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1.
Phys Rev E ; 100(3-2): 039901, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31640047

RESUMO

This corrects the article DOI: 10.1103/PhysRevE.97.012141.

2.
Phys Rev E ; 97(1-1): 012141, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29448419

RESUMO

We derive the general relations between the maximum power, maximum efficiency, and minimum dissipation for the irreversible heat engine in a nonlinear response regime. In this context, we use the minimally nonlinear irreversible model and obtain the lower and upper bounds of the above relations for the asymmetric dissipation limits. These relations can be simplified further when the system possesses the time-reversal symmetry or antisymmetry. We find that our results are the generalization of various such relations obtained earlier for different heat engines.

3.
Phys Rev E ; 93(3): 032107, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27078292

RESUMO

Nonequilibrium work relations such as Jarzynski equality and Crooks fluctuation theorem relate the free energy differences between two equilibrium states and the work distribution of nonequilibrium processes. We use the third constraint formulation of Tsallis statistics and derive the q-statistics generalization of nonequilibrium work relations.

4.
Phys Rev E Stat Nonlin Soft Matter Phys ; 84(6 Pt 1): 060101, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22304027

RESUMO

In experiments and simulations the force acting on a single biomolecular system has been observed as a fluctuating quantity if the system is driven under constant velocity. We ask the question that is analogous to transient state entropy production and work fluctuation relations whether the force fluctuations observed in the single biomolecular system satisfy a transient state fluctuationlike relation, and the answer is in the affirmative. Using a constant velocity pulling steered molecular dynamics simulation study for protein unfolding, we confirm that the force fluctuations of this single biomolecular system satisfy a transient-state fluctuationlike relation 1/γ(T,v) ln[P(v)(+f)/P(v)(-f)] = f. P(v)(±f) is the probability of positive and negative values of forces f = f · for a given unfolding velocity of magnitude v and the pulling direction n, nis the unit vector of n, and γ(T,v) is a factor that depends on initial equilibrium temperature T and the unfolding velocity. For different unfolding velocities we find that the system in the nonequilibrium pulling region displays substantial negative fluctuation in its unfolding force when velocity decreases. A negative value of force may indicate the emergence of refolding behavior during protein unfolding. We also find that γ(T,v) ~ T(-δ)v(α) and the system relaxation time τ(T,v) ~ T(δ)v(-(1+α), where α and δ are scaling exponents.


Assuntos
Contactina 1/química , Fenômenos Mecânicos , Simulação de Dinâmica Molecular , Fenômenos Biomecânicos , Entropia , Probabilidade , Estrutura Terciária de Proteína , Desdobramento de Proteína
5.
Phys Rev E Stat Nonlin Soft Matter Phys ; 82(3 Pt 1): 031129, 2010 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21230047

RESUMO

It has been shown recently that the Jarzynski equality is generalized under nonequilibrium feedback control [T. Sagawa and M. Ueda, Phys. Rev. Lett. 104, 090602 (2010)]. The presence of feedback control in physical systems should modify both the Jarzynski equality and the detailed fluctuation theorem [K. H. Kim and H. Qian, Phys. Rev. E 75, 022102 (2007)]. However, the generalized Jarzynski equality under forward feedback control has been proved by considering that the physical systems under feedback control should locally satisfy the detailed fluctuation theorem. We use the same formalism and derive the generalized detailed fluctuation theorem for nonequilibrium driven systems under feedback control. We find that the feedback control in a physical system should preserve the detailed fluctuation theorem if the system has the same feedback information measure in forward and reverse directions.

6.
J Chem Phys ; 128(1): 014105, 2008 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-18190183

RESUMO

We have explained in detail why the canonical partition function of interacting self-avoiding walk (ISAW) is exactly equivalent to the configurational average of the weights associated with growth walks, such as the interacting growth walk (IGW), if the average is taken over the entire genealogical tree of the walk. In this context, we have shown that it is not always possible to factor the density of states out of the canonical partition function if the local growth rule is temperature dependent. We have presented Monte Carlo results for IGWs on a diamond lattice in order to demonstrate that the actual set of IGW configurations available for study is temperature dependent even though the weighted averages lead to the expected thermodynamic behavior of ISAW.

7.
J Chem Phys ; 126(14): 144906, 2007 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-17444742

RESUMO

The authors present an exact enumeration study of short self-avoiding walks in two as well as in three dimensions that addresses the question, "what is the shortest walk for which the existence of all the three scaling regimes--coil, globule, and the theta--could be demonstrated." Even though they could easily demonstrate the coil and the globule phase from free energy considerations, they could demonstrate the existence of a theta temperature only by using a scaling form for the distribution of gyration radius. That even such short walks have a scaling behavior is an unexpected result of this work.


Assuntos
Algoritmos , Modelos Químicos , Modelos Moleculares , Polímeros/química , Proteínas/química , Proteínas/ultraestrutura , Simulação por Computador , Modelos Estatísticos , Peso Molecular , Transição de Fase , Conformação Proteica
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