(Q51888450)

English

Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models.

scientific article published in April 2008

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scholarly article

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models. (English)

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

quantum Monte Carlo

1 reference

based on heuristic

inferred from title

molecular knots

1 reference

based on heuristic

inferred from title

author name string

Zhirong Liu

1

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

Hue Sun Chan

2

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

language of work or name

0 references

publication date

1 April 2008

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

Journal of Chemical Physics

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

128

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Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

14

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

145104

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

DNA bending and its relation to nucleosome positioning.

1 reference

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21 January 2018

Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation

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Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

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21 January 2018

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

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21 January 2018

Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids

1 reference

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21 January 2018

Average size of random polygons with fixed knot topology

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots

1 reference

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21 January 2018

Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers

1 reference

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21 January 2018

Biochemical topology: applications to DNA recombination and replication

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21 January 2018

Topoisomerase IV, alone, unknots DNA in E. coli

1 reference

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Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation

1 reference

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Probability of DNA knotting and the effective diameter of the DNA double helix

1 reference

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21 January 2018

Effect of supercoiling on the juxtaposition and relative orientation of DNA sites

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Simplification of DNA topology below equilibrium values by type II topoisomerases

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting

1 reference

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Influence of ADP on cross-bridge-dependent activation of myofibrillar thin filaments

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21 January 2018

Mechanism of topology simplification by type II DNA topoisomerases

1 reference

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21 January 2018

Monte Carlo simulations of supercoiled DNAs confined to a plane

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition

1 reference

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21 January 2018

A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Dynamics of site juxtaposition in supercoiled DNA.

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

DNA knots reveal a chiral organization of DNA in phage capsids

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Simple model for the DNA denaturation transition.

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

DNA disentangling by type-2 topoisomerases.

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.

1 reference

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21 January 2018

Modeling of long-range electrostatic interactions in DNA.

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Flexibility of DNA.

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

The writhing number of a space curve

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Decomposition of the linking number of a closed ribbon: A problem from molecular biology

1 reference

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21 January 2018

Computation of writhe in modeling of supercoiled DNA.

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Brownian dynamics simulation of knot diffusion along a stretched DNA molecule

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

A solution for the best rotation to relate two sets of vectors

1 reference

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21 January 2018

Using quaternions to calculate RMSD

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21 January 2018

End-to-end distance vector distribution with fixed end orientations for the wormlike chain model

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Exploring conformational space with a simple lattice model for protein structure

1 reference

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21 January 2018

Cooperativity principles in protein folding.

1 reference

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21 January 2018

RNA folding energy landscapes.

1 reference

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21 January 2018

Predicting RNA pseudoknot folding thermodynamics

1 reference

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21 January 2018

Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Knotting of a DNA chain during ring closure

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

A new polynomial invariant of knots and links

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Tightness of random knotting

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Behavior of complex knots in single DNA molecules

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

1 reference

https://api.crossref.org/works/10.1063%2F1.2899022

21 January 2018

Identifiers

10.1063/1.2899022

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

1 reference

Europe PubMed Central

17 April 2018

http://europepmc.org/abstract/MED/18412482

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