561 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
Active translocation of a semiflexible polymer assisted by an ATP-based molecular motor
In this work we study the assisted translocation of a polymer across a
membrane nanopore, inside which a molecular motor exerts a force fuelled by the
hydrolysis of ATP molecules. In our model the motor switches to its active
state for a fixed amount of time, while it waits for an ATP molecule binding
and triggering the impulse, during an exponentially distributed time lapse. The
polymer is modelled as a beads-springs chain with both excluded volume and
bending contributions, and moves in a stochastic three dimensional environment
modelled with a Langevin dynamics at fixed temperature. The resulting dynamics
shows a Michaelis-Menten translocation velocity that depends on the chain
flexibility. The scaling behavior of the mean translocation time with the
polymer length for different bending values is also investigated.Comment: 10 pages, 10 figure
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
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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