Generalized Langevin equations with non-linear forces and position-dependent linear friction memory kernels, such as commonly used to describe the effective dynamics of coarse-grained variables in molecular dynamics, are rigorously derived within the Mori-Zwanzig formalism. A fluctuation-dissipation theorem relating the properties of the noise to the memory kernel is shown. The derivation also yields Volterra-type equations for the kernel, which can be used for a numerical parametrization of the model from all-atom simulations.
We present a numerical method to produce stochastic dynamics according to the generalized Langevin equation with a non-stationary memory kernel. This type of dynamics occurs when a microscopic system with an explicitly time-dependent Liouvillian is coarse-grained by means of a projection operator formalism. We show how to replace the deterministic fluctuating force in the generalized Langevin equation by a stochastic process, such that the distributions of the observables are reproduced up to moments of a given order. Thus, in combination with a method to extract the memory kernel from simulat…
Generalized Langevin dynamics (GLD) arise in the modeling of a number of systems, ranging from structured fluids that exhibit a viscoelastic mechanical response, to biological systems, and other media that exhibit anomalous diffusive phenomena. Molecular dynamics (MD) simulations that include GLD in conjunction with external and/or pairwise forces require the development of numerical integrators that are efficient, stable, and have known convergence properties. In this article, we derive a family of extended variable integrators for the Generalized Langevin equation (GLE) with a positive Prony…
We obtain the memory kernel of the generalized Langevin equation, describing a particle interacting with longitudinal phonons in a liquid. The kernel is obtained analytically at T=0 Kelvin and numerically at T>0 Kelvin. We find that it shows some non-trivial structural features like negative correlations for some range of time separations. The system is shown to have three characteristic time scales, that control the shape of the kernel, and the transition between quadratic and linear behavior of the mean squared distance (MSD). Although the derivation of the structure in the memory kernel is …
Memory effects, sometimes, can not be neglected. In the framework of continuous time random walk, memory effect is modeled by the correlated waiting times. In this paper, we derive the two-point probability distribution of the stochastic process with correlated increments as well as the one of its inverse process, and present the Langevin description of Lévy walk with memory, i.e., correlated waiting times. Based on the built Langevin picture, the properties of aging and nonstationary are discussed. The Langevin system exhibits sub-ballistic superdiffusion if the friction force is involved, wh…
The generalized Langevin equation describes anomalous dynamics. Noise is not only the origin of uncertainty but also plays a positive role in helping to detect signal with information, termed stochastic resonance (SR). This paper analyzes the anomalous resonant behaviors of the generalized Langevin system with a multiplicative dichotomous noise and an internal tempered Mittag-Leffler noise. For the system with fluctuating harmonic potential, we obtain the exact expressions of several SR, such as, the first moment, the amplitude and the autocorrelation function for the output signal as well as …
We present an efficient method for simulating a stationary Gaussian noise with an arbitrary covariance function and then study numerically the impact of time-correlated noise on the time evolution of a 1 + 1 dimensional generalized Langevin equation by comparing also to analytical results. Finally, we apply our method to the generalized Langevin equation with an external harmonic and double-well potential.
A generalized Langevin equation with fluctuating diffusivity (GLEFD) is proposed, and it is shown that the GLEFD satisfies a generalized fluctuation-dissipation relation. If the memory kernel is a power law, the GLEFD exhibits anomalous subdiffusion, non-Gaussianity, and stretched-exponential relaxation. The case in which the memory kernel is given by a single exponential function is also investigated as an analytically tractable example. In particular, the mean-square displacement and the self-intermediate-scattering function of this system show plateau structures. A numerical scheme to integ…
A Gauss-Newton method for iterative optimization of memory kernels for generalized Langevin thermostats in coarse-grained molecular dynamics simulations
It is known that in the regime of superlinear diffusion, characterized by zero integral friction (vanishing integral of the memory function), the generalized Langevin equation may have non-ergodic solutions which do not relax to equilibrium values. It is shown that the equation may have non-ergodic (non-stationary) solutions even if the integral of the memory function is finite and diffusion is normal.
The irreversible generalized Langevin equation (iGLE) contains a nonstationary friction kernel that in certain limits reduces to the GLE with space-dependent friction. For more general forms of the friction kernel, the iGLE was previously shown to be the projection of a mechanical system with a time-dependent Hamiltonian. [R. Hernandez, J. Chem. Phys. 110, 7701 (1999)] In the present work, the corresponding open Hamiltonian system is further explored. Numerical simulations of this mechanical system illustrate that the time dependence of the observed total energy and the correlations of the sol…
The Generalized Langevin Equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general non-equilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a …
We investigate the nature of the effective dynamics and statistical forces obtained after integrating out nonequilibrium degrees of freedom. To be explicit, we consider the Rouse model for the conformational dynamics of an ideal polymer chain subject to steady driving. We compute the effective dynamics for one of the many monomers by integrating out the rest of the chain. The result is a generalized Langevin dynamics for which we give the memory and noise kernels and the effective force, and we discuss the inherited nonequilibrium aspects.
The Brownian motion of a particle immersed in a medium of charged particles is considered when the system is placed in magnetic or electric fields. Coming from the Zwanzig-Caldeira-Legget particle-bath model, we modify it so that not only the charged Brownian particle (BP) but also the bath particles respond to the external fields. For stationary systems the generalized Langevin equations are derived. Arbitrarily time-dependent electric fields do not affect the memory functions, the thermal noise force, and the BP velocity correlation functions. In the case of a constant magnetic field two equ…
In molecular dynamics simulations and single molecule experiments, observables are usually measured along dynamic trajectories and then averaged over an ensemble ("bundle") of trajectories. Under stationary conditions, the time-evolution of such averages is described by the generalized Langevin equation. In contrast, if the dynamics is not stationary, it is not a priori clear which form the equation of motion for an averaged observable has. We employ the formalism of time-dependent projection operator techniques to derive the equation of motion for a non-equilibrium trajectory-averaged observa…
We consider a system in direct contact with a thermal reservoir and which, if left unperturbed, is well described by a memory-less equilibrium Langevin equation of the second order in the time coordinate. In such conditions, the strength of the noise fluctuations is set by the damping factor, in accordance with the Fluctuation and Dissipation theorem. We study the system when it is subject to a feedback mechanism, by modifying the Langevin equation accordingly. Memory terms now arise in the time evolution, which we study in a non-equilibrium steady state. Two types of feedback schemes are cons…
Any first course on polymer physics teaches that the dynamics of a tagged monomer of a polymer is anomalously subdiffusive, i.e., the mean-square displacement of a tagged monomer increases as $t^α$ for some $α<1$ until the terminal relaxation time $τ$ of the polymer. Beyond time $τ$ the motion of the tagged monomer becomes diffusive. Classical examples of anomalous dynamics in polymer physics are single polymeric systems, such as phantom Rouse, self-avoiding Rouse, self-avoiding Zimm, reptation, translocation through a narrow pore in a membrane, and many-polymeric systems such as polymer melts…
Generating an initial condition for a Langevin equation with memory is a non trivial issue. We introduce a generalisation of the Laplace transform as a useful tool for solving this problem, in which a limit procedure may send the extension of memory effects to arbitrary times in the past. This method allows us to compute average position, work, their variances and the entropy production rate of a particle dragged in a complex fluid by an harmonic potential, which could represent the effect of moving optical tweezers. For initial conditions in equilibrium we generalise the results by van Zon an…
We present an exact functional formalism to deal with linear Langevin equations with arbitrary memory kernels and driven by any noise structure characterized through its characteristic functional. No others hypothesis are assumed over the noise, neither the fluctuation dissipation theorem. We found that the characteristic functional of the linear process can be expressed in terms of noise's functional and the Green function of the deterministic (memory-like) dissipative dynamics. This object allow us to get a procedure to calculate all the Kolmogorov hierarchy of the non-Markov process. As exa…
We derive a quantum Langevin equation for a quantum spin in the presence of a magnetic field and study its dynamics in the Markovian limit using the Ohmic bath model. We extend our analysis to the Drude bath with a finite memory. We study the time evolution of the expectation values of the magnetic moments. The spin auto-correlation functions exhibit a damped oscillatory behaviour with the randomization time being determined by the damping rate and also the memory time for the Drude bath model. We also analyse the spin response function of the system for the Ohmic bath model. Our results are c…
It is shown that the solution of generalized Langevin equation can be obtained on the basis of simple comparison of the time scale for the velocity autocorrelation function of a particle (atom, molecule) and of the time scale for the corresponding memory function. The result expression for the velocity autocorrelation function contains dependence on the non-Markovity parameter, which allows one to take into account memory effects of the investigated phenomena. It is demonstrated for the cases of liquid tin and liquid lithium that the obtained expression for the velocity autocorrelation functio…
Anomalous diffusion in coupled viscoelastic media: A fractional Langevin equation approach
Pohang University of Science and Technology（浦项科技大学）；Institute for Theoretical Science, Pohang University of Science and Technology（浦项科技大学理论科学研究所）；Asia Pacific Center for Theoretical Physics（亚太理论物理中心）
Recent advances in single particle tracking and supercomputing techniques demonstrate the emergence of normal or anomalous, viscoelastic diffusion in conjunction with non-Gaussian distributions in soft, biological, and active matter systems. We here formulate a stochastic model based on a generalised Langevin equation in which non-Gaussian shapes of the probability density function and normal or anomalous diffusion have a common origin, namely a random parametrisation of the stochastic force. We perform a detailed analytical analysis demonstrating how various types of parameter distributions f…
We present a numerical method to compute non-equilibrium memory kernels based on experimental data or molecular dynamics simulations. The procedure uses a recasting of the non-stationary generalized Langevin equation, in which we expand the memory kernel in a series that can be reconstructed iteratively. Each term in the series can be computed based solely on knowledge of the two-time auto-correlation function of the observable of interest. As a proof of principle, we apply the method to crystallization from a super-cooled Lennard Jones melt. We analyze the nucleation and growth dynamics of cr…
We discuss how the first order Langevin equation for the overdamped dynamics of an interacting system has a natural time reversal of simple but surprising form, with consequences for correlation functions. This leads to the correlation of interactions as a strictly restraining term in the time-dependent diffusion tensor of the system, deriving the relation first suggested by Fixman. Applying this to the time-dependent diffusion of dilute polymer coils leads to the quantitative calibration of Kirkwood's approximation for their hydrodynamic radius. We find the generalized ``Fixman Law" for dissi…
We consider the stochastic dynamics of a system linearly coupled to a hierarchical thermal bath with two well-separated inherent timescales: one slow, and one fast. The slow part of the bath is modeled as a set of harmonic oscillators and taken into account explicitly, while the effects of the fast part of the bath are simulated by dissipative and stochastic Langevin forces, uncorrelated in space and time, acting on oscillators of the slow part of the bath. We demonstrate for this model the robust emergence of a fractional Langevin equation with a power-law decaying memory kernel. The conditio…
We consider the two- (2D) and three-dimensional (3D) Ising model on a square lattice at the critical temperature $T_c$, under Monte-Carlo spin flip dynamics. The bulk magnetisation and the magnetisation of a tagged line in the 2D Ising model, and the bulk magnetisation and the magnetisation of a tagged plane in the 3D Ising model exhibit anomalous diffusion. Specifically, their mean-square displacement increases as power-laws in time, collectively denoted as $\sim t^c$, where $c$ is the anomalous exponent. We argue that the anomalous diffusion in all these quantities for the Ising model stems …
Diffusion in nonhomogeneous media is described by a dynamical process driven by a general Levy noise and subordinated to a random time; the subordinator depends on the position. This problem is approximated by a multiplicative process subordinated to a random time: it separately takes into account effects related to the medium structure and the memory. Density distributions and moments are derived from the solutions of the corresponding Langevin equation and compared with the numerical calculations for the exact problem. Both subdiffusion and enhanced diffusion are predicted. Distribution of t…
We consider the non-Markovian Langevin evolution of a dissipative dynamical system in quantum mechanics in the path integral formalism. After discussing the role of the frequency cutoff for the interaction of the system with the heat bath and the kernel and noise correlator that follow from the most common choices, we derive an analytic expansion for the exact non-Markovian dissipation kernel and the corresponding colored noise in the general case that is consistent with the fluctuation-dissipation theorem and incorporates systematically non-local corrections. We illustrate the modifications t…
We recently showed that the dynamics of coarse-grained observables in systems out of thermal equilibrium are governed by the non-stationary generalized Langevin equation [J. Chem. Phys. 147, 214110 (2017), J. Chem. Phys. 150, 174118 (2019)]. The derivation we presented in these two articles was based on the assumption that the dynamics of the microscopic degrees of freedom was deterministic. Here we extend the discussion to stochastic microscopic dynamics. The fact that the non-stationary Generalized Langevin Equation also holds for stochastic processes implies that methods designed to estimat…
Financial market dynamics is rigorously studied via the exact generalized Langevin equation. Assuming market Brownian self-similarity, the market return rate memory and autocorrelation functions are derived, which exhibit an oscillatory-decaying behavior with a long-time tail, similar to empirical observations. Individual stocks are also described via the generalized Langevin equation. They are classified by their relation to the market memory as heavy, neutral and light stocks, possessing different kinds of autocorrelation functions.
In the Langevin formalism, the delicate balance maintained between the fluctuations in the system and their corresponding dissipation may be upset by the presence of a secondary, space-dependent stochastic force, particularly in the low friction regime. In prior work, the latter was dissipated self-consistently through an additional uniform (mean-field) friction [Shepherd and Hernandez, J. Chem. Phys., 115, 2430-2438 (2001).] An alternative approach to ensure that equipartition is satisfied relies on the use of a space-dependent friction while ignoring nonlocal correlations. The approach is ev…
In this paper, we study the diffusive limit of solutions to the generalized Langevin equation (GLE) in a periodic potential. Under the assumption of quasi-Markovianity, we obtain sharp longtime equilibration estimates for the GLE using techniques from the theory of hypocoercivity. We then prove asymptotic results for the effective diffusion coefficient in three limiting regimes: the short memory, the overdamped and the underdamped limits. Finally, we employ a recently developed spectral numerical method in order to calculate the effective diffusion coefficient for a wide range of (effective) f…
The methods of Nuclear Magnetic Resonance belong to the best developed and often used tools for studying random motion of particles in different systems, including soft biological tissues. In the long-time limit the current mathematical description of the experiments allows proper interpretation of measurements of normal and anomalous diffusion. The shorter-time dynamics is however correctly considered only in a few works that do not go beyond the standard memoryless Langevin description of the Brownian motion (BM). In the present work, the attenuation function S(t) for an ensemble of spin-bea…
Hydrodynamic memory in overdamped colloidal dynamics
Princeton Center for Theoretical Science, Princeton University（普林斯顿大学理论物理中心）；Princeton Materials Institute, Princeton University（普林斯顿大学材料研究所）；Department of Mechanical and Aerospace Engineering, Princeton University（普林斯顿大学机械与航空航天工程系）
The generalised Langevin equation with a retarded friction and a double-well potential is solved. The random force is modelled by a multiplicative noise with long jumps. Probability density distributions converge with time to a distribution similar to a Gaussian but tails have a power-law form. Dependence of the mean first passage time on model parameters is discussed. Properties of the stochastic resonance, emerging as a peak in the plot of the spectral amplification against the temperature, are discussed for various sets of the model parameters. The amplification rises with the memory and is…
The memory kernel of the self-part of the intermediate scattering function is studied. We found that the short-time behavior of the memory kernel for our MD-simulated glass-forming Ni$_{20}$Zr$_{80}$-system shows a deviation from the polynomial form predicted by MCT. By using the gaussian approximation we give a more detailed description of the short-time dynamics of the system.
We relate the memory kernel in the Nakajima-Zwanzig-Mori time-convolution approach to the reduced system propagator which is often used to obtain the kernel in the Tokuyama-Mori time-convolutionless approach. The connection provides a robust and simple formalism to compute the memory kernel for a generalized system-bath model circumventing the need to compute high order system-bath observables. We illustrate this for a model system with electron-electron and electron-phonon couplings, driven away from equilibrium.
Single-file diffusion behaves as normal diffusion at small time and as anomalous subdiffusion at large time. These properties can be described by fractional Brownian motion with variable Hurst exponent or multifractional Brownian motion. We introduce a new stochastic process called Riemann-Liouville step fractional Brownian motion which can be regarded as a special case of multifractional Brownian motion with step function type of Hurst exponent tailored for single-file diffusion. Such a step fractional Brownian motion can be obtained as solution of fractional Langevin equation with zero dampi…
We study stochastic ratchets with inertia in the limit where the time correlations become important. We have developed a Fokker-Planck type equation for the ratchet problem which includes the memory effects. It is tested with comparison to the Langevin simulations. The effect of the memory in the system is analyzed extensively. A positive feedback regime which manifests itself as instabilities is observed. This may be regarded as an illustration of stochastic resonance.
Based on Sjögren und Sjolander's Mode-Coupling(MC)-Model, we have reformulated and calculated the memory kernel (MK) of the velocity autocorrelation function (VACF)on a Ni$_{0.2}$Zr$_{0.8}$-liquid. Reformulating means here that we have constructed the memory kernel of VACF for our binary system, instead of one for one atomic system of the Sjögren und Sjolander's model. The data required for the theoretical calculations have been obtained from molecular dynamics (MD) simulations. The theoretical results then are compared with those directly obtained from computer simulation. We found, although …
We study homogenization for a class of generalized Langevin equations (GLEs) with state-dependent coefficients and exhibiting multiple time scales. In addition to the small mass limit, we focus on homogenization limits, which involve taking to zero the inertial time scale and, possibly, some of the memory time scales and noise correlation time scales. The latter are meaningful limits for a class of GLEs modeling anomalous diffusion. We find that, in general, the limiting stochastic differential equations (SDEs) for the slow degrees of freedom contain non-trivial drift correction terms and are …
