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1.
Phys Rev E ; 101(1-1): 012130, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32069645

RESUMEN

We study the properties of nonequilibrium systems modelled as spin models without defined Hamiltonian as the majority voter model. This model has transition probabilities that do not satisfy the condition of detailed balance. The lack of detailed balance leads to entropy production phenomena, which are a hallmark of the irreversibility. By considering that voters can diffuse on the lattice we analyze how the entropy production and how the critical properties are affected by this diffusion. We also explore two important aspects of the diffusion effects on the majority voter model by studying entropy production and entropy flux via time-dependent and steady-state simulations. This study is completed by calculating some critical exponents as function of the diffusion probability.

2.
Phys Rev E Stat Nonlin Soft Matter Phys ; 73(4 Pt 1): 040902, 2006 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-16711779

RESUMEN

We study the critical relaxation of the helix-coil transition in all-atom models of polyalanine chains. We show that at the critical temperature the decay of a completely helical conformation can be described by scaling relations that allow us estimating the pertinent critical exponents. The present approach opens a new way for characterizing transitions in proteins and may lead to a better understanding of their folding mechanism. An application of the technique to the 34-residue human parathyroid fragment PTH(1-34) supports universality of the helix-coil transition in homopolymers and (helical) proteins.


Asunto(s)
Modelos Químicos , Modelos Moleculares , Fragmentos de Péptidos/química , Fragmentos de Péptidos/ultraestructura , Péptidos/química , Teriparatido/análogos & derivados , Simulación por Computador , Humanos , Cinética , Movimiento (Física) , Conformación Proteica , Pliegue de Proteína , Teriparatido/química
3.
Phys Rev E Stat Nonlin Soft Matter Phys ; 66(2 Pt 2): 026130, 2002 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-12241260

RESUMEN

In this paper we study the short-time behavior of the Blume-Capel model at the tricritical point as well as along the second order critical line. Dynamic and static exponents are estimated by exploring scaling relations for the magnetization and its moments at an early stage of the dynamic evolution. Our estimates for the dynamic exponents, at the tricritical point, are z=2.215(2) and theta=-0.53(2).

4.
Phys Rev E Stat Nonlin Soft Matter Phys ; 70(6 Pt 2): 067701, 2004 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-15697566

RESUMEN

We analyze two alternative methods for determining the dynamic critical exponent z of the contact process and the Domany-Kinzel cellular automaton in Monte Carlo simulations. One method employs mixed initial conditions, as proposed for magnetic models [Phys. Lett. A 298, 325 (2002)]]; the other is based on the growth of the moment ratio m (t) = /2 starting with all sites occupied. The methods provide reliable estimates for z using the short-time dynamics of the process. Estimates of nu|| are obtained using a method suggested by Grassberger.

5.
Phys Rev E Stat Nonlin Soft Matter Phys ; 67(5 Pt 2): 057102, 2003 May.
Artículo en Inglés | MEDLINE | ID: mdl-12786323

RESUMEN

The global persistence exponent theta(g) is calculated for the two-dimensional Blume-Capel model following a quench to the critical point from both disordered states and such with small initial magnetizations. Estimates are obtained for the nonequilibrium critical dynamics on the critical line and at the tricritical point. Ising-like universality is observed along the critical line and a different value theta(g)=1.080(4) is found at the tricritical point.

6.
Artículo en Inglés | MEDLINE | ID: mdl-25375432

RESUMEN

We have investigated the dynamic critical behavior of the two-dimensional Z(5)-symmetric spin model by using short-time Monte Carlo (MC) simulations. We have obtained estimates of some critical points in its rich phase diagram and included, among the usual critical lines the study of first-order (weak) transition by looking into the order-disorder phase transition. In addition, we also investigated the soft-disorder phase transition by considering empiric methods. A study of the behavior of ß/νz along the self-dual critical line has been performed and special attention has been devoted to the critical bifurcation point, or Fateev-Zamolodchikov (FZ) point. First, by using a refinement method and taking into account simulations out of equilibrium, we were able to localize parameters of this point. In a second part of our study, we turned our attention to the behavior of the model at the early stage of its time evolution in order to find the dynamic critical exponent z as well as the static critical exponents ß and ν of the FZ point on square lattices. The values of the static critical exponents and parameters are in good agreement with the exact results, and the dynamic critical exponent z≈2.28 very close to the four-state Potts model (z≈2.29).

7.
J Chem Phys ; 126(4): 045107, 2007 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-17286517

RESUMEN

The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm earlier observations that the helix-coil transition in proteins can be described by a set of critical exponents. The high statistics of the simulations allows the authors to determine the exponent values with increased precision and support universality of the helix-coil transition in homopolymers and (helical) proteins.


Asunto(s)
Modelos Químicos , Modelos Moleculares , Péptidos/química , Simulación por Computador , Cinética , Conformación Proteica , Solventes/química
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