A sequence-dependent rigid-base model of DNA

Impact of Methylation on the Physical Properties of DNA

(2012) Alberto Pérez et al.   BIOPHYSICAL JOURNAL

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

(2012) Tomáš Dršata et al.   Journal of Chemical Theory and Computation

Nonsmooth optimization via quasi-Newton methods

(2012) Adrian S. Lewis et al.   MATHEMATICAL PROGRAMMING

Exploring polymorphisms in B-DNA helical conformations

(2012) Pablo D. Dans et al.   NUCLEIC ACIDS RESEARCH

Robust self-replication of combinatorial information via crystal growth and scission

(2012) R. Schulman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward Convergence of Experimental Studies and Theoretical Modeling of the Chromatin Fiber

(2011) Tamar Schlick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant

(2011) Garen G. Holman et al.   Nature Chemistry

Cytosine methylation alters DNA mechanical properties

(2011) Philip M. D. Severin et al.   NUCLEIC ACIDS RESEARCH

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

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

Thermal Denaturation of DNA Studied with Neutron Scattering

(2011) Andrew Wildes et al.   PHYSICAL REVIEW LETTERS

Timing molecular motion and production with a synthetic transcriptional clock

(2011) E. Franco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Origami with Complex Curvatures in Three-Dimensional Space

(2011) D. Han et al.   SCIENCE

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

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 of DNA with Explicit Solvation by Water and Ions

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

Group theory and biomolecular conformation: I. Mathematical and computational models

(2010) Gregory S Chirikjian   JOURNAL OF PHYSICS-CONDENSED MATTER

On the Stochastic Modeling of Rigid Body Systems with Application to Polymer Dynamics

(2010) J. Walter et al.   MULTISCALE MODELING & SIMULATION

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

Looping probabilities of elastic chains: A path integral approach

(2010) Ludovica Cotta-Ramusino et al.   PHYSICAL REVIEW E

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

Coarse-grained molecular dynamics modeling of DNA-carbon nanotube complexes

(2009) Jian Zou et al.   INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

Stretching and twisting of the DNA duplexes in coarse-grained dynamical models

(2009) Szymon Niewieczerzał et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

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

Using DNA mechanics to predict in vitro nucleosome positions and formation energies

(2009) Alexandre V. Morozov et al.   NUCLEIC ACIDS RESEARCH

Conformational analysis of nucleic acids revisited: Curves+

(2009) R. Lavery et al.   NUCLEIC ACIDS RESEARCH

Viral assembly: a molecular modeling perspective

(2009) Stephen C. Harvey et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Mesoscale simulations of two nucleosome-repeat length oligonucleosomes

(2009) Tamar Schlick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Simulation of DNA catenanes

(2009) Alexander Vologodskii et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations

(2009) F. Lankaš et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

An information-bearing seed for nucleating algorithmic self-assembly

(2009) R. D. Barish et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

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

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

Insights on protein-DNA recognition by coarse grain modelling

(2008) P. Poulain et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Brownian dynamics of double-stranded DNA in periodic systems with discrete salt

(2008) Steven P. Mielke et al.   PHYSICAL REVIEW E