(Q37255509)

19 August 2017

An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization (English)

1 reference

19 August 2017

0 references

4

Juan J de Pablo

1 reference

19 August 2017

Daniel M Hinckley

1

1 reference

19 August 2017

Gordon S Freeman

series ordinal

2

1 reference

19 August 2017

Jonathan K Whitmer

series ordinal

3

1 reference

19 August 2017

language of work or name

English

0 references

publication date

1 October 2013

1 reference

Journal of Chemical Physics

19 August 2017

1 reference

19 August 2017

139

1 reference

19 August 2017

14

1 reference

19 August 2017

144903

1 reference

Heat conductivity of DNA double helix

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Two-phase stretching of molecular chains

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Density of states-based molecular simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

A coarse-grain three-site-per-nucleotide model for DNA with explicit ions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Frontiers in molecular dynamics simulations of DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Forward flux sampling for rare event simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

A coarse-grained model of DNA with explicit solvation by water and ions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Chemically accurate coarse graining of double-stranded DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Mechanical and structural properties of YOYO-1 complexed DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

A mesoscale model of DNA and its renaturation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Stacked-unstacked equilibrium at the nick site of DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Escaping free-energy minima

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Electrostatic interaction between helical macromolecules in dense aggregates: an impetus for DNA poly- and meso-morphism

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Ionic effects on the elasticity of single DNA molecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

VMD: visual molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Defining the structure of irregular nucleic acids: conventions and principles

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Hybridization and renaturation kinetics of nucleic acids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Moving beyond Watson-Crick models of coarse grained DNA dynamics.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Insights on protein-DNA recognition by coarse grain modelling

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Measuring the geometry of DNA grooves.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Exploring the mechanisms of DNA hybridization on a surface

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Sequence-dependent thermodynamics of a coarse-grained DNA model.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Molecular origins of DNA flexibility: sequence effects on conformational and mechanical properties.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

DNA nanotweezers studied with a coarse-grained model of DNA.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

DNA melting in small-molecule-DNA-hybrid dimer structures: experimental characterization and coarse-grained molecular dynamics simulations

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Coarse-grained model of nucleic acid bases.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Accurate sampling using Langevin dynamics.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

A coarse grain model for DNA.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Deriving effective mesoscale potentials from atomistic simulations.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Diffusion coefficient of DNA molecules during free solution electrophoresis

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808442

Zeeman shift of two-dimensional optical signals of Mg-porphyrin dimers with circularly polarized beams

3 September 2018

1 reference

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties

21 January 2018

1 reference

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

21 January 2018

1 reference

Relaxation kinetics of dimer formation by self complementary oligonucleotides

21 January 2018

1 reference

12 December 2020

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

1 reference

12 December 2020

Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide

1 reference

12 December 2020

Stretching and twisting of the DNA duplexes in coarse-grained dynamical models

1 reference

12 December 2020

Coarse-grained model DNA: structure, sequences, stems, circles, hairpins

1 reference

12 December 2020

Thermodynamics of DNA hybridization on surfaces

1 reference

12 December 2020

A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties

1 reference

12 December 2020

DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism

1 reference

12 December 2020

A hybrid all-atom/coarse grain model for multiscale simulations of DNA

1 reference

12 December 2020

Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix

1 reference

12 December 2020

Extracting bulk properties of self-assembling systems from small simulations

1 reference

12 December 2020

A configurational interpretation of the axial phosphate spacing in polynucleotide helices and random coils

1 reference

12 December 2020

A theory of linear and helical aggregations of macromolecules

1 reference

12 December 2020

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

1 reference

12 December 2020

Ab initio determination of coarse-grained interactions in double-stranded DNA

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.4822042

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

24116642

1 reference