(Q37279310)

19 August 2017

A mesoscale model of DNA and its renaturation (English)

1 reference

19 August 2017

3

J J de Pablo

1 reference

19 August 2017

E J Sambriski

1

1 reference

19 August 2017

D C Schwartz

series ordinal

2

1 reference

19 August 2017

language of work or name

English

0 references

publication date

1 March 2009

1 reference

19 August 2017

1 reference

19 August 2017

96

1 reference

19 August 2017

5

1 reference

19 August 2017

1675-1690

1 reference

Recent advances in the study of nucleic acid flexibility by molecular dynamics

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Origins of barriers and barrierless folding in BBL.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Mesoscopic modeling for nucleic acid chain 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=2717267

Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in 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=2717267

Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Electrostatic mechanisms of DNA deformation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

From atomic to mesoscopic descriptions of the internal dynamics 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=2717267

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=2717267

Predicting sequence-dependent melting stability of short duplex DNA oligomers

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

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=2717267

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=2717267

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=2717267

The occurrence of C-H...O hydrogen bonds in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Predicting DNA duplex stability from the base sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Direct measurement of temperature-dependent solvation forces between DNA double helices

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

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=2717267

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Generalized theory of semiflexible polymers

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Heat capacity changes associated with DNA duplex formation: salt- and sequence-dependent effects

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Precipitation of DNA by polyamines: a polyelectrolyte behavior

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Kinetics of renaturation of DNA

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Molecular mechanics model of supercoiled DNA.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Supercoiled DNA energetics and dynamics by computer simulation

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Dynamics of B-DNA on the microsecond time scale.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

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=2717267

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=2717267

Measuring inter-DNA potentials in solution.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Optimal allocation of replicas in parallel tempering 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=2717267

Shear-induced migration in flowing polymer solutions: simulation of long-chain DNA in microchannels [corrected].

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Attraction between DNA molecules mediated by multivalent ions.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Atomic simulations of protein folding, using the replica exchange algorithm.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

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=2717267

Unified Description of Electrophoresis and Diffusion for DNA and Other Polyions

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Counterion-mediated, non-pairwise-additive attractions in bundles of like-charged rods

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

A mezoscopic model of nucleic acids. Part 2. An effective potential energy function 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=2717267

The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717267

Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices

20 October 2018

1 reference

12 December 2020

Effective interaction between helical biomolecules

1 reference

12 December 2020

Why is the DNA Denaturation Transition First Order?

1 reference

12 December 2020

Attractive interactions between rodlike polyelectrolytes: polarization, crystallization, and packing

1 reference

12 December 2020

Roles of stiffness and excluded volume in DNA denaturation

1 reference

12 December 2020

Self-diffusion in solutions of a 20 base pair oligonucleotide: effects of concentration and ionic strength

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

Atomistic simulation of the DNA helix-coil transition

1 reference

12 December 2020

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

1 reference

12 December 2020

Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations

1 reference

12 December 2020

Exploring the Essential Dynamics of B-DNA

1 reference

12 December 2020

10.1016/J.BPJ.2008.09.061

Identifiers

DOI

1 reference

release_c6rtcofucraxxfextn2n4tl5ue

19 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/c6rtcofucraxxfextn2n4tl5ue

24 November 2022

mapped directly with Wikidata item

1 reference

19 August 2017

PubMed publication ID

19254530

1 reference