(Q34177239)

31 July 2017

title

Monte Carlo simulations of supercoiled DNAs confined to a plane (English)

1 reference

31 July 2017

Bryant S Fujimoto

1

1 reference

31 July 2017

J Michael Schurr

series ordinal

2

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 February 2002

1 reference

31 July 2017

1 reference

31 July 2017

volume

82

1 reference

31 July 2017

issue

2

1 reference

31 July 2017

page(s)

944-962

1 reference

Dynamic bending rigidity of a 200-bp DNA in 4 mM ionic strength: a transient polarization grating study

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Electrostatic-undulatory theory of plectonemically supercoiled DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Modeling chain folding in protein-constrained circular DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

On the origin of the temperature dependence of the supercoiling free energy.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Comparison of hard-cylinder and screened Coulomb interactions in the modeling of supercoiled DNAs.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Visualization of supercoiled DNA with atomic force microscopy in situ

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Thermodynamics of the first transition in writhe of a small circular DNA by Monte Carlo simulation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Effect of bending strain on the torsion elastic constant of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Atomic force microscopy of long DNA: imaging in air and under water

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Conformational and thermodynamic properties of supercoiled DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Effects of localized bending on DNA supercoiling.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Structures and dynamics of a supercoiled DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Modeling DNA supercoils and knots with B-spline functions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Effects of chloroquine on the torsional dynamics and rigidities of linear and supercoiled DNAs at low ionic strength

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Evidence for allosteric transitions in secondary structure induced by superhelical stress.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Structure of plectonemically supercoiled DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Direct visualization of supercoiled DNA molecules in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Effect of ethidium on the torsion constants of linear and supercoiled DNAs.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Circular DNA molecules imaged in air by scanning force microscopy

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Conformations of closed DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Surface-induced DNA superhelicity.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Charge fluctuations on membrane surfaces in water

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Molecular modeling and energy refinement of supercoiled DNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301902

Effect of temperature on DNA secondary structure in the absence and presence of 0.5 M tetramethylammonium chloride

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

Electrostatic effects in short superhelical DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

Counterion-Mediated Attraction between Two Like-Charged Rods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

A portable high-quality random number generator for lattice field theory simulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

Atomic force microscopy imaging of double stranded DNA and RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

The question of long-range allosteric transitions in DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

Interactions of highly charged colloidal cylinders with applications to double-stranded

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

Conformational and thermodynamic properties of supercoiled DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

Computer simulation of protein-induced structural changes in closed circular DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975455-6

Molecular modeling of closed circular DNA thermodynamic ensembles

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/11806935

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(02)75455-6

1 reference

31 July 2017

1 reference

31 July 2017

1 reference