Related references
Note: Only part of the references are listed.Coarse-grained simulation of DNA using LAMMPS An implementation of the oxDNA model and its applications
Oliver Henrich et al.
EUROPEAN PHYSICAL JOURNAL E (2018)
A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes
Alexander Ohmann et al.
NATURE COMMUNICATIONS (2018)
Hybridization Kinetics Explains CRISPR-Cas Off-Targeting Rules
Misha Klein et al.
CELL REPORTS (2018)
Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks
Kevin M. Cherry et al.
NATURE (2018)
Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns
Grigory Tikhomirov et al.
NATURE (2017)
A spatially localized architecture for fast and modular DNA computing
Gourab Chatterjee et al.
NATURE NANOTECHNOLOGY (2017)
Fundamental Costs in the Production and Destruction of Persistent Polymer Copies
Thomas E. Ouldridge et al.
PHYSICAL REVIEW LETTERS (2017)
Enzyme-free nucleic acid dynamical systems
Niranjan Srinivas et al.
SCIENCE (2017)
The Effect of Basepair Mismatch on DNA Strand Displacement
D. W. Bo Broadwater et al.
BIOPHYSICAL JOURNAL (2016)
New Langevin and gradient thermostats for rigid body dynamics
R. L. Davidchack et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
DNA nanotechnology: understanding and optimisation through simulation
Thomas E. Ouldridge
MOLECULAR PHYSICS (2015)
Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker
Thomas E. Ouldridge et al.
ACS NANO (2013)
Programmable chemical controllers made from DNA
Yuan-Jyue Chen et al.
NATURE NANOTECHNOLOGY (2013)
DNA hybridization kinetics: zippering, internal displacement and sequence dependence
Thomas E. Ouldridge et al.
NUCLEIC ACIDS RESEARCH (2013)
On the biophysics and kinetics of toehold-mediated DNA strand displacement
Niranjan Srinivas et al.
NUCLEIC ACIDS RESEARCH (2013)
Sequence-dependent thermodynamics of a coarse-grained DNA model
Petr Sulc et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Three-Dimensional Structures Self-Assembled from DNA Bricks
Yonggang Ke et al.
SCIENCE (2012)
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
Thomas E. Ouldridge et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
A simple DNA gate motif for synthesizing large-scale circuits
Lulu Qian et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2011)
A Programmable Molecular Robot
Richard A. Muscat et al.
NANO LETTERS (2011)
Forward flux sampling for rare event simulations
Rosalind J. Allen et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2009)
Control of DNA Strand Displacement Kinetics Using Toehold Exchange
David Yu Zhang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Self-assembly of DNA into nanoscale three-dimensional shapes
Shawn M. Douglas et al.
NATURE (2009)
Multiscale modeling of emergent materials: biological and soft matter
Teemu Murtola et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2009)
PROGRAMMABLE CONTROL OF NUCLEATION FOR ALGORITHMIC SELF-ASSEMBLY
Rebecca Schulman et al.
SIAM JOURNAL ON COMPUTING (2009)
The role of collective motion in examples of coarsening and self-assembly
Stephen Whitelam et al.
SOFT MATTER (2009)
Engineering entropy-driven reactions and networks catalyzed by DNA
David Yu Zhang et al.
SCIENCE (2007)
Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles
Stephen Whitelam et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Folding DNA to create nanoscale shapes and patterns
PWK Rothemund
NATURE (2006)
Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication
RP Goodman et al.
SCIENCE (2005)
Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability
BG Moreira et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2005)
Sampling rare switching events in biochemical networks
RJ Allen et al.
PHYSICAL REVIEW LETTERS (2005)
A new class of homogeneous nucleic acid probes based on specific displacement hybridization
QQ Li et al.
NUCLEIC ACIDS RESEARCH (2002)
A DNA-fuelled molecular machine made of DNA
B Yurke et al.
NATURE (2000)