Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects

A sequence-dependent rigid-base model of DNA

(2013) O. Gonzalez et al.   JOURNAL OF CHEMICAL PHYSICS

Exploring the mechanisms of DNA hybridization on a surface

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

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

(2013) Daniel M. Hinckley et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-Grained Simulations of RNA and DNA Duplexes

(2013) Tristan Cragnolini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

(2013) Thomas E. Ouldridge et al.   NUCLEIC ACIDS RESEARCH

Coarse-graining DNA for simulations of DNA nanotechnology

(2013) Jonathan P. K. Doye et al.   PHYSICAL CHEMISTRY 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

Topotactic Interconversion of Nanoparticle Superlattices

(2013) R. J. Macfarlane et al.   SCIENCE

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

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

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

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

Building plasmonic nanostructures with DNA

(2011) Shawn J. Tan et al.   Nature Nanotechnology

Heat conductivity of the DNA double helix

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

Nanoparticle Superlattice Engineering with DNA

(2011) R. J. Macfarlane et al.   SCIENCE

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 proximity-based programmable DNA nanoscale assembly line

(2010) Hongzhou Gu et al.   NATURE

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

Mechanism of Thermal Renaturation and Hybridization of Nucleic Acids: Kramers’ Process and Universality in Watson−Crick Base Pairing†

(2009) Jean-Louis Sikorav et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transition path sampling and forward flux sampling. Applications to biological systems

(2009) Fernando A Escobedo 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

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-programmable nanoparticle crystallization

(2008) Sung Yong Park et al.   NATURE

IDT SciTools: a suite for analysis and design of nucleic acid oligomers

(2008) R. Owczarzy et al.   NUCLEIC ACIDS RESEARCH