Recent successes in coarse-grained modeling of DNA

Frontiers in Molecular Dynamics Simulations of DNA

(2011) Alberto Pérez et al.   ACCOUNTS OF CHEMICAL RESEARCH

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

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

DNA origami: a quantum leap for self-assembly of complex structures

(2011) Thomas Tørring et al.   CHEMICAL SOCIETY REVIEWS

Coarse-graining entropy, forces, and structures

(2011) Joseph F. Rudzinski 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

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

DNA Cyclization: Suppression or Enhancement by Electrostatic Repulsions?

(2011) A. G. Cherstvy   JOURNAL OF PHYSICAL CHEMISTRY B

Energy Landscape Analyses of Disordered Histone Tails Reveal Special Organization of Their Conformational Dynamics

(2011) Davit A. Potoyan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Conformational Flexibility of DNA

(2011) Andriy Marko et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A hybrid all-atom/coarse grain model for multiscale simulations of DNA

(2011) Matías Rodrigo Machado et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2011) Alexey Savelyev   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Molecular Origins of DNA Flexibility: Sequence Effects on Conformational and Mechanical Properties

(2011) Vanessa Ortiz et al.   PHYSICAL REVIEW LETTERS

DNA Origami with Complex Curvatures in Three-Dimensional Space

(2011) D. Han et al.   SCIENCE

The atomistic simulation of DNA

(2011) Charles A. Laughton et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Real-Time Atomistic Description of DNA Unfolding

(2010) Alberto Perez et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Nanomaterials Based on DNA

(2010) Nadrian C. Seeman   Annual Review of Biochemistry

Chromatin Dynamics

(2010) Michael R. Hübner et al.   Annual Review of Biophysics

Chromatin Ionic Atmosphere Analyzed by a Mesoscale Electrostatic Approach

(2010) Hin Hark Gan et al.   BIOPHYSICAL JOURNAL

Electrostatic Origin of Salt-Induced Nucleosome Array Compaction

(2010) Nikolay Korolev et al.   BIOPHYSICAL JOURNAL

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

(2010) Alex Morriss-Andrews et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Modeling Studies of Chromatin Fiber Structure as a Function of DNA Linker Length

(2010) Ognjen Perišić et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Intrinsic Z-DNA Is Stabilized by the Conformational Selection Mechanism of Z-DNA-Binding Proteins

(2010) Sangsu Bae et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Development of coarse-graining DNA models for single-nucleotide resolution analysis

(2010) K. Doi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Physics of DNA: unravelling hidden abilities encoded in the structure of ‘the most important molecule’

(2010) Alexei A. Kornyshev   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

DNA curvature and flexibility in vitro and in vivo

(2010) Justin P. Peters et al.   QUARTERLY REVIEWS OF BIOPHYSICS

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

(2010) Qianqian Cao et al.   Soft Matter

Nucleosome Assembly Depends on the Torsion in the DNA Molecule: A Magnetic Tweezers Study

(2009) Pooja Gupta et al.   BIOPHYSICAL JOURNAL

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

(2009) Alexey Savelyev et al.   BIOPHYSICAL JOURNAL

Probing the Conformational Distributions of Subpersistence Length DNA

(2009) Alexander J. Mastroianni 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

A Mesoscale Model of DNA and Its Renaturation

(2009) E.J. Sambriski et al.   BIOPHYSICAL JOURNAL

Coarse-grained ions without charges: Reproducing the solvation structure of NaCl in water using short-ranged potentials

(2009) Robert C. DeMille et al.   JOURNAL OF CHEMICAL PHYSICS

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

Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl

(2009) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle

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

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

(2009) Richard Lavery 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 multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

Polyionic Charge Density Plays a Key Role in Differential Recognition of Mobile Ions by Biopolymers

(2008) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Analysis of DNA Elasticity

(2008) R. P. Linna et al.   PHYSICAL REVIEW LETTERS

DNA Bending Stiffness on Small Length Scales

(2008) Chongli Yuan et al.   PHYSICAL REVIEW LETTERS