Finding transition paths and rate coefficients through accelerated Langevin dynamics.

نویسندگان

  • L Y Chen
  • S C Ying
  • T Ala-Nissila
چکیده

We present a technique to resolve the rare event problem for a Langevin equation describing a system with thermally activated transitions. A transition event within a given time interval (0,t(f)) can be described by a transition path that has an activation part during (0,t(M)) and a deactivation part during (t(M),t(f))(0<t(M)<t(f)). The activation path is governed by a Langevin equation with negative friction while the deactivation path by the standard Langevin equation with positive friction. Each transition path carries a given statistical weight from which rate constants and related physical quantities can be obtained as averages over all possible paths. We demonstrate how this technique can be used to calculate activation rates of a particle in a two dimensional potential for a wide range of temperatures where standard molecular dynamics techniques are inefficient.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Gaussian Approximations for Transition Paths in Molecular Dynamics

This paper is concerned with transition paths within the framework of the overdamped Langevin dynamics model of chemical reactions. We aim to give an efficient description of typical transition paths in the small temperature regime. We adopt a variational point of view and seek the best Gaussian approximation, with respect to Kullback-Leibler divergence, of the non-Gaussian distribution of the ...

متن کامل

Simulating rare events in equilibrium or nonequilibrium stochastic systems.

We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the phase-space density and are suitable for equilibrium or nonequilibrium systems in stationary state. All the methods use a series of interfaces in phase space, between the initial and final states, t...

متن کامل

Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations

The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...

متن کامل

Stochastic gradient method with accelerated stochastic dynamics

In this paper, we propose a novel technique to implement stochastic gradient methods, which are beneficial for learning from large datasets, through accelerated stochastic dynamics. A stochastic gradient method is based on mini-batch learning for reducing the computational cost when the amount of data is large. The stochasticity of the gradient can be mitigated by the injection of Gaussian nois...

متن کامل

Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations

Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Physical review. E, Statistical, nonlinear, and soft matter physics

دوره 65 4 Pt 1  شماره 

صفحات  -

تاریخ انتشار 2002