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

Extinction statistics in N random interacting species

A randomly interacting N-species Lotka-Volterra system in the presence of a Gaussian multiplicative noise is analyzed. The investigation is focused on the role of this external noise into the statistical properties of the extinction times of the populations. The distributions show a Gaussian shape for each noise intensity value investigated. A monotonic behavior of the mean extinction time as a function of the noise intensity is found, while a nonmonotonic behavior of the width of the extinction time probability distribution characterizes the dynamical evolution.Comment: 9 pages, 4 figures, Presented at the 19th Marian Smoluchowski Symposium on Statistical Physics, Krakow, Poland, May 14-17, 200

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

Resonant activation in piecewise linear asymmetric potentials

7 páginas, 8 figuras.-- PACS number(s): 05.40.−a, 05.45.−a, 02.50.EyThis work analyzes numerically the role played by the asymmetry of a piecewise linear potential, in the presence of both a Gaussian white noise and a dichotomous noise, on the resonant activation phenomenon. The features of the asymmetry of the potential barrier arise by investigating the stochastic transitions far behind the potential maximum, from the initial well to the bottom of the adjacent potential well. Because of the asymmetry of the potential profile together with the random external force uniform in space, we find, for the different asymmetries: (1) an inversion of the curves of the mean first passage time in the resonant region of the correlation time τ of the dichotomous noise, for low thermal noise intensities; (2) a maximum of the mean velocity of the Brownian particle as a function of τ; and (3) an inversion of the curves of the mean velocity and a very weak current reversal in the miniratchet system obtained with the asymmetrical potential profiles investigated. An inversion of the mean first passage time curves is also observed by varying the amplitude of the dichotomous noise, behavior confirmed by recent experiments.The authors acknowledge financial support from Spanish MICINN through Project No. FIS2008- 01240, cofunded by FEDER funds, and the Italian Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR).Peer reviewe

Stability measures in metastable states with Gaussian colored noise

We present a study of the escape time from a metastable state of an overdamped Brownian particle, in the presence of colored noise generated by Ornstein-Uhlenbeck process. We analyze the role of the correlation time on the enhancement of the mean first passage time through a potential barrier and on the behavior of the mean growth rate coefficient as a function of the noise intensity. We observe the noise enhanced stability effect for all the initial unstable states used, and for all values of the correlation time $\tau_c$ investigated. We can distinguish two dynamical regimes characterized by weak and strong correlated noise respectively, depending on the value of $\tau_c$ with respect to the relaxation time of the system.Comment: 6 pages, 7 figure

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

Michaelis-Menten dynamics of a polymer chain out of a dichotomous ATP-based motor

We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The machine activation rate can be put in relationship with the available ATP concentration in the solution, which gives the necessary energy supply. The translocation time shows a monotonic behavior as a function of the activation frequency and the velocity follows a Michaelis-Menten law that arises naturally in this description. The estimation of the stall force of the motor follows a corrected Michaelis-Menten law which still is to be checked in experimental investigation. The results presented agree with recent biological experimental findings.Comment: 12 pages, 8 figure