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

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

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

Molecular machines

(2013) Ron Elber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse-grained simulations of DNA overstretching

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

Two-domain DNA strand displacement

(2013) LUCA CARDELLI   MATHEMATICAL STRUCTURES IN COMPUTER SCIENCE

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

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

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

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

Complex shapes self-assembled from single-stranded DNA tiles

(2012) Bryan Wei et al.   NATURE

Nucleic Acid Based Molecular Devices

(2011) Yamuna Krishnan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

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

Expanding the Rule Set of DNA Circuitry with Associative Toehold Activation

(2011) Xi Chen   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics

(2011) Anthony J. Genot et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Challenges and opportunities for structural DNA nanotechnology

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

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

(2011) L. Qian et al.   SCIENCE

NUPACK: Analysis and design of nucleic acid systems

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

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

Robustness and modularity properties of a non-covalent DNA catalytic reaction

(2010) D. Y. Zhang et al.   NUCLEIC ACIDS RESEARCH

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

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

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators

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

DNA as a universal substrate for chemical kinetics

(2010) D. Soloveichik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Langevin thermostat for rigid body dynamics

(2009) Ruslan L. Davidchack et al.   JOURNAL OF CHEMICAL PHYSICS

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

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

Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations

(2008) Richard Owczarzy et al.   BIOCHEMISTRY

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra

(2008) Yu He et al.   NATURE

Programming biomolecular self-assembly pathways

(2008) Peng Yin et al.   NATURE

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