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M. A. A. da Silva

Publications and source records attributed to M. A. A. da Silva.

6 recordsLinked to original sources

Scaling Analysis of Random Walks with Persistence Lengths: Application to Self-Avoiding Walks

We develop an approach for performing scaling analysis of $N$-step Random Walks (RWs). The mean square end-to-end distance, $\langle\vec{R}_{N}^{2}\rangle$, is written in terms of inner persistence lengths (IPLs), which we define by the ensemble averages of dot products between the walker's position and displacement vectors, at the $j$-th step. For RW models statistically invariant under orthogonal transformations, we analytically introduce a relation between $\langle\vec{R}_{N}^{2}\rangle$ and the persistence length, $λ_{N}$, which is defined as the mean end-to-end vector projection in the first step direction. For Self-Avoiding Walks (SAWs) on 2D and 3D lattices we introduce a series expansion for $λ_{N}$, and by Monte Carlo simulations we find that $λ_{\infty}$ is equal to a constant; the scaling corrections for $λ_{N}$ can be second and higher order corrections to scaling for $\langle\vec{R}_{N}^{2}\rangle$. Building SAWs with typically one hundred steps, we estimate the exponents $ν_{0}$ and $Δ_{1}$ from the IPL behavior as function of $j$. The obtained results are in excellent agreement with those in the literature. This shows that only an ensemble of paths with the same length is sufficient for determining the scaling behavior of $\langle\vec{R}_{N}^{2}\rangle$, being that the whole information needed is contained in the inner part of the paths.

cond-mat.stat-mech↗

The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics

Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process with two consecutive and independent stages, namely the search mechanism and the overall productive stabilization; ($ii$) the folding kinetics results from a mechanism as fast as can be; and ($iii$) at nanoscale dimensions, local thermal fluctuations may have important role on the folding kinetics. Here the first stage of folding process (search mechanism) is focused exclusively. The effects and consequences of local thermal fluctuations on the configurational kinetics, treated here in the context of non extensive statistical mechanics, is analyzed in detail through the dependence of the characteristic time of folding ($τ$) on the temperature $T$ and on the nonextensive parameter $q$.The model used consists of effective residues forming a chain of 27 beads, which occupy different sites of a $3-$D infinite lattice, representing a single protein chain in solution. The configurational evolution, treated by Monte Carlo simulation, is driven mainly by the change in free energy of transfer between consecutive configurations. ...

physics.bio-ph↗

Amnestically induced persistence in random walks

We study how the Hurst exponent $α$ depends on the fraction $f$ of the total time $t$ remembered by non-Markovian random walkers that recall only the distant past. We find that otherwise nonpersistent random walkers switch to persistent behavior when inflicted with significant memory loss. Such memory losses induce the probability density function of the walker's position to undergo a transition from Gaussian to non-Gaussian. We interpret these findings of persistence in terms of a breakdown of self-regulation mechanisms and discuss their possible relevance to some of the burdensome behavioral and psychological symptoms of Alzheimer's disease and other dementias.

cond-mat.stat-mech↗

Stochastic Modelling Approach to the Incubation Time of Prionic Diseases

Transmissible spongiform encephalopathies like the bovine spongiform encephalopathy (BSE) and the Creutzfeldt-Jakob disease (CJD) in humans are neurodegenerative diseases for which prions are the attributed pathogenic agents. A widely accepted theory assumes that prion replication is due to a direct interaction between the pathologic (PrPsc) form and the host encoded (PrPc) conformation, in a kind of an autocatalytic process. Here we show that the overall features of the incubation time of prion diseases are readily obtained if the prion reaction is described by a simple mean-field model. An analytical expression for the incubation time distribution then follows by associating the rate constant to a stochastic variable log normally distributed. The incubation time distribution is then also shown to be log normal and fits the observed BSE data very well. The basic ideas of the theoretical model are then incorporated in a cellular automata model. The computer simulation results yield the correct BSE incubation time distribution at low densities of the host encoded protein.

cond-mat.stat-mech↗

The R0 Approach to Epidemic-non-Epidemic Phases Revisited

In this work, we revisit the basic reproduction rate $\mathcal{R}_{0}$ definition for analysis of epidemic-non-epidemic phases describing the dynamics of the discrete stochastic version of the epidemic $SIR$ model based on the Master Equation formalism. One shows that it is a very precise and efficient way to determine the epidemic threshold; using its most primitive concept, we can find exact results.

physics.bio-ph↗

Dynamical Monte Carlo method for stochastic epidemic models

In this work we introduce a new approach to Dynamical Monte Carlo methods to simulate markovian processes. We apply this approach to formulate and study an epidemic generalized SIRS model. The results are in excellent agreement with the fourth order Runge-Kutta method in a region of deterministic solution. Introducing local stochastic interactions, the Runge-Kutta method is no longer applicable. Thus, we solve the system described by a set of stochastic differential equations by a Dynamical Monte Carlo technique and check the solutions self-consistently with a stochastic version of the Euler method. We also analyzed the results under the herd-immunity concept.

physics.bio-ph↗