In this paper we present an algorithm which allows single-stage direct Langevin dynamics simulations of transitions over arbitrary high energy barriers employing the concept of the energy-dependent temperature (EDT). In our algorithm, simulation time required for the computation of the corresponding switching rate does not increase with energy barrier. This is achieved by using in simulations an effective temperature which depends on the system energy: around the energy minima this temperature is high and tends towards the room temperature when the energy approaches the saddle point value. Switching times computed via our EDT algorithm show an excellent agreement with results obtained with the established forward flux sampling (FFS) method. As the simulation time required by our method does not increase with the energy barrier, we achieve a very large speedup when compared even to the highly optimized FFS version. In addition, our method does not suffer from stability problems occurring in multi-stage algorithms (like FFS and 'energy bounce' methods) due to the multiplication of a large number of transition probabilities between the interfaces.
The non--static generalized Langevin equation and its corresponding Fokker--Planck equation for the position of a viscous fluid particle were solved in closed form for a time dependent external force. Its solution for a constant external force was obtained analytically. The non--Markovian stochastic differential equation, associated to the dynamics of the position under a colored noise, was then applied to the description of the dynamics and persistence time of particles constrained within absorbing barriers. Comparisons with molecular dynamics were very satisfactory.
Bistable systems present two degenerate metastable configurations separated by an energy barrier. Thermal or quantum fluctuations can promote the transition between the configurations at a rate which depends on the dynamical properties of the local environment (i.e., a thermal bath). In the case of classical systems, strong system-bath interaction has been successfully modelled by the Generalised Langevin Equation (GLE) formalism. Here we show that the efficient GLE algorithm introduced in Phys. Rev. B 89, 134303 (2014) can be extended to include some crucial aspects of the quantum fluctuation…
Initial stages of thin film growth in the presence of island-edge barriers
研究了一种亚单层薄膜生长模型，在该模型中原子与岛边缘的附着受到能垒的阻碍。预测了岛密度N_s作为通量F和温度T的函数的新行为。例如，N_s与F^X成比例，其中X= 2 i ^*/（i^*+3），其中i^* 是临界岛尺寸，与标准结果X=i^*/（i^*+2）形成对比。该理论适用于表面活性剂介导的生长和化学气相沉积。它解释了最近的实验，这些实验与标准理论不一致。
Non-Gaussian Fluctuation and Non-Markovian Effect in the Nuclear Fusion Process: Langevin Dynamics Emerging from Quantum Molecular Dynamics Simulations
We propose a novel stochastic method to generate Brownian paths conditioned to start at an initial point and end at a given final point during a fixed time $t_{f}$ under a given potential $U(x)$. These paths are sampled with a probability given by the overdamped Langevin dynamics. We show that these paths can be exactly generated by a local Stochastic Partial Differential Equation (SPDE). This equation cannot be solved in general. We present several approximations that are valid either in the low temperature regime or in the presence of barrier crossing. We show that this method warrants the g…
We analyze multiple new issues concerning activated relaxation in glassy hard sphere fluids and molecular and polymer liquids based on the Elastically Collective Nonlinear Langevin Equation (ECNLE) theory. By invoking a high temperature reference state, a near universality of the apparent dynamic localization length scale is predicted for liquids of widely varying fragility, a result that is relevant to recent simulation studies and quasi-elastic neutron scattering measurements. In contrast, in the same format strongly non-universal behavior is found for the activation barrier that controls lo…
We introduce a generalized Langevin model system for different non-Markovian effects in the well and barrier regions of a potential, and use it to numerically study the dependence of the barrier-crossing time. In the appropriate limits, our model interpolates between the theoretical barrier-crossing-time predictions by Grote and Hynes (GH), as well as by Pollak et al., which for a single barrier memory time can differ by several orders of magnitude. Our model furthermore allows to test an analytic rate theory for space-inhomogeneous memory, which disagrees with our numerical results in the lon…
We present a path integral formalism to compute potentials for nonequilibrium steady states, reached by a multiplicative stochastic dynamics. We develop a weak-noise expansion, which allows the explicit evaluation of the potential in arbitrary dimensions and for any stochastic prescription. We apply this general formalism to study noise-induced phase transitions. We focus on a class of multiplicative stochastic lattice models and compute the steady state phase diagram in terms of the noise intensity and the lattice coupling. We obtain, under appropriate conditions, an ordered phase induced by …
We study a polar tracer, having a concave surface, immersed in a two-dimensional suspension of active particles. Using Brownian dynamics simulations, we measure the distributions and auto-correlation functions of forces and torque exerted by active particles on the tracer. The tracer experiences a finite average force along its polar axis, while all the correlation functions show exponential decay in time. Using these insights we construct the full coarse-grained Langevin description for tracer position and orientation, where the active particles are subsumed into an effective self-propulsion …
The waiting time distribution (WTD) is a common tool for analysing discrete stochastic processes in classical and quantum systems. However, there are many physical examples where the dynamics is continuous and only approximately discrete, or where it is favourable to discuss the dynamics on a discretized and a continuous level in parallel. An example is the hindered motion of particles through potential landscapes with barriers. In the present paper we propose a consistent generalisation of the WTD from the discrete case to situations where the particles perform continuous barrier-crossing cha…
We investigate memory effects in barrier-crossing in the overdamped setting. We focus on the scenario where the hidden degrees of freedom relax on exactly the same time scale as the observable. As a prototypical model, we analyze tagged-particle diffusion in a single file confined to a bi-stable potential. We identify the signatures of memory and explain their origin. The emerging memory is a result of the projection of collective many-body eigenmodes onto the motion of a tagged-particle. We are interested in the "confining" (all background particles in front of the tagged-particle) and "pushi…
A common problem that affects simulations of complex systems within the computational physics and chemistry communities is the so-called sampling problem or rare event problem where proper sampling of energy landscapes is impeded by the presences of high kinetic barriers that hinder transitions between metastable states on typical simulation time scales. Many enhanced sampling methods have been developed to address this sampling problem and more efficiently sample rare event systems. An interesting idea, coming from the field of statistics, was introduced in a recent work (Y. Lu, J. Lu, and J.…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized Langevin equation until the latter reproduces in a faithful way a set of molecular dynamics trajectories. In particular, using solvated proline dipeptide as a test case, we report evidence that ~100 short trajectories initiated at the top of a high barrier encode all the information needed to reconstruct free energy, friction, and mass profiles, including non-Mark…
We focus on the energy landscape of a simple mean-field model of glasses and analyze activated barrier-crossing by combining the Kac-Rice method for high-dimensional Gaussian landscapes with dynamical field theory. In particular, we consider Langevin dynamics at low temperature in the energy landscape of the pure spherical $p$-spin model. We select as initial condition for the dynamics one of the many unstable index-1 saddles in the vicinity of a reference local minimum. We show that the associated dynamical mean-field equations admit two solutions: one corresponds to falling back to the origi…
The dielectric response of non-interacting dipoles is discussed in the framework of the classical model of stochastic reorientations in an asymmetric double well potential (ADWP). In the nonlinear regime, this model exhibits some pecularities in the static response. We find that the saturation behavior of the symmetric double well potential model does not follow the Langevin function and only in the linear regime the standard results are recovered. If a finite asymmetry is assumed, the nonlinear susceptibilities are found to change the sign at a number of characteristic temperatures that depen…
The time evolution of the thermally activated decay rates is considered. This evolution is of particular importance for the recent nanoscale experiments discussed in the literature, where the potential barrier is relatively low (or the temperature is relatively high). The single-molecule pulling is one example of such experiments. The decay process is modeled in the present work through computer solving the stochastic (Langevin) equations. Altogether about a hundred of high precision rates have been obtained and analyzed. The rates are registered at the absorption point located far beyond the …
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular trajectories, a direct evaluation of friction is far more elusive, and one typically evaluates it indirectly via memoryless reaction rate theories. Here, using memory-kernel extraction methods founded on a generalised Langevin equation (GLE) formalism, we directly calculate the memory-dependent friction for eight fast-folding proteins, taken from a published se…
