相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami
Hyungmin Jun et al.
NUCLEIC ACIDS RESEARCH (2021)
Automated sequence design of 2D wireframe DNA origami with honeycomb edges
Hyungmin Jun et al.
NATURE COMMUNICATIONS (2019)
Autonomously designed free-form 2D DNA origami
Hyungmin Jun et al.
SCIENCE ADVANCES (2019)
Programmed coherent coupling in a synthetic DNA-based excitonic circuit
Etienne Boulais et al.
NATURE MATERIALS (2018)
New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions
Jejoong Yoo et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2018)
Optical determination of the electronic coupling and intercalation geometry of thiazole orange homodimer in DNA
Paul D. Cunningham et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
Photophysics of J-Aggregate-Mediated Energy Transfer on DNA
James L. Banal et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2017)
Structure and conformational dynamics of scaffolded DNA origami nanoparticles
Keyao Pan et al.
NUCLEIC ACIDS RESEARCH (2017)
Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies
Reza Sharifi Sedeh et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis
Soma Dhakal et al.
NANOSCALE (2016)
De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation
Christopher Maffeo et al.
NUCLEIC ACIDS RESEARCH (2016)
DNA NANOTECHNOLOGY Designer nanoscale DNA assemblies programmed from the top down
Remi Veneziano et al.
SCIENCE (2016)
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
Benedict E. K. Snodin et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Complex wireframe DNA origami nanostructures with multi-arm junction vertices
Fei Zhang et al.
NATURE NANOTECHNOLOGY (2015)
DNA brick crystals with prescribed depths
Yonggang Ke et al.
NATURE CHEMISTRY (2014)
Structure-based model for light-harvesting properties of nucleic acid nanostructures
Keyao Pan et al.
NUCLEIC ACIDS RESEARCH (2014)
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
Marco Pasi et al.
NUCLEIC ACIDS RESEARCH (2014)
A single-stranded architecture for cotranscriptional folding of RNA nanostructures
Cody Geary et al.
SCIENCE (2014)
Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
Keyao Pan et al.
NATURE COMMUNICATIONS (2014)
Temperature Dependence of the DNA Double Helix at the Nanoscale: Structure, Elasticity, and Fluctuations
Sam Meyer et al.
BIOPHYSICAL JOURNAL (2013)
Using collective variables to drive molecular dynamics simulations
Giacomo Fiorin et al.
MOLECULAR PHYSICS (2013)
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
Jejoong Yoo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
A DNA tweezer-actuated enzyme nanoreactor
Minghui Liu et al.
NATURE COMMUNICATIONS (2013)
Design and Development of Nanosized DNA Assemblies in Polypod-like Structures as Efficient Vehicles for Immunostimulatory CpG Motifs to Immune Cells
Kohta Mohri et al.
ACS NANO (2012)
Molecular Dynamics of a DNA Holliday Junction: The Inverted Repeat Sequence d(CCGGTACCGG)4
Elizabeth G. Wheatley et al.
BIOPHYSICAL JOURNAL (2012)
Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations
Olof Allner et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations
Bill R. Miller et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Complex shapes self-assembled from single-stranded DNA tiles
Bryan Wei et al.
NATURE (2012)
Hidden complexity in the isomerization dynamics of Holliday junctions
Changbong Hyeon et al.
NATURE CHEMISTRY (2012)
Exploring polymorphisms in B-DNA helical conformations
Pablo D. Dans et al.
NUCLEIC ACIDS RESEARCH (2012)
The Role of Defects on the Assembly and Stability of DNA Nanostructures
Daniel G. Greene et al.
SMALL (2012)
ProDy: Protein Dynamics Inferred from Theory and Experiments
Ahmet Bakan et al.
BIOINFORMATICS (2011)
Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations
Naveen Michaud-Agrawal et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
DNA-Directed Artificial Light-Harvesting Antenna
Palash K. Dutta et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
Camille J. Delebecque et al.
SCIENCE (2011)
DNA Origami with Complex Curvatures in Three-Dimensional Space
Dongran Han et al.
SCIENCE (2011)
Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers
Qin Cai et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
Jerome Henin et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Molecular robots guided by prescriptive landscapes
Kyle Lund et al.
NATURE (2010)
Differential stability of DNA crossovers in solution mediated by divalent cations
Peter Varnai et al.
NUCLEIC ACIDS RESEARCH (2010)
A Rare Nucleotide Base Tautomer in the Structure of an Asymmetric DNA Junction
Patricia Khuu et al.
BIOCHEMISTRY (2009)
CHAMBER: Comprehensive Support for CHARMM Force Fields Within the AMBER Software
Michael F. Crowley et al.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (2009)
Self-assembly of DNA into nanoscale three-dimensional shapes
Shawn M. Douglas et al.
NATURE (2009)
A DNA nanomachine that maps spatial and temporal pH changes inside living cells
Souvik Modi et al.
NATURE NANOTECHNOLOGY (2009)
Folding DNA into Twisted and Curved Nanoscale Shapes
Hendrik Dietz et al.
SCIENCE (2009)
Adaptive biasing force method for scalar and vector free energy calculations
Eric Darve et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
Xiang-Jun Lu et al.
NATURE PROTOCOLS (2008)
Nanoparticle therapeutics: an emerging treatment modality for cancer
Mark E. Davis et al.
NATURE REVIEWS DRUG DISCOVERY (2008)
Towards a molecular dynamics consensus view of B-DNA flexibility
Alberto Perez et al.
NUCLEIC ACIDS RESEARCH (2008)
Engineering entropy-driven reactions and networks catalyzed by DNA
David Yu Zhang et al.
SCIENCE (2007)
DNA nanomachines
Jonathan Bath et al.
NATURE NANOTECHNOLOGY (2007)
Folding DNA to create nanoscale shapes and patterns
PWK Rothemund
NATURE (2006)
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
P Yakovchuk et al.
NUCLEIC ACIDS RESEARCH (2006)
Scalable molecular dynamics with NAMD
JC Phillips et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
SB Dixit et al.
BIOPHYSICAL JOURNAL (2005)
Exploring the essential dynamics of B-DNA
A Pérez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
Stacked-unstacked equilibrium at the nick site of DNA
E Protozanova et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides.: I.: Research design and results on d(CpG) steps
DL Beveridge et al.
BIOPHYSICAL JOURNAL (2004)
Conformational model of the Holliday junction transition deduced from molecular dynamics simulations
J Yu et al.
NUCLEIC ACIDS RESEARCH (2004)
Definitions and analysis of DNA Holliday junction geometry
J Watson et al.
NUCLEIC ACIDS RESEARCH (2004)
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
XJ Lu et al.
NUCLEIC ACIDS RESEARCH (2003)
DNA basepair step deformability inferred from molecular dynamics simulations
F Lankas et al.
BIOPHYSICAL JOURNAL (2003)
Free-energy perturbation calculations of DNA destabilization by base substitutions:: The effect of neutral guanine thymine, adenine cytosine and adenine difluorotoluene mismatches
J Florián et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2000)
Structures of helical junctions in nucleic acids
DMJ Lilley
QUARTERLY REVIEWS OF BIOPHYSICS (2000)