Simulating the entropic collapse of coarse-grained chromosomes (Q42007630)

15 October 2017

Simulating the entropic collapse of coarse-grained chromosomes (English)

1 reference

15 October 2017

Tyler N Shendruk

1

1 reference

15 October 2017

Martin Bertrand

2

1 reference

15 October 2017

Hendrick W de Haan

3

1 reference

15 October 2017

James L Harden

4

1 reference

15 October 2017

Gary W Slater

5

1 reference

15 October 2017

language of work or name

English

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publication date

1 February 2015

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15 October 2017

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15 October 2017

108

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15 October 2017

4

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15 October 2017

810-820

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Physical manipulation of the Escherichia coli chromosome reveals its soft nature

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Entropy-based mechanism of ribosome-nucleoid segregation in E. coli cells

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Fundamental measure theory for hard-sphere mixtures: a review

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

The fractal globule as a model of chromatin architecture in the cell

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Entropy as the driver of chromosome segregation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Modeling the separation of macromolecules: a review of current computer simulation methods

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Experimental evidence for the influence of molecular crowding on nuclear architecture

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

DNA-protein interactions and bacterial chromosome architecture

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Chromosome organization and segregation in bacteria

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Structural and physical aspects of bacterial chromosome segregation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

At the heart of the chromosome: SMC proteins in action

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

A-tract clusters may facilitate DNA packaging in bacterial nucleoid

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

SMC proteins and chromosome mechanics: from bacteria to humans

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Effect of repulsive and attractive interactions on depletion forces in colloidal suspensions: a density functional theory treatment

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Topological domain structure of the Escherichia coli chromosome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Information content and complexity in the high-order organization of DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

SMC proteins in bacteria: condensation motors for chromosome segregation?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Macromolecular crowding and the mandatory condensation of DNA in bacteria

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Phase separation in cytoplasm, due to macromolecular crowding, is the basis for microcompartmentation.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

The effect of volume occupancy upon the thermodynamic activity of proteins: some biochemical consequences

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Phase separation between nucleoid and cytoplasm in Escherichia coli as defined by immersive refractometry

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

A Transition to a Compact Form of DNA in Polymer Solutions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Induction of entropic segregation: the first step is the hardest.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Depletion potentials in highly size-asymmetric binary hard-sphere mixtures: comparison of simulation results with theory

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Hard-sphere fluids in annular wedges: density distributions and depletion potentials.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Chromosome segregation in Escherichia coli division: a free energy-driven string model.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Hard-sphere fluid adsorbed in an annular wedge: the depletion force of hard-body colloidal physics.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Depletion potential between large spheres immersed in a multicomponent mixture of small spheres.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Phase diagram of the adhesive hard sphere fluid.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Depletion force between two large spheres suspended in a bath of small spheres: onset of the Derjaguin limit

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Collapse of a semiflexible polymer in poor solvent.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Metastable intermediates in the condensation of semiflexible polymers

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Polymer-mediated compaction and internal dynamics of isolated Escherichia coli nucleoids.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Osmotic compaction of supercoiled DNA into a bacterial nucleoid

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Theory of molecular crowding in Brownian hard-sphere liquids

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes

2 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336370

Accurate calculation of three-body depletion interactions

2 December 2018

1 reference

12 December 2020

Self-association of polynucleosome chains by macromolecular crowding

1 reference

12 December 2020

Mesoscopic description of solvent effects on polymer dynamics

1 reference

12 December 2020

Density functional for additive mixtures

1 reference

12 December 2020

Large discrete transition in a single DNA molecule appears continuous in the ensemble

1 reference

12 December 2020

Elongation/compaction of giant DNA caused by depletion interaction with a flexible polymer

1 reference

12 December 2020

Quantifying the effects of neglecting many-body interactions in coarse-grained models of complex fluids

1 reference

12 December 2020

Time scale of entropic segregation of flexible polymers in confinement: implications for chromosome segregation in filamentous bacteria

1 reference

12 December 2020

Depletion potential in hard-sphere mixtures: theory and applications

1 reference

12 December 2020

Effect of confinement on the collapsing mechanism of a flexible polymer chain

1 reference

12 December 2020

Switchable self-protected attractions in DNA-functionalized colloids

1 reference

12 December 2020

Simulation study of the coil-globule transition of a polymer in solvent

1 reference

12 December 2020

Coarse-grained molecular dynamics simulations of depletion-induced interactions for soft matter systems

1 reference

12 December 2020

Depletion forces between nonspherical objects

1 reference

12 December 2020

Free-energy model for the inhomogeneous hard-sphere fluid mixture and density-functional theory of freezing

1 reference

12 December 2020

10.1016/J.BPJ.2014.11.3487

Identifiers

DOI

1 reference

15 October 2017

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0 references

1 reference

15 October 2017

PubMed publication ID

25692586

1 reference