Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics

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

DNA Melting in Small-Molecule−DNA-Hybrid Dimer Structures: Experimental Characterization and Coarse-Grained Molecular Dynamics Simulations

(2010) Tatiana R. Prytkova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

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

A Mesoscale Model of DNA and Its Renaturation

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

The self-assembly of DNA Holliday junctions studied with a minimal model

(2009) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

Brownian dynamics simulations of single-stranded DNA hairpins

(2009) Martin Kenward et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration

(2009) Milo M. Lin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations

(2009) Srinivasaraghavan Kannan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis

(2009) E. J. Sambriski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Pathway of Oligomeric DNA Melting Investigated by Molecular Dynamics Simulations

(2008) Ka-Yiu Wong et al.   BIOPHYSICAL JOURNAL

Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes

(2008) Ernesto E. Borrero et al.   JOURNAL OF CHEMICAL PHYSICS

Optimization of expanded ensemble methods

(2008) Fernando A. Escobedo et al.   JOURNAL OF CHEMICAL PHYSICS

United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials

(2008) Agustí Emperador et al.   Journal of Chemical Theory and Computation

Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways

(2008) E J Sambriski et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

RNA secondary structures: complex statics and glassy dynamics

(2008) S Wolfsheimer et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Origins of barriers and barrierless folding in BBL

(2008) S. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA