Ref HAL: hal-01063014_v1
PMID 25204752
Ref Arxiv: 1408.2945
DOI: 10.1088/1478-3975/11/5/056006
WoS: 000343670600021
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22 Citations
Résumé:

In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or the flow chamber) and hence compete for recruiting the available motors, potentially depleting the reservoir and affecting cytoskeletal transport. In this work we provide a theoretical framework to study, analytically and numerically, how motor density profiles and crowding along cytoskeletal filaments depend on the competition of motors for their binding sites. We propose two models in which finite processive motor proteins actively advance along cytoskeletal filaments and are continuously exchanged with the motor pool. We first look at homogeneous reservoirs and then examine the effects of free motor diffusion in the surrounding medium. We consider as a reference situation recent in vitro experimental setups of kinesin-8 motors binding and moving along microtubule filaments in a flow chamber. We investigate how the crowding of linear motor proteins moving on a filament can be regulated by the balance between supply (concentration of motor proteins in the flow chamber) and demand (total number of polymerised tubulin heterodimers). We present analytical results for the density profiles of bound motors, the reservoir depletion, and propose novel phase diagrams that present the formation of jams of motor proteins on the filament as a function of two tuneable experimental parameters: the motor protein concentration and the concentration of tubulins polymerized into cytoskeletal filaments. Extensive numerical simulations corroborate the analytical results for parameters in the experimental range and also address the effects of diffusion of motor proteins in the reservoir.

Commentaires: 31 pages, 10 figures

Ref HAL: hal-01052685_v1
Ref Arxiv: 1403.7959
DOI: 10.1021/ma500635h
WoS: 000339462900033
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8 Citations
Résumé:

We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from a state of minimal entropy. We investigate the dynamics of several quantities such as the total and local winding angles and metric quantities. The results of simulations performed in two and three dimensions, with and without self-avoidance, are explained by a theory based on scaling arguments and on a balance between frictional and entropic forces. The early stage of the dynamics is particularly rich, being characterized by three coexisting phases.

Ref HAL: hal-00872108_v1
Ref Arxiv: 1301.2777
DOI: 10.1103/PhysRevLett.110.068301
WoS: 000314686700013
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14 Citations
Résumé:

The relaxation dynamics of a polymer wound around a fixed obstacle constitutes a fundamental instance of polymer with twist and torque and it is of relevance also for DNA denaturation dynamics. We investigate it by simulations and Langevin equation analysis. The latter predicts a relaxation time scaling as a power of the polymer length times a logarithmic correction related to the equilibrium fluctuations of the winding angle. The numerical data support this result and show that at short times the winding angle decreases as a power-law. This is also in agreement with the Langevin equation provided a winding-dependent friction is used, suggesting that such reduced description of the system captures the basic features of the problem.

Commentaires: 4 pages, 5 figures, published in Phys. Rev. Lett. 110, 068301 (2013)

PMID 22587051
Ref Arxiv: 1111.4323
DOI: 10.1103/PhysRevE.85.031120
WoS: 000301773200004
Ref. & Cit.: NASA ADS
22 Citations
Résumé:

We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature $T=T_c$ using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as $\tau \sim L^{2.26(2)}$, exceeding the Rouse time $\sim L^{2.18}$. We investigate the probability distribution function, the velocity autocorrelation function, the survival probability and boundary behaviour of the underlying stochastic process. These quantities scale as expected from a fractional Brownian motion with a Hurst exponent $H=0.44(1)$. We discuss similarities and differences with unbiased polymer translocation.

Commentaires: 7 pages, 8 figures Journal: Phys. Rev. E 85, 031120 (2012)

DOI: 10.1016/j.nuclphysb.2012.07.021
WoS: 000308450500006
41 Citations
Résumé:

Above the upper critical dimension, the breakdown of hyperscaling is associated with dangerous irrelevant variables in the renormalization group formalism at least for systems with periodic boundary conditions. While these have been extensively studied, there have been only a few analyses of finite-size scaling with free boundary conditions. The conventional expectation there is that, in contrast to periodic geometries, finite-size scaling is Gaussian, governed by a correlation length commensurate with the lattice extent. Here, detailed numerical studies of the five-dimensional Ising model indicate that this expectation is unsupported, both at the infinite-volume critical point and at the pseudocritical point where the finite-size susceptibility peaks. Instead the evidence indicates that finite-size scaling at the pseudocritical point is similar to that in the periodic case. An analytic explanation is offered which allows hyperscaling to be extended beyond the upper critical dimension.

Ref HAL: hal-00872287_v1
PMID 22661582
Ref Arxiv: 1211.1303
DOI: 10.1093/nar/gks475
WoS: 000309927100002
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15 Citations
Résumé:

In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.

Commentaires: 13 pages, 11 figures, 1 table, Supplementary Data available in Appendix Journal: Nucleic Acids Research, 2012, Vol. 40, No. 18 e138

Ref HAL: hal-00653816_v1
Ref Arxiv: 1112.4666
DOI: 10.1088/1742-5468/2012/02/P02010
WoS: 000300904900011
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1 Citation
Résumé:

We consider by means of Monte Carlo simulations the relaxation in the paramagnetic phase of the anti-ferromagnetic Ising model on a triangular lattice and of a fully-frustrated Ising model on a square lattice. In contradistinction to previous studies of the second model, we show that spin-spin correlation functions do not decay with a stretched-exponential law at low temperature but that both models display an exponential decay with logarithmic corrections that are interpreted as the signature of topological defects.

Commentaires: 12 pages, 9 figures