The effects of bead inertia on the Rouse model

1988 ◽  
Vol 89 (11) ◽  
pp. 6972-6981 ◽  
Author(s):  
J. D. Schieber ◽  
Hans Christian Öttinger
Keyword(s):  
Rouse Model

scholarly journals Rouse model with fluctuating internal friction

2021 ◽  
Vol 65 (5) ◽  
pp. 903-923
Author(s):  
R. Kailasham ◽  
Rajarshi Chakrabarti ◽  
J. Ravi Prakash
Keyword(s):  
Internal Friction ◽  
Rouse Model

scholarly journals Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C Paradox

2019 ◽  
Author(s):  
Guang Shi ◽  
D. Thirumalai
Keyword(s):  
Cell Population ◽  
Genome Organization ◽  
Large Cell ◽  
Spatial Distance ◽  
Chromosome Organization ◽  
Conformational Heterogeneity ◽  
Interphase Chromosome ◽  
Length Scales ◽  
Rouse Model ◽  
Contact Probability

AbstractHi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH data show that in some cases the distance between one pair of loci, with larger Hi-C readout, is paradoxically larger compared to another pair with a smaller value of the contact probability. Here, we show that the FISH-Hi-C paradox can be resolved using a theory based on a Generalized Rouse Model for Chromosomes (GRMC). The FISH-Hi-C paradox arises because the cell population is highly heterogeneous, which means that a given contact is present in only a fraction of cells. Insights from the GRMC is used to construct a theory, without any adjustable parameters, to extract the distribution of subpopulations from the FISH data, which quantitatively reproduces the Hi-C data. Our results show that heterogeneity is pervasive in genome organization at all length scales, reflecting large cell-to-cell variations.

scholarly journals Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes

2019 ◽  
Vol 47 (12) ◽  
pp. 6195-6207 ◽  
Author(s):  
Marius Socol ◽  
Renjie Wang ◽  
Daniel Jost ◽  
Pascal Carrivain ◽  
Cédric Vaillant ◽  
...  
Keyword(s):  
Structural Properties ◽  
Single Particle Tracking ◽  
Chemical Parameters ◽  
Chromosome Conformation ◽  
Formation Reaction ◽  
Rouse Model ◽  
Physico Chemical ◽  
Capture Techniques

Abstract DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of –0.3 to –0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in ‘theta’ conditions, in which they are poised for compartmentalization and phase separation.

The Rouse model

2009 ◽  
pp. 244-247
Author(s):  
Richard Boyd ◽  
Grant Smith
Keyword(s):  
Rouse Model

The Simulation of Aggregated Colloids Under Flow

1992 ◽  
Vol 289 ◽  
Author(s):  
John R. Melrose
Keyword(s):  
Shear Rate ◽  
Large Scale ◽  
Shear Thinning ◽  
High Shear ◽  
Shear Rates ◽  
Rouse Model ◽  
High Shear Rates ◽  
Structural Breakdown ◽  
Large Scale Simulations ◽  
Low Shear

AbstractAn overview is given of theories of aggregates under flow. These generally assume some sort of structural breakdown as the shear rate is increased. Models vary with both the rigidity of the bonding and the level of treatment of hydrodynamics. Results are presented for simulations of a Rouse model of non-rigid, (i.e. central force) weakly bonded aggregates. In large scale simulations different structures are observed at low and high shear rates. The change from one structure to another is associated with a change in the rate of shear thinning. The model captures low shear rate features of real systems absent in previous models: this feature is ascribed to agglomerate deformations. Quantitatively, the model is two orders of magnitude out from experiment but some scaling is possible.

scholarly journals Viscoelastic Properties of Unentangled Multicyclic Polystyrenes

Polymers ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 973 ◽  
Author(s):  
Zhi-Chao Yan ◽  
Md. Hossain ◽  
Michael Monteiro ◽  
Dimitris Vlassopoulos
Keyword(s):  
Molecular Weight ◽  
Shear Viscosity ◽  
Viscoelastic Properties ◽  
Dilution Effect ◽  
The Other ◽  
Low Molecular Weight ◽  
Zero Shear Viscosity ◽  
Rouse Model ◽  
Loop Size ◽  
Linear Chains

We report on the viscoelastic properties of linear, monocyclic, and multicyclic polystyrenes with the same low molecular weight. All polymers investigated were found to exhibit unentangled dynamics. For monocyclic polymers without inner loops, a cyclic-Rouse model complemented by the contribution of unlinked chains (whose fraction was determined experimentally) captured the observed rheological response. On the other hand, multicyclic polymers with inner loops were shown to follow a hierarchical cyclic-Rouse relaxation with the outer loops relaxing first, followed by the inner loop relaxation. The influence of unlinked linear chains was less significant in multicyclic polymers with inner loops. The isofrictional zero-shear viscosity decreased with increasing number of constrained segments on the coupling sites, which was attributed to the decreasing loop size and the dilution effect due to the hierarchical relaxation.

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