-replicating materials of DNA-functionalized colloids

(2009) Mirjam E. Leunissen et al.   Soft Matter

Recent advances in the study of nucleic acid flexibility by molecular dynamics

(2008) Modesto Orozco et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology