Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

Characterizing the bending and flexibility induced by bulges in DNA duplexes

(2015) John S. Schreck et al.   JOURNAL OF CHEMICAL PHYSICS

Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

(2015) Christian Matek et al.   Scientific Reports

Gels of DNA Nanostars Never Crystallize

(2014) Lorenzo Rovigatti et al.   ACS Nano

Modeling DNA Thermodynamics under Torsional Stress

(2014) Qian Wang et al.   BIOPHYSICAL JOURNAL

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

(2014) Daniel M. Hinckley et al.   JOURNAL OF CHEMICAL PHYSICS

A nucleotide-level coarse-grained model of RNA

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

A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment

(2014) Christopher Maffeo et al.   Journal of Chemical Theory and Computation

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

(2014) Lorenzo Rovigatti et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Role of Loop Stacking in the Dynamics of DNA Hairpin Formation

(2014) Majid Mosayebi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Close encounters with DNA

(2014) C Maffeo et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Ultrafast cooling reveals microsecond-scale biomolecular dynamics

(2014) Mark E. Polinkovsky et al.   Nature Communications

Programmable energy landscapes for kinetic control of DNA strand displacement

(2014) Robert R. F. Machinek et al.   Nature Communications

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

(2014) Nikolay Korolev et al.   Polymers

Beyond the Helix Pitch: Direct Visualization of Native DNA in Aqueous Solution

(2013) Shinichiro Ido et al.   ACS Nano

Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

(2013) Thomas E. Ouldridge et al.   ACS Nano

Sequence and Temperature Dependence of the End-to-End Collision Dynamics of Single-Stranded DNA

(2013) Takanori Uzawa et al.   BIOPHYSICAL JOURNAL

Coarse-grained simulations of DNA overstretching

(2013) Flavio Romano et al.   JOURNAL OF CHEMICAL PHYSICS

A sequence-dependent rigid-base model of DNA

(2013) O. Gonzalez 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

Approaching the Limit: Can One DNA Strand Assemble into Defined Nanostructures?

(2013) Cheng Tian et al.   LANGMUIR

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

(2013) Jiří Šponer et al.   METHODS

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

(2013) Petr Šulc et al.   Natural Computing

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

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

On the biophysics and kinetics of toehold-mediated DNA strand displacement

(2013) Niranjan Srinivas et al.   NUCLEIC ACIDS RESEARCH

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

(2013) Alessandro Bosco et al.   NUCLEIC ACIDS RESEARCH

Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory

(2013) Arnošt Mládek 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

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

DNA Gridiron Nanostructures Based on Four-Arm Junctions

(2013) D. Han et al.   SCIENCE

Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami

(2012) Reza M. Zadegan et al.   ACS Nano

Controlling the Chirality of DNA Nanocages

(2012) Chuan Zhang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Sequence-dependent thermodynamics of a coarse-grained DNA model

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

DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism

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

Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level

(2012) Elías Herrero-Galán et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Electromagnetic Torque Tweezers: A Versatile Approach for Measurement of Single-Molecule Twist and Torque

(2012) Xander J. A. Janssen et al.   NANO LETTERS

DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response

(2012) Anton Kuzyk et al.   NATURE

End-to-end attraction of duplex DNA

(2012) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering

(2012) Adelene Y. L. Sim et al.   PHYSICAL REVIEW E

Cryo-EM structure of a 3D DNA-origami object

(2012) X.-c. Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-Dimensional Structures Self-Assembled from DNA Bricks

(2012) Y. Ke et al.   SCIENCE

A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads

(2012) S. M. Douglas et al.   SCIENCE

Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”

(2012) Francesca Mocci et al.   Soft Matter

Recent successes in coarse-grained modeling of DNA

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

Frontiers in Molecular Dynamics Simulations of DNA

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

DNA Cage Delivery to Mammalian Cells

(2011) Anthony S. Walsh et al.   ACS Nano

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

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

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

The Label-Free Unambiguous Detection and Symbolic Display of Single Nucleotide Polymorphisms on DNA Origami

(2011) Hari K. K. Subramanian et al.   NANO LETTERS

Challenges and opportunities for structural DNA nanotechnology

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

Do monovalent mobile ions affect DNA's flexibility at high salt content?

(2011) Alexey Savelyev   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The atomistic simulation of DNA

(2011) Charles A. Laughton et al.   Wiley Interdisciplinary Reviews-Computational Molecular 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

Extracting bulk properties of self-assembling systems from small simulations

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

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

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

DNA–DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density

(2010) Christopher Maffeo 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

DNA self-assembly: from 2D to 3D

(2009) Chuan Zhang et al.   FARADAY DISCUSSIONS

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

High-Resolution Structural Analysis of a DNA Nanostructure by cryoEM

(2009) Takayuki Kato et al.   NANO LETTERS

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal

(2009) Jianping Zheng et al.   NATURE

Folding DNA into Twisted and Curved Nanoscale Shapes

(2009) H. Dietz et al.   SCIENCE

Determination of phase diagrams via computer simulation: methodology and applications to water, electrolytes and proteins

(2008) C Vega et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

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

(2008) Stephen Whitelam et al.   Soft Matter