An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
出版年份 2013 全文链接
标题
An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
作者
关键词
-
出版物
JOURNAL OF CHEMICAL PHYSICS
Volume 139, Issue 14, Pages 144903
出版商
AIP Publishing
发表日期
2013-10-08
DOI
10.1063/1.4822042
参考文献
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。- Exploring the mechanisms of DNA hybridization on a surface
- (2013) Terry J. Schmitt et al. JOURNAL OF CHEMICAL PHYSICS
- Mean-Field Interactions between Nucleic-Acid-Base Dipoles can Drive the Formation of a Double Helix
- (2013) Yi He et al. PHYSICAL REVIEW LETTERS
- Two-phase stretching of molecular chains
- (2013) A. V. Savin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Zeeman shift of two-dimensional optical signals of Mg-porphyrin dimers with circularly polarized beams
- (2012) Justo J. Rodriguez et al. 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
- 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
- Density of States–Based Molecular Simulations
- (2012) Sadanand Singh et al. Annual Review of Chemical and Biomolecular Engineering
- Frontiers in Molecular Dynamics Simulations of DNA
- (2011) Alberto Pérez et al. ACCOUNTS OF CHEMICAL RESEARCH
- Thermodynamics of DNA hybridization on surfaces
- (2011) Terry J. Schmitt et al. JOURNAL OF CHEMICAL PHYSICS
- Moving beyond Watson–Crick models of coarse grained DNA dynamics
- (2011) Margaret C. Linak et al. JOURNAL OF CHEMICAL PHYSICS
- Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
- (2011) Ana-Maria Florescu et al. JOURNAL OF CHEMICAL PHYSICS
- Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
- (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
- CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work
- (2011) Hiroo Kenzaki et al. Journal of Chemical Theory and Computation
- Computational Model for Predicting Experimental RNA and DNA Nearest-Neighbor Free Energy Rankings
- (2011) Charles A. Johnson et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Flux Tempered Metadynamics
- (2011) Sadanand Singh et al. JOURNAL OF STATISTICAL PHYSICS
- A hybrid all-atom/coarse grain model for multiscale simulations of DNA
- (2011) Matías Rodrigo Machado et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Heat conductivity of the DNA double helix
- (2011) Alexander V. Savin et al. PHYSICAL REVIEW B
- Molecular Origins of DNA Flexibility: Sequence Effects on Conformational and Mechanical Properties
- (2011) Vanessa Ortiz et al. PHYSICAL REVIEW LETTERS
- 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
- Extracting bulk properties of self-assembling systems from small simulations
- (2010) Thomas E Ouldridge et al. JOURNAL OF PHYSICS-CONDENSED MATTER
- Mechanical and structural properties of YOYO-1 complexed DNA
- (2010) K. Gunther et al. NUCLEIC ACIDS RESEARCH
- 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
- Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides
- (2010) Moritz Julian Hoefert et al. Soft Matter
- A Mesoscale Model of DNA and Its Renaturation
- (2009) E.J. Sambriski et al. BIOPHYSICAL JOURNAL
- Coarse-grained model of nucleic acid bases
- (2009) Maciej Maciejczyk et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Stretching and twisting of the DNA duplexes in coarse-grained dynamical models
- (2009) Szymon Niewieczerzał et al. JOURNAL OF PHYSICS-CONDENSED MATTER
- Forward flux sampling for rare event simulations
- (2009) Rosalind J Allen et al. JOURNAL OF PHYSICS-CONDENSED MATTER
- 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
- PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
- (2009) Srinivasa M. Gopal et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Insights on protein-DNA recognition by coarse grain modelling
- (2008) P. Poulain et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways
- (2008) E J Sambriski et al. JOURNAL OF PHYSICS-CONDENSED MATTER
- Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
- (2008) Alessandro Laio et al. REPORTS ON PROGRESS IN PHYSICS
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started