Well-Posedness and Long Time Behavior of Singular Langevin Stochastic Differential Equations✩ Renming Songa, Longjie Xieb,∗
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Mathematical and Algorithmic Analysis of Modified Langevin Dynamics
Zofia Trstanova Mathematical and Algorithmic Analysis of Modified Langevin Dynamics Summary In statistical physics, the macroscopic information of interest for the systems under consideration can be inferred from averages over microscopic configurations distributed according to probability measures µ characterizing the thermodynamic state of the system. Due to the high dimensionality of the system (which is proportional to the number of particles), these configurations are most often sampled using trajectories of stochastic differential equations or Markov chains ergodic for the probability measure µ, which describes a system at constant temperature. One popular stochastic process allowing to sample this measure is the Langevin dynamics. In practice, the Langevin dynamics cannot be analytically integrated, its solution is therefore approximated with a numerical scheme. The numerical analysis of such discretization schemes is by now well-understood when the kinetic energy is the standard quadratic kinetic energy. One important limitation of the estimators of the ergodic averages are their possibly large statistical errors. Under certain assumptions on potential and kinetic energy, it can be shown that a central limit theorem holds true. The asymptotic variance may be large due to the metastability of the Langevin process, which occurs as soon as the probability measure µ is multimodal. In this thesis, we consider the discretization of modified Langevin dynamics which improve the sampling of the Boltzmann–Gibbs distribution by introducing a more general kinetic energy function U instead of the standard quadratic one. We have in fact two situations in mind: (a) Adaptively Restrained (AR) Langevin dynamics, where the kinetic energy vanishes for small momenta, while it agrees with the standard kinetic energy for large momenta. -
From Stochastic to Deterministic Langevin Equations
Abstract In the first part of this thesis we review the concept of stochastic Langevin equations. We state a simple example and explain its physical meaning in terms of Brownian motion. We then calculate the mean square displacement and the velocity autocorrelation function by solving this equation. These quantities are related to the diffusion coefficient in terms of the Green-Kuba formula, and will be defined properly. In the second part of the thesis we introduce a deterministic Langevin equation which models Brownian motion in terms of deterministic chaos, as suggested in recent research literature. We solve this equation by deriving a recurrence relation. We review Takagi function techniques of dynamical systems theory and apply them to this model. We also apply the correlation function technique. Finally, we derive, for the first time, an exact formula for the diffusion coefficient as a function of a control parameter for this model. Acknowledgement I would like to thank my supervisor Dr Rainer Klages for his excellent guid- ance and support throughout my thesis work. Special thanks to Dr Wolfram Just for some useful hints. i Contents 1 Introduction 1 2 Stochastic Langevin Equation 3 2.1 What is Brownian motion? . 3 2.2 The Langevin equation . 4 2.3 Calculation of the mean square displacement . 5 2.4 Derivation of the velocity autocorrelation function . 8 3 Deterministic Langevin Equation 10 3.1 Langevin equation revisited . 10 3.2 Solving the deterministic Langevin equation . 11 3.3 Calculation of the Diffusion Coefficient . 14 3.3.1 Correlation function technique . 15 3.3.2 Takagi function technique . -
Mathematical and Algorithmic Analysis of Modified Langevin Dynamics. Mathe- Matical Physics [Math-Ph]
Mathematical and algorithmic analysis of modified Langevin dynamics Zofia Trstanova To cite this version: Zofia Trstanova. Mathematical and algorithmic analysis of modified Langevin dynamics. Mathe- matical Physics [math-ph]. Université Grenoble Alpes, 2016. English. NNT : 2016GREAM054. tel-01682721 HAL Id: tel-01682721 https://tel.archives-ouvertes.fr/tel-01682721 Submitted on 12 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour obtenir le grade de DOCTEUR DE L’UNIVERSITÉ DE GRENOBLE Spécialité : Mathématiques appliquées Arrêté ministérial : 7 août 2006 Présentée par Zofia Trstanova Thèse dirigée par Stephane Redon et codirigée par Gabriel Stoltz préparée au sein INRIA Grenoble Rhônes-Alpes et Laboratoire Jean Kuntzmann et de Ecole Doctorale Mathématiques, Sciences et Technologies de l’Information, Informatique Mathematical and Algorithmic Analysis of Modified Langevin Dynamics Thèse soutenue publiquement le 25 novembre 2016, devant le jury composé de : M. Jean-Louis Barrat Professeur à l’Université Joseph Fourier, Président M. Benedict Leimkuhler Professeur à l’Université d’Edimbourg, Rapporteur M. Grigorios A. Pavliotis Professeur à l’Imperial College London, Rapporteur M. Mathias Rousset Chargé de Recherche à l’Inria Rennes, Examinateur M. Stephane Redon Chargé de Recherche à l’Inria Rhônes-Alpes Grenoble, Directeur de thèse M. -
CLASSICAL LANGEVIN DYNAMICS DERIVED from QUANTUM MECHANICS Håkon Hoel Anders Szepessy 1. Langevin Molecular Dynamics. Langevin
DISCRETE AND CONTINUOUS doi:10.3934/dcdsb.2020135 DYNAMICAL SYSTEMS SERIES B Volume 25, Number 10, October 2020 pp. 4001{4038 CLASSICAL LANGEVIN DYNAMICS DERIVED FROM QUANTUM MECHANICS H˚akon Hoel Chair of Mathematics for Uncertainty Quantification RWTH Aachen University Germany Anders Szepessy∗ Institutionen f¨orMatematik Kungl. Tekniska H¨ogskolan 100 44 Stockholm, Sweden Abstract. The classical work by Zwanzig [J. Stat. Phys. 9 (1973) 215-220] derived Langevin dynamics from a Hamiltonian system of a heavy particle coupled to a heat bath. This work extends Zwanzig's model to a quantum system and formulates a more general coupling between a particle system and a heat bath. The main result proves, for a particular heat bath model, that ab initio Langevin molecular dynamics, with a certain rank one friction ma- trix determined by the coupling, approximates for any temperature canonical quantum observables, based on the system coordinates, more accurately than any Hamiltonian system in these coordinates, for large mass ratio between the system and the heat bath nuclei. 1. Langevin molecular dynamics. Langevin dynamics for (unit mass) particle N systems with position coordinates XL : [0; 1) ! R and momentum coordinates N PL : [0; 1) ! R , defined by dXL(t) = PL(t)dt (1) 1=2 dPL(t) = −∇λ XL(t) dt − κP¯ L(t)dt + (2¯κT ) dW (t) ; is used for instance to simulate molecular dynamics in the canonical ensemble of constant temperature T , volume and number of particles, where W denotes the standard Wiener process with N independent components. The purpose of this work is to precisely determine both the potential λ : RN ! R and the friction matrixκ ¯ 2 RN×N in this equation, from a quantum mechanical model of a molecular system including weak coupling to a heat bath. -
A Multi-Scale Method for Dynamics Simulation in Continuum Solvent
A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation Li Xiao,1,2 Qin Cai,1,2 Zhilin Li,5 Hongkai Zhao,3 and Ray Luo1,2,4 1. Departments of Biomedical Engineering, 2. Molecular Biology and Biochemistry, 3. Mathematics , and 4. Chemical Engineering and Materials Science, University of California, Irvine, CA 92697 5. Department of Mathematics, North Carolina State University, Raleigh, NC 27695 Abstract A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design. 1 Introduction To model a biomolecular system, there are different levels of approximation. The most accurate approach is the high level quantum description [1], which explicitly accounts for the electronic structures in the molecules. However the computational cost of this approach is high for large and complex biomolecular systems. The most efficient approach is the coarse-grained description [2], which averages atomic structures and properties. The intermediate approach is the atom-based description, which preserves the atomic details in molecular structures and models the effects of electronic structure through a few empirical energy terms [3]. -
Time Integrators for Molecular Dynamics
Entropy 2014, 16, 138-162; doi:10.3390/e16010138 OPEN ACCESS entropy ISSN 1099-4300 www.mdpi.com/journal/entropy Article Time Integrators for Molecular Dynamics Nawaf Bou-Rabee Department of Mathematical Sciences, Rutgers University—Camden, 311 N 5th Street, Camden, NJ 08102, USA; E-Mail: [email protected]; Tel.: +1-856-225-6093; Fax: +1-856-225-6602 Received: 19 September 2013; in revised form: 20 November 2013 / Accepted: 4 December 2013 / Published: 27 December 2013 Abstract: This paper invites the reader to learn more about time integrators for Molecular Dynamics simulation through a simple MATLAB implementation. An overview of methods is provided from an algorithmic viewpoint that emphasizes long-time stability and finite-time dynamic accuracy. The given software simulates Langevin dynamics using an explicit, second-order (weakly) accurate integrator that exactly reproduces the Boltzmann-Gibbs density. This latter feature comes from adding a Metropolis acceptance-rejection step to the integrator. The paper discusses in detail the properties of the integrator. Since these properties do not rely on a specific form of a heat or pressure bath model, the given algorithm can be used to simulate other bath models including, e.g., the widely used v-rescale thermostat. Keywords: explicit integrators; Metropolis algorithm; ergodicity; weak accuracy MSC Classification: 82C80 (Primary); 82C31, 65C30, 65C05 (Secondary) 1. Introduction Molecular Dynamics (MD) simulation refers to the time integration of Hamilton’s equations often coupled to a heat or pressure bath [1–5]. From its early use in computing equilibrium dynamics of homogeneous molecular systems [6–13] and pico- to nano-scale protein dynamics [14–23], the method has evolved into a general purpose tool for simulating statistical properties of heterogeneous molecular systems [24]. -
2 Molecular and Stochastic Dynamics
2 Molecular and stochastic dynamics In this chapter we discuss the most commonly used ensembles in molecular simulations and the different equations of motion that can be used to generate each ensemble. For generating a canonical ensemble one can use stochastic dynamics with or without inertia. The temperature in a simulation can also be maintained by coupling to a heat bath. We compare the different methods for generating constant temperature trajectories using several test systems. 7 2 Molecular and stochastic dynamics 2.1 Equations of motion We will briefly introduce two ways to describe classical dynamics. For a more thorough treatment see Goldstein [7] or Landau and Lifshitz [8]. Lagrangian dynamics Classical dynamics can be described in the most general way with the Lagrangian ap- ´Øµ proach. The equations of motion are expressed using generalized coordinates Õ . These coordinates do not have to be coordinates in the usual sense, which span a high dimensional space, like Cartesian coordinates, they should be seen as ’just’ variables. Î Ä Given the kinetic energy à and the potential energy , the Lagrangian of the system is defined as: ´Õ ´Øµ մصص Ã Î Ä (2.1) մص where is the derivative of Õ with respect to time: ´Øµ dÕ ´Øµ Õ (2.2) dØ Õ Ø The kinetic and potential can both be a function of Õ , and explicitly. Lagrange’s equations of motion are: Ä d Ä ¼ ½Æ (2.3) Ø Õ Õ d The elegance of this formulation is that it is completely independent of the choice of co- ordinates Õ.