arXiv subjects

A. Caliri

Publications and source records attributed to A. Caliri.

3 recordsLinked to original sources

arXiv2016

Entropic formulation for the protein folding process: hydrophobic stability correlates with folding rates

We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our main tool of investigation is a 3D lattice model provided with a ten-letter alphabet, the stereochemical model. This model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. In order to characterize the folding characteristic time (τ) by two distinct sampling methods, first we present two sets of 10^{3} MC simulations for a fast protein-like sequence. For these sets of folding times, τ and τ_{q} were obtained with the application of the standard Metropolis algorithm (MA), and a modified algorithm (M_{q}A). The results for τ_{q}reveal two things: i) the hydrophobic chain-solvent interactions plus a set of inter-residues steric constraints are enough to emulate the first stage of the process: for each one of the 10^{3} MC performed simulations, the native is always found without exception, ii) the ratio τ_{q}/τ~1/3 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides an innate efficiency to the chain escapes from energetic and steric traps. ...

physics.bio-ph↗

arXiv2010

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↗

arXiv2003

The Predictive Power of R0 in an Epidemic Probabilistic System

An important issue in theoretical epidemiology is the epidemic threshold phenomenon, which specify the conditions for an epidemic to grow or die out. In standard (mean-field-like) compartmental models the concept of the basic reproductive number, R0, has been systematically employed as a predictor for epidemic spread and as an analytical tool to study the threshold conditions. Despite the importance of this quantity, there are no general formulation of R0 when one considers the spread of a disease in a generic finite population, involving, for instance, arbitrary topology of inter-individual interactions and heterogeneous mixing of susceptible and immune individuals. The goal of this work is to study this concept in a generalized stochastic system described in terms of global and local variables. In particular, the dependence of R0 on the space of parameters that define the model is investigated; it is found that near of the ``classical'' epidemic threshold transition the uncertainty about the strength of the epidemic process still is significantly large. The forecasting attributes of R0 for a discrete finite system is discussed and generalized; in particular, it is shown that, for a discrete finite system, the pretentious predictive power of R0 is significantly reduced.

physics.bio-ph↗