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

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

(2011) Juan J. de Pablo   Annual Review of Physical Chemistry

Solution Structures of Rat Amylin Peptide: Simulation, Theory, and Experiment

(2010) Allam S. Reddy et al.   BIOPHYSICAL JOURNAL

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

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

A Mesoscale Model of DNA and Its Renaturation

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

Coarse-grained ions without charges: Reproducing the solvation structure of NaCl in water using short-ranged potentials

(2009) Robert C. DeMille et al.   JOURNAL OF CHEMICAL PHYSICS

The impact of monovalent ion force field model in nucleic acids simulations

(2009) Agnes Noy 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

Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations

(2008) Richard Owczarzy et al.   BIOCHEMISTRY

Packaging Double-Helical DNA into Viral Capsids: Structures, Forces, and Energetics

(2008) Anton S. Petrov et al.   BIOPHYSICAL JOURNAL

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

Portal Motor Velocity and Internal Force Resisting Viral DNA Packaging in Bacteriophage ϕ29

(2007) John Peter Rickgauer et al.   BIOPHYSICAL JOURNAL