Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

(2017) Luvena L. Ong et al.   NATURE

Predicting DNA hybridization kinetics from sequence

(2017) Jinny X. Zhang et al.   Nature Chemistry

The Beauty and Utility of DNA Origami

(2017) Pengfei Wang et al.   Chem

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

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

Effects of co-ordination number on the nucleation behaviour in many-component self-assembly

(2016) Aleks Reinhardt et al.   FARADAY DISCUSSIONS

Self-Assembly of Structures with Addressable Complexity

(2016) William M. Jacobs et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Self-assembly of fully addressable DNA nanostructures from double crossover tiles

(2016) Wen Wang et al.   NUCLEIC ACIDS RESEARCH

DNA brick self-assembly with an off-lattice potential

(2016) Aleks Reinhardt et al.   Soft Matter

Design principles for rapid folding of knotted DNA nanostructures

(2016) Vid Kočar et al.   Nature Communications

Effects of co-ordination number on the nucleation behaviour in many-component self-assembly

(2016) Aleks Reinhardt et al.   FARADAY DISCUSSIONS

Mechanisms of Virus Assembly

(2015) Jason D. Perlmutter et al.   Annual Review of Physical Chemistry

Modelling DNA origami self-assembly at the domain level

(2015) Frits Dannenberg et al.   JOURNAL OF CHEMICAL PHYSICS

Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

(2015) William M. Jacobs et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2015) Benedict E. K. Snodin et al.   JOURNAL OF CHEMICAL PHYSICS

Guiding the folding pathway of DNA origami

(2015) Katherine E. Dunn et al.   NATURE

Order through entropy

(2015) Daan Frenkel   NATURE MATERIALS

Programmable self-assembly

(2015) Ludovico Cademartiri et al.   NATURE MATERIALS

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

(2015) John S. Schreck et al.   NUCLEIC ACIDS RESEARCH

Rational design of self-assembly pathways for complex multicomponent structures

(2015) William M. Jacobs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Compact DNA Cube with Side Length 10 nm

(2015) Max B. Scheible et al.   Small

Self-assembly protocol design for periodic multicomponent structures

(2015) William M. Jacobs et al.   Soft Matter

Undesired usage and the robust self-assembly of heterogeneous structures

(2015) Arvind Murugan et al.   Nature Communications

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

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

DNA brick crystals with prescribed depths

(2014) Yonggang Ke et al.   Nature Chemistry

Numerical Evidence for Nucleated Self-Assembly of DNA Brick Structures

(2014) Aleks Reinhardt et al.   PHYSICAL REVIEW LETTERS

Programmable energy landscapes for kinetic control of DNA strand displacement

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

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

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

Coarse-grained simulations of DNA overstretching

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

Design Space for Complex DNA Structures

(2013) Bryan Wei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Isothermal Self-Assembly of Complex DNA Structures under Diverse and Biocompatible Conditions

(2013) Cameron Myhrvold et al.   NANO LETTERS

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

Coarse-graining DNA for simulations of DNA nanotechnology

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

Sequence-dependent thermodynamics of a coarse-grained DNA model

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

Complex shapes self-assembled from single-stranded DNA tiles

(2012) Bryan Wei et al.   NATURE

Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature

(2012) J.-P. J. Sobczak et al.   SCIENCE

Three-Dimensional Structures Self-Assembled from DNA Bricks

(2012) Y. Ke et al.   SCIENCE

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

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

Design principles for self-assembly with short-range interactions

(2011) S. Hormoz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Monodisperse self-assembly in a model with protein-like interactions

(2009) Alex W. Wilber et al.   JOURNAL OF CHEMICAL PHYSICS

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

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

Programming DNA Tube Circumferences

(2008) P. Yin et al.   SCIENCE

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

(2008) Stephen Whitelam et al.   Soft Matter

Domain Nucleation Rates and Interfacial Line Tensions in Supported Bilayers of Ternary Mixtures Containing Galactosylceramide

(2007) Craig D. Blanchette et al.   BIOPHYSICAL JOURNAL