78 research outputs found
Translocation time of periodically forced polymer chains
We show the presence of both a minimum and clear oscillations in the
frequency dependence of the translocation time of a polymer described as a
unidimensional Rouse chain driven by a spatially localized oscillating linear
potential. The observed oscillations of the mean translocation time arise from
the synchronization between the very mean translocation time and the period of
the external force. We have checked the robustness of the frequency value for
the minimum translocation time by changing the damping parameter, finding a
very simple relationship between this frequency and the correspondent
translocation time. The translocation time as a function of the polymer length
has been also evaluated, finding a precise scaling. Furthermore, the role
played by the thermal fluctuations described as a Gaussian uncorrelated noise
has been also investigated, and the analogies with the resonant activation
phenomenon are commented.Comment: 7 pages, 11 figures. Physical Review E (in press
An integrative approach for modeling and simulation of Heterocyst pattern formation in Cyanobacteria strands
A comprehensive approach to cellular differentiation in cyanobacteria is
developed. To this aim, the process of heterocyst cell formation is studied
under a systems biology point of view. By relying on statistical physics
techniques, we translate the essential ingredients and mechanisms of the
genetic circuit into a set of differential equations that describes the
continuous time evolution of combined nitrogen, PatS, HetR and NtcA
concentrations. The detailed analysis of these equations gives insight into the
single cell dynamics. On the other hand, the inclusion of diffusion and noisy
conditions allows simulating the formation of heterocysts patterns in
cyanobacteria strains. The time evolution of relevant component concentrations
are calculated allowing for a comparison with experiments. Finally, we discuss
the validity and the possible improvements of the model.Comment: 20 pages (including the supporting information), 8 figure
Thermal and mechanical properties of a DNA model with solvation barrier
We study the thermal and mechanical behavior of DNA denaturation in the frame
of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent
interaction. By analyzing the melting transition of a homogeneous A-T sequence,
we are able to set suitable values of the parameters of the model and study the
formation and stability of bubbles in the system. Then, we focus on the case of
the P5 promoter sequence and use the Principal Component Analysis of the
trajectories to extract the main information on the dynamical behavior of the
system. We find that this analysis method gives an excellent agreement with
previous biological results.Comment: Physical Review E (in press
Elastic traits of the extensible discrete wormlike chain model
Polymer models play the special role of elucidating the elementary features describing the physics of long molecules and become essential to interpret the measurements of their magnitudes. In this work the end-to-end distance of an extensible discrete wormlike chain polymer as a function of the applied force has been calculated both numerically and analytically, the latter as an effective approximation. The numerical evaluation uses the transfer matrix formalism to obtain an exact calculation of the partition function, while the analytic derivations generalize the simple phenomenological formulas largely used up to now. The obtained formulas are simple enough to be implemented in the fit analysis of experimental data of semiflexible extensible polymers, with the result that the elastic parameters obtained are compatible with previous measurements, and more, their accuracy strongly improves in a large range of chain extensibility
Force spectroscopy analysis in polymer translocation
This paper reports the force spectroscopy analysis of a polymer that
translocates from one side of a membrane to the other side through an extended
pore, pulled by a cantilever that moves with constant velocity against the
damping and the potential barrier generated by the reaction of the membrane
walls. The polymer is modeled as a beads-springs chain with both excluded
volume and bending contributions, and moves in a stochastic three dimensional
environment described by a Langevin dynamics at fixed temperature. The force
trajectories recorded at different velocities reveal two unexplored exponential
regimes: the force increases when the first part of the chain enters the pore,
and then decreases when the first monomer reaches the trans region. The
spectroscopy analysis of the force values permit the estimation of the free
energy barrier as well as the limit force to permit the translocation. The
stall force to maintain the polymer fixed has been also calculated
independently, and its value confirms the force spectroscopy outcomes.Comment: arXiv admin note: text overlap with arXiv:1705.0517
Translocation of a polymer chain driven by a dichotomous noise
We consider the translocation of a one-dimensional polymer through a pore
channel helped by a motor driven by a dichotomous noise with time exponential
correlation. We are interested in the study of the translocation time, mean
velocity and stall force of the system as a function of the mean driving
frequency. We find a monotonous translocation time, in contrast with the mean
velocity which shows a pronounced maximum at a given frequency. Interestingly,
the stall force shows a nonmonotonic behavior with the presence of a minimum.
The influence of the spring elastic constant to the mean translocation times
and velocities is also presented.Comment: 11 pages, 7 figure
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