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1.
J Chem Phys ; 160(2)2024 Jan 14.
Artículo en Inglés | MEDLINE | ID: mdl-38189619

RESUMEN

We investigate the "roughness" of the energy landscape of a system that diffuses in a heterogeneous medium with a random position-dependent friction coefficient α(x). This random friction acting on the system stems from spatial inhomogeneity in the surrounding medium and is modeled using the generalized Caldira-Leggett model. For a weakly disordered medium exhibiting a Gaussian random diffusivity D(x) = kBT/α(x) characterized by its average value ⟨D(x)⟩ and a pair-correlation function ⟨D(x1)D(x2)⟩, we find that the renormalized intrinsic diffusion coefficient is lower than the average one due to the fluctuations in diffusivity. The induced weak internal friction leads to increased roughness in the energy landscape. When applying this idea to diffusive motion in liquid water, the dissociation energy for a hydrogen bond gradually approaches experimental findings as fluctuation parameters increase. Conversely, for a strongly disordered medium (i.e., ultrafast-folding proteins), the energy landscape ranges from a few to a few kcal/mol, depending on the strength of the disorder. By fitting protein folding dynamics to the escape process from a metastable potential, the decreased escape rate conceptualizes the role of strong internal friction. Studying the energy landscape in complex systems is helpful because it has implications for the dynamics of biological, soft, and active matter systems.

2.
Entropy (Basel) ; 25(7)2023 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-37509959

RESUMEN

In statistical mechanics, the ergodic hypothesis (i.e., the long-time average is the same as the ensemble average) accompanying anomalous diffusion has become a continuous topic of research, being closely related to irreversibility and increasing entropy. While measurement time is finite for a given process, the time average of an observable quantity might be a random variable, whose distribution width narrows with time, and one wonders how long it takes for the convergence rate to become a constant. This is also the premise of ergodic establishment, because the ensemble average is always equal to the constant. We focus on the time-dependent fluctuation width for the time average of both the velocity and kinetic energy of a force-free particle described by the generalized Langevin equation, where the stationary velocity autocorrelation function is considered. Subsequently, the shortest time scale can be estimated for a system transferring from a stationary state to an effective ergodic state. Moreover, a logarithmic spatial potential is used to modulate the processes associated with free ballistic diffusion and the control of diffusion, as well as the minimal realization of the whole power-law regime. The results presented suggest that non-ergodicity mimics the sparseness of the medium and reveals the unique role of logarithmic potential in modulating diffusion behavior.

3.
Soft Matter ; 18(45): 8687-8699, 2022 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-36349834

RESUMEN

The two-state stochastic phenomenon is observed in various systems and is attracting more interest, and it can be described by the two-state random walk (TSRW) model. The TSRW model is a typical two-state renewal process alternating between the continuous-time random walk state and the Lévy walk state, in both of which the sojourn time distributions follow a power law. In this paper, by discussing the statistical properties and calculating the ensemble averaged and time averaged mean squared displacement, the ergodic property and the ultimate diffusive behavior of the aging TSRW is studied. Results reveal that because of the two-state intermittent feature, ergodicity and nonergodicity can coexist in the aging TSRW, which behave as the time scalings of the time averages and ensemble averages not being identically equal. In addition, we find that the unique state occupation mechanism caused by the diverging mean of the sojourn times of one state, determines the aging TSRW's ultimate diffusive behavior at extremely large timescales, i.e., instead of the term with the larger diffusion exponent, the diffusion is surprisingly characterized by the term with the smaller one, which is distinctly different from previous conclusions and known results. At last, we note that the Lévy walk with rests model which also displays aging and ergodicity breaking, can be generalized by the TSRW model.

4.
Soft Matter ; 17(42): 9786-9798, 2021 Nov 03.
Artículo en Inglés | MEDLINE | ID: mdl-34657952

RESUMEN

Within the framework of a space-time correlated continuous-time random walk model, anomalous diffusion of particles moving in the velocity field is studied in this paper. The weak asymptotic form ω(t) ∼ t-(1+α), 1 < α < 2 for large t, is considered to be the waiting time distribution. The analytical results reveal that the diffusion in the velocity field, i.e., the mean squared displacement, can display a multi-fractional form caused by dispersive bias and space-time correlation. The numerical results indicate that the multi-fractional diffusion leads to a crossover phenomenon in-between the process at an intermediate timescale, followed by a steady state which is always determined by the largest diffusion exponent term. In addition, the role of velocity and weak asymptotics is discussed. The extremely small fluid velocity can characterize the diffusion by a diffusion coefficient instead of diffusion exponent, which is distinctly different from the former definition. In particular, for the waiting time displaying a weak asymptotic property, if the anomalous part is suppressed by the normal part, a second crossover phenomenon appears at an intermediate timescale, followed by a steady normal diffusion, which implies that the anomalies underlying the process are smoothed out at large timescales. Moreover, we discuss that the consideration of bias and correlation could help to avoid a possible not readily noticeable mistake in studying the topic concerned in this paper, which may be helpful in the relevant experimental research.

5.
J Chem Phys ; 146(20): 204103, 2017 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-28571326

RESUMEN

We study numerically and analytically the barrier escape dynamics of a particle driven by an underlying correlated Lévy noise for a smooth metastable potential. A "quasi-monochrome-color" Lévy noise, i.e., the first-order derivative variable of a linear second-order differential equation subjected to a symmetric α-stable white Lévy noise, also called the harmonic velocity Lévy noise, is proposed. Note that the time-integral of the noise Green function of this kind is equal to zero. This leads to the existence of underlying negative time correlation and implies that a step in one direction is likely followed by a step in the other direction. By using the noise of this kind as a driving source, we discuss the competition between long flights and underlying negative correlations in the metastable dynamics. The quite rich behaviors in the parameter space including an optimum α for the stationary escape rate have been found. Remarkably, slow diffusion does not decrease the stationary rate while a negative correlation increases net escape. An approximate expression for the Lévy-Kramers rate is obtained to support the numerically observed dependencies.

6.
Phys Rev E ; 109(1-1): 014130, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38366502

RESUMEN

Anomalous diffusive behaviors are observed in highly inhomogeneous but relatively stable environments such as intracellular media and are increasingly attracting attention. In this paper we develop a coupled continuous-time random walk model in which the waiting time is power-law coupled with the local environmental diffusion coefficient. We provide two forms of the waiting time density, namely, a heavy-tailed density and an exponential density. For different waiting time densities, anomalous diffusions with the diffusion exponent between 0 and 2 and Brownian yet non-Gaussian diffusion can be realized within the present model. The diffusive behaviors are analyzed and discussed by deriving the mean-squared displacement and probability density function. In addition we derive the effective jump length density corresponding to the decoupled form to help distinguish the diffusion types. Our model unifies two kinds of anomalous diffusive behavior with different characteristics in the same inhomogeneous environment into a theoretical framework. The model interprets the random motion of particles in a complex inhomogeneous environment and reproduces the experimental results of different biological and physical systems.

7.
J Chem Phys ; 138(8): 084104, 2013 Feb 28.
Artículo en Inglés | MEDLINE | ID: mdl-23464137

RESUMEN

We derive an integral form of multidimensional master equation for a markovian process, in which the transition function is obtained in terms of a set of discrete Langevin equations. The solution of master equation, namely, the probability density function is calculated by using the Monte-Carlo composite sampling method. In comparison with the usual Langevin-trajectory simulation, the present approach decreases effectively coarse-grained error. We apply the master equation to investigate time-dependent barrier escape rate of a particle from a two-dimensional metastable potential and show the advantage of this approach in the calculations of quantities that depend on the probability density function.


Asunto(s)
Cadenas de Markov , Método de Montecarlo , Factores de Tiempo
8.
Phys Rev E ; 105(5): L052105, 2022 May.
Artículo en Inglés | MEDLINE | ID: mdl-35706220

RESUMEN

We develop a unified Hamiltonian approach to the diffusion of a particle coupled to a dissipative environment, an archetypal model widely invoked to interpret condensed phase phenomena, such as polymerization and cold-atom diffusion in optical lattices. By appropriate choices of the coupling functions, we reformulate phenomenological diffusion models by adding otherwise ignored space-momentum terms. We thus numerically predict a variety of diffusion regimes, from diffusion saturation to superballistic diffusion. With reference to ultracold atoms in optical lattices, we also show that time correlated external noises prevent superdiffusion from exceeding Richardson's law. Some of these results are unexpected and call for experimental validation.

9.
Phys Rev E ; 105(1-1): 014122, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-35193269

RESUMEN

The phenomenon of the two-state process is observed in various systems and is increasingly attracting attention, such that there is a need for a theoretical model of the process. In this paper, we present a prototypal two-state random walk (TSRW) model of a renewal process alternating between the continuous-time random walk (CTRW) state and Lévy walk (LW) state. The jump length distribution of the CTRW state is assumed to be Gaussian whereas the time distributions of the two states are both considered to follow a power law. The diffusive behavior is analyzed and discussed by calculating the mean squared displacement (MSD) analytically and numerically. The results reveal that it displays strong anomalous diffusive behaviors caused by random motions of both states, i.e., two anomalous diffusion terms coexist in the expression of the MSD, and the time distribution which has the heavier tail determines their forms. Moreover, because the two diffusion terms originate from different mechanisms, we find that the diffusion can be characterized by either the term with the largest diffusion exponent or the term with the largest diffusion coefficient at long timescales, which shows very different properties from the single-state process. In addition, the two-state nature of the process of the particle moving in a velocity field makes the TSRW model applicable to describe it. Results obtained from the two-state model reveal that the diffusion can even exhibit subdiffusive behavior, which is significantly different from known results obtained using the single-state model.

10.
Phys Rev E ; 104(1-1): 014114, 2021 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-34412352

RESUMEN

For the Debye Brownian oscillator, we present a series solution to the generalized Langevin equation describing the motion of a particle. The external potential is considered to be a harmonic potential and the spectral density of driven noise is a hard cutoff at high finite frequencies. The results are in agreement with both numerical calculations and Monte Carlo simulations. We demonstrate abnormal weak ergodic breaking; specifically, the long-time average of the observable vanishes but the corresponding ensemble average continues to oscillate with time. This Debye Brownian oscillator does not arrive at an equilibrium state and undergoes underdamped-like motion for any model parameter. Nevertheless, ergodic behavior and equilibrium can be recovered concurrently using a strong bound potential. We give an understanding of the behavior as being the consequence of discrete breather modes in the lattices similar to the formation of an additional periodic signal. Furthermore, we compare the results calculated by cutting off separately the spectral density and the correlation function of colored noise.

11.
Phys Rev E ; 103(3-1): 032136, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33862786

RESUMEN

We investigate ergodic time scales in single-particle tracking by introducing a covariance measure Ω(Δ;t) for the time-averaged relative square displacement recorded in lag-time Δ at elapsed time t. The present model is established in the generalized Langevin equation with a power-law memory function. The ratio Ω(Δ;Δ)/Ω(Δ;t) is shown to obey a universal scaling law for long but finite times and is used to extract the effective ergodic time. We derive a finite-time-averaged Green-Kubo relation and find that, to control the deviations in measurement results from ensemble averages, the ratio Δ/t must be neither too small nor close to unity. Our paper connects the experimental self-averaging property of a tracer with the theoretic velocity autocorrelation function and sheds light on the transition to ergodicity.

12.
Phys Rev E ; 101(6-1): 062131, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-32688488

RESUMEN

A time-dependent generalized Kubo relation is derived by introducing the notion of a diffusion function for a particle confined in a harmonic potential. The relation reduces to the standard Kubo relation as a special case but holds for anomalous diffusion, nonergodic processes, and bounded motion. We analyze in detail the behaviors of the diffusion and memory functions and report a generalized Stokes-Einstein relation concerning anomalous diffusion. Furthermore, we demonstrate that when a high finite-frequency cutoff is imposed on the noise spectral density, a breakdown in ergodicity accompanied by the appearance of nonstationarity in the velocity autocorrelation function occurs in forced systems. This breakdown is taken as explicit evidence for either decay-spring-memory or recovering-force effects leading to nonexponential relaxation kinematics.

13.
Phys Rev E ; 102(6-1): 062122, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33465995

RESUMEN

The diffusion of space-time correlated continuous-time random walk moving in the velocity field, which includes the fluid flowing freely and the fluid flowing through porous media, is investigated in this paper. Results reveal that it presents anomalous diffusion merely caused by space-time correlation in the freely flowing fluid, and the bias from the velocity field only supplies a standard advection, which is verified by the corresponding generalized diffusion equation which includes a standard advection term. However, the diffusion in the fluid flowing through porous media, i.e., the mean squared displacement, can display a bifractional form of which one originates from space-time correlation and the other one originates from dispersive bias caused by sticking of the porous media. The fractional advection term emerging in the corresponding generalized diffusion equation confirms the results. Moreover, the coexistence of correlation and dispersive bias result in crossover phenomenon in-between the diffusive process at an intermediate timescale, but just as the definition of diffusion, the one owning the largest diffusion exponent always prevails at large timescales. However, since the two fractional diffusions originate from a different mechanism, even if it owns the smaller diffusion exponent, that one can dominate the diffusion if it fluctuates much stronger than the other one, which no longer obeys the previous conclusion.

14.
Phys Rev E ; 100(5-1): 052149, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31869967

RESUMEN

The generalized Einstein relation (GER) for nonergodic processes is investigated within the framework of the generalized Langevin equation. The conditions for anomalous relaxation such as long-tail decay and non-vanishing velocity autocorrelation function (VAF) are proposed and distinguished. For the stationary nonergodic process, if the initial preparation of the particle velocity is non-thermal, an asymptotic GER occurs in a departure from the usual result. It is shown that the GER holding is a necessary condition rather than a full condition for the system being close to equilibrium. For the nonergodic process of the second type due to cutoff of high frequencies, the VAF oscillates with time, the GER holds but the equilibrium fails in the long-time limit. Applications to some practical examples confirm the present theoretical findings.

15.
Phys Rev E ; 97(6-1): 062143, 2018 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-30011451

RESUMEN

We carry out a detailed study of escape dynamics of a particle driven by a white noise over a metastable potential corrugated by spatial disorder in the form of zero-mean random correlated potential. The approach of double-averaging over test particles and statistic ensemble is proposed to calculate the escape rate in a finite-size random rough metastable potential, moreover, the interference mechanism of test particles multi-passing over the saddle point is considered. Through analyzing the dependence of the steady escape rate on various modelled potentials and parameters, we demonstrate that the obstruction induced by roughness leads to a decrease in the steady escape rate with the increase of rough intensity. We also add the random correlated potential into the vicinity of the saddle-point of metastable potentials of three kinds and show an enhancement phenomenon of escape rate similar to the previous study of a surmounting fluctuating sharp barrier.

16.
Phys Rev E Stat Nonlin Soft Matter Phys ; 76(6 Pt 1): 061119, 2007 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-18233826

RESUMEN

Anomalous transport of a particle subjected to non-Ohmic damping of the power delta in a tilted periodic potential is investigated via Monte Carlo simulation of the generalized Langevin equation. It is found that the system exhibits two relative motion modes: the locked state and the running state. In an environment of sub-Ohmic damping (0=2D_(eff)(delta){t(delta_eff} . Our result shows that the effective power index delta_(eff) can be enhanced and is a nonmonotonic function of the temperature and the driving force. The mixture of the two motion modes also leads to a breakdown of the hysteresis loop of the mobility.

17.
Phys Rev E ; 95(3-1): 032107, 2017 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-28415276

RESUMEN

We study a frequency-dependent damping model of hyperdiffusion within the generalized Langevin equation. The model allows for the colored noise defined by its spectral density, assumed to be proportional to ω^{δ-1} at low frequencies with 0<δ<1 (sub-Ohmic damping) or 1<δ<2 (super-Ohmic damping), where the frequency-dependent damping is deduced from the noise by means of the fluctuation-dissipation theorem. It is shown that for super-Ohmic damping and certain parameters, the diffusive process of the particle in a titled periodic potential undergos sequentially four time regimes: thermalization, hyperdiffusion, collapse, and asymptotical restoration. For analyzing transition phenomenon of multidiffusive states, we demonstrate that the first exist time of the particle escaping from the locked state into the running state abides by an exponential distribution. The concept of an equivalent velocity trap is introduced in the present model; moreover, reformation of ballistic diffusive system is also considered as a marginal situation but does not exhibit the collapsed state of diffusion.

18.
Phys Rev E Stat Nonlin Soft Matter Phys ; 73(6 Pt 1): 061103, 2006 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-16906805

RESUMEN

Heat conduction in a one-dimensional non-Markovian damping channel between two heat baths separated by a finite distance is studied numerically. It is found that the Fourier heat law is not obeyed for a finite-size underdamped channel under a Gaussian white noise and the coefficient of heat conductivity is a nonmonotonic function of the channel length in the sub-Ohmic damping case. The key dynamic feature is that the system does not approach the stationary state when it arrives at the cold bath for the former, and the system exhibits different diffusive behaviors from ballistic diffusion to subdiffusion at initial and asymptotic periods of time for the latter. We evaluate a damping-dependent critical separation size between two heat baths above which the heat conductivity becomes independent of the separation.

19.
Phys Rev E Stat Nonlin Soft Matter Phys ; 73(3 Pt 1): 031103, 2006 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-16605496

RESUMEN

Diffusive behavior of a particle in a two-dimensional random correlated potential with Gaussian distribution and exponential correlation is investigated via Langevin simulation. Our results show that superdiffusion appears only in the early period of the time of evolution and there does not exist an intermediate time for the occurrence of the whole issue from subdiffusion to superdiffusion. Whether the asymptotic situation of the particle could be arrived before the simulation stops is strongly influenced by the finite-size effect of the random correlated potential simulated. By applying the random correlated potential to the decay of a metastable system, we find that the escape rate of a particle is decreased by hill effect of the random potential.

20.
Phys Rev E Stat Nonlin Soft Matter Phys ; 74(4 Pt 1): 041125, 2006 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-17155040

RESUMEN

We present numerical studies of anomalous diffusion in periodic potentials by simulating a generalized Langevin equation. It is proved that the particle driven by a thermal colored noise with the spectral density vanishing at zero frequency allows superdiffusive motion. It is found that the system subjected to sub- or superohmic damping exhibits two motion modes in a corrugated plane: running oscillated state and mixed running and oscillating states, respectively. Induced, the anomalous power can be enhanced up twice for the latter case and thus a wide range of diffusive regimes is observed with changing titled force.

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