arXiv subjects

A. Pelizzola

Publications and source records attributed to A. Pelizzola.

At least 19 recordsLinked to original sources

arXiv2020

Simple Exclusion Processes with Local Resetting

We investigate the stationary state of Symmetric and Totally Asymmetric Simple Exclusion Processes with local resetting, on a one-dimensional lattice with periodic boundary conditions, using mean-field approximations, which appear to be exact in the thermodynamic limit, and kinetic Monte Carlo simulations. In both cases we find that in the thermodynamic limit the models exhibit three different regimes, depending on how the resetting rate scales with the system size. The Totally Asymmetric version of the model has a particularly rich behaviour, especially in an intermediate resetting regime where the resetting rate vanishes as the inverse of the system size, exhibiting 4 different phases, including phase separation.

cond-mat.stat-mech↗

arXiv2020

Dynamical transitions in a driven diffusive model with interactions

We study the dynamics of an asymmetric simple exclusion process with open boundaries and local interactions using a pair approximation which generalizes the 2-node cluster mean field theory and the Markov chain approach to kinetics and shares with these approaches the property of reproducing exact results for the bulk current-density relation and the steady state phase diagrams. We find that the relaxation rate exhibits a dynamical transition, with no static counterpart, analogous to that found without interactions. Remarkably, for some values of the model's parameters, we find 2 dynamical transitions in the same low density phase. We study the dynamics of relaxation to the steady state on both sides of these transitions and make an attempt at providing a physical interpretation for this phenomenon. Results from numerical approaches and a modified Domain Wall Theory confirm the picture provided by the pair approximation.

cond-mat.stat-mech↗

arXiv2020

Unbalanced Langmuir kinetics affects TASEP dynamical transitions: mean-field theory

In a previous study we developed a mean-field theory of dynamical transitions for the totally-asymmetric simple-exclusion process (TASEP) with open boundaries and Langmuir kinetics, in the so-called balanced regime, characterized by equal binding and unbinding rates. Here we show that simply including the possibility of unbalanced rates gives rise to an unexpectedly richer dynamical phase diagram. In particular, the current work predicts an unusual type of dynamical transition, which exhibits certain similarities with first-order phase transitions of equilibrium systems. We also point out that different types of dynamical transition are accompanied by different structural changes in the (mean-field) relaxation spectrum.

cond-mat.stat-mech↗

arXiv2013

Nonequilibrium dynamics of an exactly solvable Ising-like model and protein translocation

Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model is then applied to the protein translocation phenomenon, taking inspiration from a recent experiment on the green fluorescent protein pulled by a molecular motor. The average translocation time is evaluated exactly, and the analysis of single trajectories shows that translocation proceeds through an intermediate state, similar to that observed in the experiment.

physics.bio-ph↗

arXiv2011

Direction dependent mechanical unfolding and Green Fluorescent Protein as a force sensor

An Ising--like model of proteins is used to investigate the mechanical unfolding of the Green Fluorescent Protein along different directions. When the protein is pulled from its ends, we recover the major and minor unfolding pathways observed in experiments. Upon varying the pulling direction, we find the correct order of magnitude and ranking of the unfolding forces. Exploiting the direction dependence of the unfolding force at equilibrium, we propose a force sensor whose luminescence depends on the applied force.

cond-mat.soft↗

arXiv2010

Pathways of mechanical unfolding of FnIII_{10}: low force intermediates

We study the mechanical unfolding pathways of the $FnIII_{10}$ domain of fibronectin by means of an Ising--like model, using both constant force and constant velocity protocols. At high forces and high velocities our results are consistent with experiments and previous computational studies. Moreover, the simplicity of the model allows us to probe the biologically relevant low force regime, where we predict the existence of two intermediates with very close elongations. The unfolding pathway is characterized by stochastic transitions between these two intermediates.

cond-mat.soft↗

arXiv2009

Equilibrium properties and force-driven unfolding pathways of RNA molecules

The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a simple two--state behaviour for the hairpin and the presence of intermediate states for the ribozyme. Nonequilibrium simulations give the possible unfolding pathways for the ribozyme, and the dominant pathway corresponds to the experimentally observed one.

cond-mat.soft↗

arXiv2009

Fluctuation relations in non-equilibrium stationary states of Ising models

Fluctuation relations for the entropy production in non equilibrium stationary states of Ising models are investigated by Monte Carlo simulations. Systems in contact with heat baths at two different temperatures or subject to external driving will be studied. In the first case, by considering different kinetic rules and couplings with the baths, the behavior of the probability distributions of the heat exchanged in a time $τ$ with the thermostats, both in the disordered and in the low temperature phase, are discussed. The fluctuation relation is always verified in the large $τ$ limit and deviations from linear response theory are observed. Finite-$τ$ corrections are shown to obey a scaling behavior. In the other case the system is in contact with a single heat bath but work is done by shearing it. Also for this system the statistics collected for the mechanical work shows the validity of the fluctuation relation and preasymptotic corrections behave analogously to the case with two baths.

cond-mat.stat-mech↗

arXiv2008

Mechanical unfolding and refolding pathways of ubiquitin

Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a Go model with binary variables. The exponential dependence of the time constants on the force is verified, and folding and unfolding lengths are computed, with good agreement with experimental results. Furthermore, the model exhibits intermediate kinetic states, as observed in experiments. Unfolding and refolding pathways and intermediate states, obtained by tracing single secondary structure elements, are consistent with simulations of previous all-atom models and with the experimentally observed step sizes.

cond-mat.soft↗

arXiv2007

Downhill versus two-state protein folding in a statistical mechanical model

The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein 1BBL, a candidate for downhill folding behavior, and comparing it to the WW domain of protein PIN1, a two-state folder of comparable size, the authors show that there are qualitative differences in both the equilibrium and kinetic properties of the two molecules. However, the barrierless scenario which would be expected if 1BBL were a true downhill folder is observed only at low enough temperature.

q-bio.BM↗

arXiv2007

Protein mechanical unfolding: a model with binary variables

A simple lattice model, recently introduced as a generalization of the Wako--Saitô model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model proteins, together with their energy landscape, are studied on the basis of the exact solution of the model. Afterwards, the kinetic response of the molecules to a force is considered, discussing both force clamp and dynamic loading protocols and showing that theoretical expectations are verified. The kinetic parameters characterizing the protein unfolding are evaluated by using computer simulations and agree nicely with experimental results, when these are available. Finally, the extended Jarzynski equality is exploited to investigate the possibility of reconstructing the free energy landscape of proteins with pulling experiments.

cond-mat.soft↗

arXiv2007

An Ising-Like model for protein mechanical unfolding

The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a model is generalized by including the effect of an external force, and its thermodynamics turns out to be exactly solvable. We consider two molecules, the 27th immunoglobulin domain of titin and protein PIN1. In the case of titin we determine equilibrium force-extension curves and study nonequilibrium phenomena in the frameworks of dynamic loading and force clamp protocols, verifying theoretical laws and finding the position of the kinetic barrier which hinders the unfolding of the molecule. The PIN1 molecule is used to check the possibility of computing the free energy landscape as a function of the molecule length by means of an extended form of the Jarzynski equality.

cond-mat.soft↗

arXiv2005

Exactness of the cluster variation method and factorization of the equilibrium probability for the Wako-Saito-Munoz-Eaton model of protein folding

I study the properties of the equilibrium probability distribution of a protein folding model originally introduced by Wako and Saito, and later reconsidered by Munoz and Eaton. The model is a one-dimensional model with binary variables and many-body, long-range interactions, which has been solved exactly through a mapping to a two-dimensional model of binary variables with local constraints. Here I show that the equilibrium probability of this two-dimensional model factors into the product of local cluster probabilities, each raised to a suitable exponent. The clusters involved are single sites, nearest-neighbour pairs and square plaquettes, and the exponents are the coefficients of the entropy expansion of the cluster variation method. As a consequence, the cluster variation method is exact for this model.

cond-mat.stat-mech↗

arXiv2004

Two-dimensional lattice-fluid model with water-like anomalies

We investigate a lattice-fluid model defined on a two-dimensional triangular lattice, with the aim of reproducing qualitatively some anomalous properties of water. Model molecules are of the "Mercedes Benz" type, i.e., they possess a D3 (equilateral triangle) symmetry, with three bonding arms. Bond formation depends both on orientation and local density. We work out phase diagrams, response functions, and stability limits for the liquid phase, making use of a generalized first order approximation on a triangle cluster, whose accuracy is verified, in some cases, by Monte Carlo simulations. The phase diagram displays one ordered (solid) phase which is less dense than the liquid one. At fixed pressure the liquid phase response functions show the typical anomalous behavior observed in liquid water, while, in the supercooled region, a reentrant spinodal is observed.

cond-mat.soft↗

arXiv2000

Folding transitions of the square--diagonal two--dimensional lattice

The phase diagram of a vertex model introduced by P. Di Francesco (Nucl. Phys. B 525, 507 1998) representing the configurations of a square lattice which can fold with different bending energies along the main axes and the diagonals has been studied by Cluster Variation Method. A very rich structure with partially and completely folded phases, different disordered phases and a flat phase is found. The crumpling transition between a disordered and the flat phase is first-order. The CVM results are confimed by the analysis of the ground states and of the two limits where the model reduces to an Ising model.

cond-mat.stat-mech↗

arXiv1997

Critical behaviour of the three-dimensional gonihedric Ising Model

We use the cluster variation method (CVM) and Monte Carlo simulations to investigate the phase structure of the 3d gonihedric Ising actions defined by Savvidy and Wegner. This model corresponds to the usual three-dimensional cubic Ising model with nearest, next to the nearest, and plaquette interactions in the region with degenerate lamellar ground states. The picture of the phase diagram given by the CVM is in good agreement with the results of Monte Carlo simulations, and it is shown that the gonihedric model is in the same universality class of the ordinary three-dimensional Ising model.

cond-mat.stat-mech↗

arXiv1996

New critical behaviour of the three-dimensional Ising model with nearest-neighbor, next-nearest-neighbor and plaquette interactions

The critical and multicritical behavior of the simple cubic Ising model with nearest-neighbor, next-nearest-neighbor and plaquette interactions is studied using the cube and star-cube approximations of the cluster variation method and the recently proposed cluster variation--Padé approximant method. Particular attention is paid to the line of critical end points of the ferromagnetic-paramagnetic phase transition: its (multi)critical exponents are calculated, and their values suggest that the transition belongs to a novel universality class. A rough estimate of the crossover exponent is also given.

cond-mat.stat-mech↗

arXiv1996

The Phase Diagram of the Gonihedric 3d Ising Model via CVM

We use the cluster variation method (CVM) to investigate the phase structure of the 3d gonihedric Ising actions defined by Savvidy and Wegner. The geometrical spin cluster boundaries in these systems serve as models for the string worldsheets of the gonihedric string embedded in ${\bf Z}^3$. The models are interesting from the statistical mechanical point of view because they have a vanishing bare surface tension. As a result the action depends only on the angles of the discrete surface and not on the area, which is the antithesis of the standard 3d Ising model. The results obtained with the CVM are in good agreement with Monte Carlo simulations for the critical temperatures and the order of the transition as the self-avoidance coupling $κ$ is varied. The value of the magnetization critical exponent $β= 0.062 \pm 0.003$, calculated with the cluster variation--Padè approximant method, is also close to the simulation results.

hep-lat↗