Sequence-dependent thermodynamics of a coarse-grained DNA model

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

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

Quantitative Prediction of the Phase Diagram of DNA-Functionalized Nanosized Colloids

(2012) Bianca M. Mladek et al.   PHYSICAL REVIEW LETTERS

Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

(2012) Cristiano De Michele et al.   Soft Matter

Frontiers in Molecular Dynamics Simulations of DNA

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

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

(2011) Juan C. Araque 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 Programmable Molecular Robot

(2011) Richard A. Muscat et al.   NANO LETTERS

Heat conductivity of the DNA double helix

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

Thermomechanics of DNA: Theory of Thermal Stability under Load

(2011) Cristiano Nisoli et al.   PHYSICAL REVIEW LETTERS

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

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Extracting bulk properties of self-assembling systems from small simulations

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

Direct Observation of Multiple Pathways of Single-Stranded DNA Stretching

(2010) Wuen-shiu Chen et al.   PHYSICAL REVIEW LETTERS

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

(2010) Thomas E. Ouldridge et al.   PHYSICAL REVIEW LETTERS

Sequence dependence of DNA bending rigidity

(2010) S. Geggier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule derivation of salt dependent base-pair free energies in DNA

(2010) J. M. Huguet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Reversible gels of patchy particles: Role of the valence

(2009) John Russo et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

(2009) Daniel Svozil et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

(2009) David Yu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Stretching of a single-stranded DNA: Evidence for structural transition

(2009) Garima Mishra et al.   PHYSICAL REVIEW E

Mechanism for a Directional, Processive, and Reversible DNA Motor

(2009) Jonathan Bath et al.   Small

A Unified Poland-Scheraga Model of Oligo- and Polynucleotide DNA Melting: Salt Effects and Predictive Power

(2008) Daniel Jost et al.   BIOPHYSICAL JOURNAL

Programming biomolecular self-assembly pathways

(2008) Peng Yin et al.   NATURE

Nature and magnitude of aromatic stacking of nucleic acid bases

(2008) Jiří Šponer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion

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

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

(2008) Stephen Whitelam et al.   Soft Matter