1,720,996 research outputs found
Transport and fluctuation-dissipation relations in asymptotic and preasymptotic diffusion across channels with variable section
No full textDiffusion properties of self-propelled particles in cellular flows
Full text linkWe study the dynamics of a self-propelled particle advected by a steady laminar flow. The persistent motion of the self-propelled particle is described by an active Ornstein–Uhlenbeck process. We focus
on the diffusivity properties of the particle as a function of persistence time and free-diffusion coefficient, revealing non-monotonic behaviors, with the occurrence of a minimum and a steep growth
in the regime of large persistence time. In the latter limit, we obtain an analytical prediction for the scaling of the diffusion coefficient with the parameters of the active force. Our study sheds light on the
effect of a flow-field on the diffusion of active particles, such as living microorganisms and motile phytoplankton in fluids
Protein translocation in narrow pores: Inferring bottlenecks from native structure topology
No full textCoarse-grained simulations of protein translocation across narrow pores suggest that the transport is characterized by long stall events. The translocation bottlenecks and the associated free-energy barriers are found to be strictly related to the structural properties of the protein native structure. The ascending ramps of the free-energy profile systematically correspond to regions of the chain denser in long range native contacts formed with the untranslocated portion of the protein. These very regions are responsible for the stalls occurring during the protein transport along the nanopore. The decomposition of the free energy in internal energy and entropic terms shows that the dominant energetic contribution can be estimated on the base of the protein native structure only. Interestingly, the essential features of the dynamics are retained in a reduced phenomenological model of the process describing the evolution of a suitable collective variable in the associated free-energy landscape
Correlated escape of active particles across a potential barrier
Full text linkWe study the dynamics of one-dimensional active particles confined in a double-well potential, focusing on the escape properties of the system, such as the mean escape time from a well. We first consider a single-particle both in near and far-from-equilibrium regimes by varying the persistence time of the active force and the swim velocity. A non-monotonic behavior of the mean escape time is observed with the persistence time of the activity, revealing the existence of an optimal choice of the parameters favoring the escape process. For small persistence times, a Kramers-like formula with an effective potential obtained within the unified colored noise approximation is shown to hold. Instead, for large persistence times, we developed a simple theoretical argument based on the first passage theory, which explains the linear dependence of the escape time with the persistence of the active force. In the second part of the work, we consider the escape on two active particles mutually repelling. Interestingly, the subtle interplay of active and repulsive forces may lead to a correlation between particles, favoring the simultaneous jump across the barrier. This mechanism cannot be observed in the escape process of two passive particles. Finally, we find that in the small persistence regime, the repulsion favors the escape, such as in passive systems, in agreement with our theoretical predictions, while for large persistence times, the repulsive and active forces produce an effective attraction, which hinders the barrier crossing
Reaction Spreading in Systems with Anomalous Diffusion
No full textWe briefly review some aspects of the anomalous diffusion, and itsrelevance in reactive systems. In particular we considerstrong anoma-lousdiffusion characterized by the moment behaviour〈x(t)q〉∼tqν(q),whereν(q) is a non constant function, and we discuss its consequences.Even in the apparently simple caseν(2) = 1/2, strong anomalous dif-fusion may correspond to non trivial features, such as non Gaussianprobability distribution and peculiar scaling of large order moments.When a reactive term is added to a normal diffusion process, onehas a propagating front with a constant velocity. The presence ofanomalous diffusion by itself does not guarantee a changing inthefront propagation scenario; a key factor to select linear intime orfaster front propagation has been identified in the shape of the prob-ability distribution tail in absence of reaction. In addition, we discussthe reaction spreading on graphs, underlying the major roleof theconnectivity properties of these structures, characterized by thecon-nectivity dimension.
Testing Simplified Proteins Models of the hPin1 WW Domain
Full text linkAbstractThe WW domain of the human Pin1 protein for its simple topology and large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of this work is to compare the reliability of the chemically based Sorenson/Head-Gordon (SHG) model and a standard native centric model in reproducing, through molecular dynamics simulations, some of the well known features of the folding transition of this small domain. Our results show that the Gō model correctly reproduces the cooperative, two-state, folding mechanism of the WW-domain, while the SHG model predicts a transition occurring in two stages: a collapse, followed by a structural rearrangement. The lack of a cooperative folding in the SHG simulations appears to be related to the nonfunnel shape of the energy landscape featuring a partitioning of the native valley in subbasins corresponding to different chain chiralities. However, the SHG approach remains more reliable in estimating the Φ-values with respect to Gō-like description. This may suggest that the WW-domain folding process is stirred by energetic and topological factors as well, and it highlights the better suitability of chemically based models in simulating mutations
Non-anomalous diffusion is not always Gaussian
No full textThrough the analysis of unbiased random walks on fractal trees and continuous time random
walks, we show that even if a process is characterized by a mean square displacement (MSD)
growing linearly with time (standard behaviour) its diffusion properties can be not
trivial. In particular, we show that the following scenarios are consistent with a linear
increase of MSD with time: (i) the high-order moments, ⟨x(t)q⟩ for q > 2 and the probability density of the process exhibit multiscaling; (ii)
the random walk on certain fractal graphs, with non integer spectral dimension, can
display a fully standard diffusion; (iii) positive order moments satisfying standard
scaling does not imply an exact scaling property of the probability density
Probability distribution functions of sub- and super-diffusive systems
Full text linkWe study the anomalous transport in systems of random walks (RW's) on
comb-like lattices with fractal sidebranches, showing subdiffusion, and in a
system of Brownian particles driven by a random shear along the x-direction,
showing a superdiffusive behavior. In particular, we discuss whether scaling
and universality are present or not in the shapes of the particle distribution
along the preferential transport direction (x-axis).Comment: latex: 13 pages, 9 pdf figures, regular articl
Transport of active particles in an open-wedge channel
Full text linkThe transport of independent active Brownian particles within a two-dimensional narrow channel, modeled as an open-wedge, is studied both numerically and theoretically. We show that the active force tends to localize the particles near the walls, thus reducing the effect of the entropic force which, instead, is prevailing in the case of passive particles. As a consequence, the exit of active particles from the smaller side of the channel is facilitated with respect to their passive counterpart. By continuously re-injecting particles in the middle of the wedge, we obtain a steady regime whose properties are investigated in the presence and absence of an external constant driving field. We characterize the statistics and properties of the exit process from the two opposite sides of the channel, also by making a comparison between the active case and passive case. Our study reveals the existence of an optimal value of the persistence time of the active force which is able to guarantee the maximal efficiency in the transport process
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