TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami

Force-Induced Unravelling of DNA Origami

(2018) Megan C. Engel et al.   ACS Nano

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Coarse-grained simulation of DNA using LAMMPS

(2018) Oliver Henrich et al.   EUROPEAN PHYSICAL JOURNAL E

A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo

(2018) Suping Li et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Sequence-Dependent Persistence Lengths of DNA

(2017) Jonathan S. Mitchell et al.   Journal of Chemical Theory and Computation

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs

(2017) Simón Poblete et al.   NUCLEIC ACIDS RESEARCH

Pore translocation of knotted DNA rings

(2017) Antonio Suma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Simulation of the Self-Assembly of a Small DNA Origami

(2016) Benedict E. K. Snodin et al.   ACS Nano

Multiscale simulation of DNA

(2016) Pablo D Dans et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars

(2016) J. Fernandez-Castanon et al.   JOURNAL OF CHEMICAL PHYSICS

Automated design of DNA origami

(2016) Veikko Linko et al.   NATURE BIOTECHNOLOGY

De novoreconstruction of DNA origami structures through atomistic molecular dynamics simulation

(2016) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

Diamond family of nanoparticle superlattices

(2016) W. Liu et al.   SCIENCE

Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments

(2016) Wujie Wang et al.   Scientific Reports

Conformationally Gated Charge Transfer in DNA Three-Way Junctions

(2015) Yuqi Zhang et al.   Journal of Physical Chemistry Letters

Knotting dynamics of DNA chains of different length confined in nanochannels

(2015) Antonio Suma et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Structural diversity of supercoiled DNA

(2015) Rossitza N. Irobalieva et al.   Nature Communications

Pore Translocation of Knotted Polymer Chains: How Friction Depends on Knot Complexity

(2015) Antonio Suma et al.   ACS Macro Letters

A nucleotide-level coarse-grained model of RNA

(2014) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

Knotting and Unknotting Dynamics of DNA Strands in Nanochannels

(2014) Cristian Micheletti et al.   ACS Macro Letters

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Topological friction strongly affects viral DNA ejection

(2013) D. Marenduzzo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

(2013) J. Yoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence-dependent thermodynamics of a coarse-grained DNA model

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

Recent successes in coarse-grained modeling of DNA

(2012) Davit A. Potoyan et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

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

A primer to scaffolded DNA origami

(2011) Carlos Ernesto Castro et al.   NATURE METHODS

Challenges and opportunities for structural DNA nanotechnology

(2011) Andre V. Pinheiro et al.   Nature Nanotechnology

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures

(2011) Do-Nyun Kim et al.   NUCLEIC ACIDS RESEARCH

Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA

(2011) J. S. Mitchell et al.   NUCLEIC ACIDS RESEARCH

Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases

(2011) Guillaume Witz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

(2010) Pablo D. Dans et al.   Journal of Chemical Theory and Computation

Excluded Volume Effects on Semiflexible Ring Polymers

(2010) Fabian Drube et al.   NANO LETTERS

Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

(2009) Alexey Savelyev et al.   BIOPHYSICAL JOURNAL

Rapid prototyping of 3D DNA-origami shapes with caDNAno

(2009) Shawn M. Douglas et al.   NUCLEIC ACIDS RESEARCH

DNA supercoiling and its role in DNA decatenation and unknotting

(2009) Guillaume Witz et al.   NUCLEIC ACIDS RESEARCH

DNA–DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting

(2009) Davide Marenduzzo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

Assembling Materials with DNA as the Guide

(2008) F. A. Aldaye et al.   SCIENCE