A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations

(2014) Nikolay Korolev et al.   BIOPOLYMERS

Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids

(2014) Alexander Mirzoev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

MagiC: Software Package for Multiscale Modeling

(2013) Alexander Mirzoev et al.   Journal of Chemical Theory and Computation

Coarse-Grained Simulations of RNA and DNA Duplexes

(2013) Tristan Cragnolini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-graining DNA for simulations of DNA nanotechnology

(2013) Jonathan P. K. Doye et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions

(2013) Yanping Fan et al.   PLoS One

Unwrapping of Nucleosomal DNA Ends: A Multiscale Molecular Dynamics Study

(2012) Karine Voltz et al.   BIOPHYSICAL JOURNAL

Coarse-grained molecular simulations of large biomolecules

(2012) Shoji Takada   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modelling chromatin structure and dynamics: status and prospects

(2012) Nikolay Korolev et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse-graining of multiprotein assemblies

(2012) Marissa G Saunders et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The polyelectrolyte properties of chromatin

(2012) Nikolay Korolev et al.   Soft Matter

Recent successes in coarse-grained modeling of DNA

(2012) Davit A. Potoyan et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Force spectroscopy of chromatin fibers: Extracting energetics and structural information from Monte Carlo simulations

(2011) Nick Kepper et al.   BIOPOLYMERS

Coarse-graining entropy, forces, and structures

(2011) Joseph F. Rudzinski et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-graining errors and numerical optimization using a relative entropy framework

(2011) Aviel Chaimovich et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

A coarse-grain three-site-per-nucleotide model for DNA with explicit ions

(2011) Gordon S. Freeman et al.   JOURNAL OF CHEMICAL PHYSICS

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Is DNA’s Rigidity Dominated by Electrostatic or Nonelectrostatic Interactions?

(2011) Alexey Savelyev et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Do monovalent mobile ions affect DNA's flexibility at high salt content?

(2011) Alexey Savelyev   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids

(2011) Jan Lipfert et al.   Nature Communications

Electrostatic Origin of Salt-Induced Nucleosome Array Compaction

(2010) Nikolay Korolev et al.   BIOPHYSICAL JOURNAL

Exploring the Conformational Space of Chromatin Fibers and Their Stability by Numerical Dynamic Phase Diagrams

(2010) René Stehr et al.   BIOPHYSICAL JOURNAL

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

(2010) Pablo D. Dans et al.   Journal of Chemical Theory and Computation

A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions

(2010) Robert C. DeMille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nucleosome accessibility governed by the dimer/tetramer interface

(2010) Vera Böhm et al.   NUCLEIC ACIDS RESEARCH

The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association

(2010) Abdollah Allahverdi et al.   NUCLEIC ACIDS RESEARCH

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

(2010) Thomas E. Ouldridge et al.   PHYSICAL REVIEW LETTERS

Chemically accurate coarse graining of double-stranded DNA

(2010) A. Savelyev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interaction of double-stranded DNA with a nanosphere: a coarse-grained molecular dynamics simulation study

(2010) Qianqian Cao et al.   Soft Matter

Cation-induced polyelectrolyte–polyelectrolyte attraction in solutions of DNA and nucleosome core particles

(2009) Nikolay Korolev et al.   ADVANCES IN COLLOID AND INTERFACE SCIENCE

Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

(2009) Alexey Savelyev et al.   BIOPHYSICAL JOURNAL

Computer Modeling Reveals that Modifications of the Histone Tail Charges Define Salt-Dependent Interaction of the Nucleosome Core Particles

(2009) Ye Yang et al.   BIOPHYSICAL JOURNAL

Systematic coarse-graining of molecular models by the Newton inversion method

(2009) Alexander Lyubartsev et al.   FARADAY DISCUSSIONS

A Tale of Tails: How Histone Tails Mediate Chromatin Compaction in Different Salt and Linker Histone Environments†

(2009) Gaurav Arya et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle

(2009) Christopher K. Materese et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation

(2009) Nikolay Korolev et al.   NUCLEIC ACIDS RESEARCH

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

(2009) S. A. Grigoryev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Effect of Internucleosomal Interaction on Folding of the Chromatin Fiber

(2008) René Stehr et al.   BIOPHYSICAL JOURNAL

Nucleosome Geometry and Internucleosomal Interactions Control the Chromatin Fiber Conformation

(2008) Nick Kepper et al.   BIOPHYSICAL JOURNAL

HELFIT: Helix fitting by a total least squares method

(2008) Purevjav Enkhbayar et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Coarse-grained force field for the nucleosome from self-consistent multiscaling

(2008) Karine Voltz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY