Moving beyond Watson–Crick models of coarse grained DNA dynamics

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

(2011) Juan C. Araque 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

Transient Hoogsteen base pairs in canonical duplex DNA

(2011) Evgenia N. Nikolova et al.   NATURE

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

(2011) Vanessa Ortiz et al.   PHYSICAL REVIEW LETTERS

Structure, location and interactions of G-quadruplexes

(2010) Julian L. Huppert   FEBS Journal

Analysis of a DNA simulation model through hairpin melting experiments

(2010) Margaret C. Linak et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

(2010) Robert C. DeMille 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

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

Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides

(2010) Moritz Julian Hoefert et al.   Soft Matter

Coarse-Grained Brownian Dynamics Simulations of the 10-23 DNAzyme

(2009) Martin Kenward et al.   BIOPHYSICAL JOURNAL

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

(2009) Alexey Savelyev et al.   BIOPHYSICAL JOURNAL

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

Coarse-grained model of nucleic acid bases

(2009) Maciej Maciejczyk et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

(2009) Srinivasa M. Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess 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

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

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