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

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

HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA

(2010) Samuela Pasquali et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Extracting bulk properties of self-assembling systems from small simulations

(2010) Thomas E Ouldridge et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

DNA Lipoplexes: Formation of the Inverse Hexagonal Phase Observed by Coarse-Grained Molecular Dynamics Simulation

(2010) Josephine Corsi et al.   LANGMUIR

Twist-writhe partitioning in a coarse-grained DNA minicircle model

(2010) Mehmet Sayar et al.   PHYSICAL REVIEW E

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

DNA nanomechanics: How proteins deform the double helix

(2009) Nils B. Becker 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

A Replicable Tetrahedral Nanostructure Self-Assembled from a Single DNA Strand

(2009) Zhe Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Circular DNA Logic Gates with Strand Displacement

(2009) Cheng Zhang et al.   LANGMUIR

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

Self-assembly of a nanoscale DNA box with a controllable lid

(2009) Ebbe S. Andersen et al.   NATURE

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

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

(2009) F. Lankaš 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

Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging

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

Mechanism for a Directional, Processive, and Reversible DNA Motor

(2009) Jonathan Bath et al.   Small

Self-Assembly of a DNA Dodecahedron from 20 Trisoligonucleotides withC3h Linkers

(2008) Jan Zimmermann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

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

Supercoiling and Local Denaturation of Plasmids with a Minimalist DNA Model

(2008) Fabio Trovato et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

DNA and lipid bilayers: self-assembly and insertion

(2008) S. Khalid et al.   Journal of the Royal Society Interface

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra

(2008) Yu He et al.   NATURE

Molecular dynamics of a κB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation

(2008) Cameron Mura et al.   NUCLEIC ACIDS RESEARCH

Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion

(2008) S. J. Green et al.   PHYSICAL REVIEW LETTERS

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

(2008) F. Ding et al.   RNA

The role of collective motion in examples of coarsening and self-assembly

(2008) Stephen Whitelam et al.   Soft Matter