An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

Exploring the mechanisms of DNA hybridization on a surface

(2013) Terry J. Schmitt et al.   JOURNAL OF CHEMICAL PHYSICS

Mean-Field Interactions between Nucleic-Acid-Base Dipoles can Drive the Formation of a Double Helix

(2013) Yi He et al.   PHYSICAL REVIEW LETTERS

Two-phase stretching of molecular chains

(2013) A. V. Savin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Zeeman shift of two-dimensional optical signals of Mg-porphyrin dimers with circularly polarized beams

(2012) Justo J. Rodriguez et al.   JOURNAL OF CHEMICAL PHYSICS

The effect of topology on the structure and free energy landscape of DNA kissing complexes

(2012) Flavio Romano et al.   JOURNAL OF CHEMICAL PHYSICS

Sequence-dependent thermodynamics of a coarse-grained DNA model

(2012) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

Ab initio determination of coarse-grained interactions in double-stranded DNA

(2012) Chia Wei Hsu et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-Grained Model DNA: Structure, Sequences, Stems, Circles, Hairpins

(2012) Lance E. Edens et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism

(2012) Christian Matek et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Density of States–Based Molecular Simulations

(2012) Sadanand Singh et al.   Annual Review of Chemical and Biomolecular Engineering

Frontiers in Molecular Dynamics Simulations of DNA

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

Thermodynamics of DNA hybridization on surfaces

(2011) Terry J. Schmitt et al.   JOURNAL OF CHEMICAL PHYSICS

Moving beyond Watson–Crick models of coarse grained DNA dynamics

(2011) Margaret C. Linak et al.   JOURNAL OF CHEMICAL PHYSICS

Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide

(2011) Ana-Maria Florescu 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

A coarse-grain three-site-per-nucleotide model for DNA with explicit ions

(2011) Gordon S. Freeman et al.   JOURNAL OF CHEMICAL PHYSICS

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

(2011) Hiroo Kenzaki et al.   Journal of Chemical Theory and Computation

Computational Model for Predicting Experimental RNA and DNA Nearest-Neighbor Free Energy Rankings

(2011) Charles A. Johnson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Flux Tempered Metadynamics

(2011) Sadanand Singh et al.   JOURNAL OF STATISTICAL PHYSICS

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

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

Heat conductivity of the DNA double helix

(2011) Alexander V. Savin et al.   PHYSICAL REVIEW B

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

(2011) Vanessa Ortiz et al.   PHYSICAL REVIEW LETTERS

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

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

(2010) Robert C. DeMille 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

Mechanical and structural properties of YOYO-1 complexed DNA

(2010) K. Gunther et al.   NUCLEIC ACIDS RESEARCH

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

A Mesoscale Model of DNA and Its Renaturation

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

Coarse-grained model of nucleic acid bases

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

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

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

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

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

Insights on protein-DNA recognition by coarse grain modelling

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

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

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS