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 $L^2$ 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