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Title
Coarse-graining DNA for simulations of DNA nanotechnology
Authors
Keywords
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Journal
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Volume 15, Issue 47, Pages 20395
Publisher
Royal Society of Chemistry (RSC)
Online
2013-10-03
DOI
10.1039/c3cp53545b
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- (2013) Thomas E. Ouldridge et al. ACS Nano
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- (2013) Emanuel Pfitzner et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- The enabled state of DNA nanotechnology
- (2013) Veikko Linko et al. CURRENT OPINION IN BIOTECHNOLOGY
- Coarse-grained simulations of DNA overstretching
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- (2013) O. Gonzalez et al. JOURNAL OF CHEMICAL PHYSICS
- Exploring the mechanisms of DNA hybridization on a surface
- (2013) Terry J. Schmitt et al. JOURNAL OF CHEMICAL PHYSICS
- Perspective: Coarse-grained models for biomolecular systems
- (2013) W. G. Noid JOURNAL OF CHEMICAL PHYSICS
- Coarse-Grained Simulations of RNA and DNA Duplexes
- (2013) Tristan Cragnolini et al. JOURNAL OF PHYSICAL CHEMISTRY B
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- (2013) Fei Zhang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- 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
- Strong bending of the DNA double helix
- (2013) A. Vologodskii et al. NUCLEIC ACIDS RESEARCH
- Mean-Field Interactions between Nucleic-Acid-Base Dipoles can Drive the Formation of a Double Helix
- (2013) Yi He et al. PHYSICAL REVIEW LETTERS
- Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry
- (2013) X. Zhang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching using fluorescence microscopy
- (2013) G. A. King et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- DNA Origami with Double-Stranded DNA As a Unified Scaffold
- (2012) Yang Yang et al. ACS Nano
- An Autonomous and Controllable Light-Driven DNA Walking Device
- (2012) Mingxu You et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- LAMMPS framework for dynamic bonding and an application modeling DNA
- (2012) Carsten Svaneborg COMPUTER PHYSICS COMMUNICATIONS
- Coarse-grained molecular simulations of large biomolecules
- (2012) Shoji Takada CURRENT OPINION IN STRUCTURAL BIOLOGY
- Coarse-graining of multiprotein assemblies
- (2012) Marissa G Saunders et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Recent developments in single-molecule DNA mechanics
- (2012) Zev Bryant et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Computer simulation studies of self-assembling macromolecules
- (2012) Wataru Shinoda et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble
- (2012) Thomas E. Ouldridge JOURNAL OF CHEMICAL PHYSICS
- The effect of topology on the structure and free energy landscape of DNA kissing complexes
- (2012) Flavio Romano et al. JOURNAL OF CHEMICAL PHYSICS
- Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA
- (2012) David A. Sivak et al. JOURNAL OF CHEMICAL PHYSICS
- Sequence-dependent thermodynamics of a coarse-grained DNA model
- (2012) Petr Šulc et al. JOURNAL OF CHEMICAL PHYSICS
- Ab initio determination of coarse-grained interactions in double-stranded DNA
- (2012) Chia Wei Hsu et al. JOURNAL OF CHEMICAL PHYSICS
- Coarse-Grained Model DNA: Structure, Sequences, Stems, Circles, Hairpins
- (2012) Lance E. Edens et al. JOURNAL OF PHYSICAL CHEMISTRY B
- DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism
- (2012) Christian Matek et al. JOURNAL OF PHYSICAL CHEMISTRY B
- DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response
- (2012) Anton Kuzyk et al. NATURE
- A DNA-based molecular motor that can navigate a network of tracks
- (2012) Shelley F. J. Wickham et al. Nature Nanotechnology
- The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
- (2012) Jiří Šponer et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Modeling the mechanical properties of DNA nanostructures
- (2012) Jean Michel Arbona et al. PHYSICAL REVIEW E
- Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements
- (2012) X. Zhang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- Bullied no more: when and how DNA shoves proteins around
- (2012) Jonathan M. Fogg et al. QUARTERLY REVIEWS OF BIOPHYSICS
- Extreme Bendability of DNA Less than 100 Base Pairs Long Revealed by Single-Molecule Cyclization
- (2012) R. Vafabakhsh et al. SCIENCE
- Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature
- (2012) J.-P. J. Sobczak et al. SCIENCE
- Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures
- (2012) M. Langecker 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
- Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link
- (2012) Cristiano De Michele et al. Soft Matter
- Frontiers in Molecular Dynamics Simulations of DNA
- (2011) Alberto Pérez et al. ACCOUNTS OF CHEMICAL RESEARCH
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- (2011) Juan J. de Pablo Annual Review of Physical Chemistry
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- (2011) Jordi Poater et al. CHEMICAL COMMUNICATIONS
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- (2011) Terry J. Schmitt et al. JOURNAL OF CHEMICAL PHYSICS
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- (2011) Margaret C. Linak et al. JOURNAL OF CHEMICAL PHYSICS
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- (2011) Thomas E. Ouldridge et al. JOURNAL OF CHEMICAL PHYSICS
- A coarse-grain three-site-per-nucleotide model for DNA with explicit ions
- (2011) Gordon S. Freeman et al. JOURNAL OF CHEMICAL PHYSICS
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- (2011) John H. Allen et al. JOURNAL OF PHYSICAL CHEMISTRY B
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- Direct observation of stepwise movement of a synthetic molecular transporter
- (2011) Shelley F. J. Wickham et al. Nature Nanotechnology
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- (2011) Do-Nyun Kim et al. NUCLEIC ACIDS RESEARCH
- Multiscale modeling of soft matter: scaling of dynamics
- (2011) Dominik Fritz et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Heat conductivity of the DNA double helix
- (2011) Alexander V. Savin et al. PHYSICAL REVIEW B
- DNA Origami with Complex Curvatures in Three-Dimensional Space
- (2011) D. Han et al. SCIENCE
- Application of a coarse-grained model for DNA to homo- and heterogeneous melting equilibria
- (2010) Nicholas B. Tito et al. CHEMICAL PHYSICS LETTERS
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- (2010) E. Sanz et al. JOURNAL OF CHEMICAL PHYSICS
- 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
- A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics
- (2010) Pablo D. Dans et al. Journal of Chemical Theory and Computation
- DNA Melting in Small-Molecule−DNA-Hybrid Dimer Structures: Experimental Characterization and Coarse-Grained Molecular Dynamics Simulations
- (2010) Tatiana R. Prytkova et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions
- (2010) Robert C. DeMille et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Development of coarse-graining DNA models for single-nucleotide resolution analysis
- (2010) K. Doi et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
- Direct Observation of Multiple Pathways of Single-Stranded DNA Stretching
- (2010) Wuen-shiu Chen et al. PHYSICAL REVIEW LETTERS
- DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
- (2010) Thomas E. Ouldridge 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
- Single-molecule derivation of salt dependent base-pair free energies in DNA
- (2010) J. M. Huguet et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- DNA curvature and flexibility in vitro and in vivo
- (2010) Justin P. Peters et al. QUARTERLY REVIEWS OF BIOPHYSICS
- Universal two-step crystallization of DNA-functionalized nanoparticles
- (2010) Wei Dai et al. Soft Matter
- Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides
- (2010) Moritz Julian Hoefert et al. Soft Matter
- On the Chirality of Self-Assembled DNA Octahedra
- (2009) Yu He et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA
- (2009) Alexey Savelyev et al. BIOPHYSICAL JOURNAL
- A Mesoscale Model of DNA and Its Renaturation
- (2009) E.J. Sambriski et al. BIOPHYSICAL JOURNAL
- The self-assembly of DNA Holliday junctions studied with a minimal model
- (2009) Thomas E. Ouldridge et al. JOURNAL OF CHEMICAL PHYSICS
- Brownian dynamics simulations of single-stranded DNA hairpins
- (2009) Martin Kenward et al. JOURNAL OF CHEMICAL PHYSICS
- DNA nanomechanics: How proteins deform the double helix
- (2009) Nils B. Becker et al. JOURNAL OF CHEMICAL PHYSICS
- Langevin thermostat for rigid body dynamics
- (2009) Ruslan L. Davidchack et al. JOURNAL OF CHEMICAL PHYSICS
- Reversible gels of patchy particles: Role of the valence
- (2009) John Russo 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
- Self-assembly of DNA into nanoscale three-dimensional shapes
- (2009) Shawn M. Douglas et al. NATURE
- Self-assembly of a nanoscale DNA box with a controllable lid
- (2009) Ebbe S. Andersen et al. NATURE
- A DNA nanomachine that maps spatial and temporal pH changes inside living cells
- (2009) Souvik Modi et al. Nature Nanotechnology
- Rapid prototyping of 3D DNA-origami shapes with caDNAno
- (2009) Shawn M. Douglas et al. NUCLEIC ACIDS RESEARCH
- A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
- (2009) Richard Lavery et al. NUCLEIC ACIDS RESEARCH
- On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations
- (2009) F. Lankaš et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis
- (2009) E. J. Sambriski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Folding DNA into Twisted and Curved Nanoscale Shapes
- (2009) H. Dietz et al. SCIENCE
- Mechanism for a Directional, Processive, and Reversible DNA Motor
- (2009) Jonathan Bath et al. Small
- Self-assembly of sparsely distributed molecules: An efficient cluster algorithm
- (2008) A. Bhattacharyay et al. CHEMICAL PHYSICS LETTERS
- Supercoiling and Local Denaturation of Plasmids with a Minimalist DNA Model
- (2008) Fabio Trovato et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra
- (2008) Yu He et al. NATURE
- Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion
- (2008) S. J. Green et al. PHYSICAL REVIEW LETTERS
- Conformational flexibility facilitates self-assembly of complex DNA nanostructures
- (2008) C. Zhang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The role of collective motion in examples of coarsening and self-assembly
- (2008) Stephen Whitelam et al. Soft Matter
- Optical Measurement of Mechanical Forces Inside Short DNA Loops
- (2007) Hari Shroff et al. BIOPHYSICAL JOURNAL
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