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.
We propose here two new recommendation methods, based on the appropriate normalization of already existing similarity measures, and on the convex combination of the recommendation scores derived from similarity between users and between objects. We v
alidate the proposed measures on three relevant data sets, and we compare their performance with several recommendation systems recently proposed in the literature. We show that the proposed similarity measures allow to attain an improvement of performances of up to 20% with respect to existing non-parametric methods, and that the accuracy of a recommendation can vary widely from one specific bipartite network to another, which suggests that a careful choice of the most suitable method is highly relevant for an effective recommendation on a given system. Finally, we studied how an increasing presence of random links in the network affects the recommendation scores, and we found that one of the two recommendation algorithms introduced here can systematically outperform the others in noisy data sets.
We present a study of the DNA translocation of the bacteriophage phi 29 packaging molecular motor. From the experimental available information we present a model system based in an stochastic fashing potential, which reproduces the experimental obser
vations such as: detailed trajectories, steps and substeps, spatial correlation, and velocity. Moreover the model allows the evaluation of power and efficiency of this motor. We have found that the maximum power regime does not correspond with that of the maximum efficiency. These informations can stimulate further experiments.
We investigate the role of the noise in the mating behavior between individuals of Nezara viridula (L.), by analyzing the temporal and spectral features of the non-pulsed type female calling song emitted by single individuals. We have measured the th
reshold level for the signal detection, by performing experiments with the calling signal at different intensities and analyzing the insect response by directionality tests performed on a group of male individuals. By using a sub-threshold signal and an acoustic Gaussian noise source, we have investigated the insect response for different levels of noise, finding behavioral activation for suitable noise intensities. In particular, the percentage of insects which react to the sub-threshold signal, shows a non-monotonic behavior, characterized by the presence of a maximum, for increasing levels of the noise intensity. This constructive interplay between external noise and calling signal is the signature of the non-dynamical stochastic resonance phenomenon. Finally, we describe the behavioral activation statistics by a soft threshold model which shows stochastic resonance. We find that the maximum of the ensemble average of the input-output cross-correlation occurs at a value of the noise intensity very close to that for which the behavioral response has a maximum.
In this work we study the noise induced effects on the dynamics of short polymers crossing a potential barrier, in the presence of a metastable state. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecul
ar dynamics by taking into account both the interactions between adjacent monomers and introducing a Lennard-Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion with a Gaussian uncorrelated noise. We find a nonmonotonic behaviour of the mean first passage time and the most probable translocation time, of the polymer centre of inertia, as a function of the polymer length at low noise intensity. We show how thermal fluctuations influence the motion of short polymers, by inducing two different regimes of translocation in the molecule transport dynamics. In this context, the role played by the length of the molecule in the translocation time is investigated.
The study of the noise induced effects on the dynamics of a chain molecule crossing a potential barrier, in the presence of a metastable state, is presented. A two-dimensional stochastic version of the Rouse model for a flexible polymer has been adop
ted to mimic the molecular dynamics and to take into account the interactions between adjacent monomers. We obtain a nonmonotonic behavior of the mean first passage time and its standard deviation, of the polymer centre of inertia, with the noise intensity. These findings reveal a noise induced effect on the mean crossing time. The role of the polymer length is also investigated.
We study a Langevin equation derived from the Michaelis-Menten (MM) phenomenological scheme for catalysis accompanying a spontaneous replication of molecules, which may serve as a simple model of cell-mediated immune surveillance against cancer. We e
xamine how two different and statistically independent sources of noise - dichotomous multiplicative noise and additive Gaussian white noise - influence the populations extinction time. This quantity is identified as the mean first passage time of the system across the zero population state. We observe the effects of resonant activation (RA) and noise-enhanced stability (NES) and we report the evidence for competitive co-occurrence of both phenomena in a given regime of noise parameters. We discuss the statistics of first passage times in this regime and the role of different pseudo-potential profiles on the RA and NES phenomena. The RA/NES coexistence region brings an interesting interpretation for the growth kinetics of cancer cells population, as the NES effect enhancing the stability of the tumoral state becomes strongly reduced by the RA phenomenon.
We investigate a stochastic version of a simple enzymatic reaction which follows the generic Michaelis-Menten kinetics. At sufficiently high concentrations of reacting species, the molecular fluctuations can be approximated as a realization of a Brow
nian dynamics for which the model reaction kinetics takes on the form of a stochastic differential equation. After eliminating a fast kinetics, the model can be rephrased into a form of a one-dimensional overdamped Langevin equation. We discuss physical aspects of environmental noises acting in such a reduced system, pointing out the possibility of coexistence of dynamical regimes where noise-enhanced stability and resonant activation phenomena can be observed together.
