Generalized Langevin Equation: An Introductory Review for Biophysicists

2019 ◽  
Vol 14 (04) ◽  
pp. 171-196
Author(s):  
Shin-Ho Chung ◽  
Michael Roper

An introductory, pedagogical review of the generalized Langevin equation (GLE) within the classical regime is presented. It is intended to be accessible to biophysicists with an interest in molecular dynamics (MD). Section 1 presents why the equation may be of interest within biophysical modeling. A detailed elementary first principles derivation of the (multidimensional) Kac–Zwanzig model is presented. The literature is reviewed with a focus on biophysical applications and representation by Markovian stochastic differential equations. The relationship with the Mori–Zwanzig formalism is discussed. The framework of model reduction and approximation is emphasized. Some open problems are identified.

2020 ◽  
Author(s):  
Forough Hassanibesheli ◽  
Niklas Boers ◽  
Jürgen Kurths

<p>A complex system is a system composed of highly interconnected components in which the collective property of an underlying system cannot be described by dynamical behavior of the individual parts. Typically, complex systems are governed by nonlinear interactions and intricate fluctuations, thus to retrieve dynamics of a system, it is required to characterize and asses interactions between deterministic tendencies and random fluctuations. </p><p>For systems with large numbers of degrees of freedom, interacting across various time scales, deriving time-evolution equations from data is computationally expensive. A possible way to circumvent this problem is to isolate a small number of relatively slow degrees of freedom that may suffice to characterize the underlying dynamics and solve the governing motion equation for the reduced-dimension system in the framework of stochastic differential equations(SDEs).  For some specific example settings, we have studied the performance of three stochastic dimension-reduction methods (Langevin equation(LE), generalized Langevin Equation(GLE) and Empirical Model Reduction(EMR)) to model various synthetic and real-world time series. In this study corresponding numerical simulations of all models have been examined by probability distribution function(PDF) and Autocorrelation function(ACF) of the average simulated time series as statistical benchmarks for assessing the differnt models' performance. </p><p>First we reconstruct the Niño-3 monthly sea surface temperature (SST) indices averages across (5°N–5°S, 150°–90°W) from 1891 to 2015 using the three aforementioned stochastic models. We demonstrate that all these considered models can reproduce the same skewed and heavy-tailed distributions of Niño-3 SST, comparing ACFs, GLE exhibits a tendency towards achieving a higher accuracy than LE and EMR. A particular challenge for deriving the underlying dynamics of complex systems from data is given by situations of abrupt transitions between alternative states. We show how the Kramers-Moyal approach to derive drift and diffusion terms for LEs can help in such situations. A prominent example of such 'Tipping Events' is given by the Dansgaard-Oeschger events during previous glacial intervals. We attempt to obtain the statistical properties of high-resolution, 20yr average, δ<sup>18</sup>O and Ca<sup>+</sup><sup>2</sup> collected from the same ice core from the NGRIP on the GICC05 time scale. Through extensive analyses of various systems, our results signify that stochastic differential equation models considering memory effects are comparatively better approaches for understanding  complex systems.</p><p> </p>


Author(s):  
Adrien Laurent ◽  
Gilles Vilmart

AbstractWe derive a new methodology for the construction of high-order integrators for sampling the invariant measure of ergodic stochastic differential equations with dynamics constrained on a manifold. We obtain the order conditions for sampling the invariant measure for a class of Runge–Kutta methods applied to the constrained overdamped Langevin equation. The analysis is valid for arbitrarily high order and relies on an extension of the exotic aromatic Butcher-series formalism. To illustrate the methodology, a method of order two is introduced, and numerical experiments on the sphere, the torus and the special linear group confirm the theoretical findings.


2016 ◽  
Author(s):  
Ιωάννης Σταματίου

Σε αυτή τη διατριβή αντικείμενο έρευνας είναι η αριθμητική επίλυση στοχαστι- κών διαφορικών εξισώσεων (ΣΔΕ), οι οποίες έχουν λύση σε ένα συγκεκριμένο χωρίο. Ο στόχος μας ειναι η κατασκευή άμεσων αριθμητικών σχημάτων τα οποία διατηρούν αυτό το χωρίο, κυρίως σε περιπτώσεις όπου οι συντελεστές των ΣΔΕ είναι μη-γραμμικοί. Είναι γνωστό ότι το με βήμα προς τα εμπρός σχήμα Euler αποκλίνει σε υπερ- γραμμικά προβλήματα και η ελεγχόμενη μέθοδος Euler δε διατηρεί απαραίτητα τη δομή του αρχικού προβλήματος. Προτείνουμε ένα νέο αριθμητικό σχήμα, χρησιμοποιώντας την Ημι-Διακριτή μέθοδο, για διάφορες κλάσεις στοχαστικών διαφορικών εξισώσεων. Για κάποια υπεργραμμικά προβλήματα (όπως το Heston 3/2-μοντέλο) καθώς και για υπο- γραμμικά (όπως το CEV μοντέλο), τα οποία εμφανίζονται στο πεδίο των χρημα- τοοικονομικών μαθηματικών, κατασκευάζουμε ένα αριθμητικό σχήμα το οποίο διατηρεί τη θετικότητα. Παραπέρα, εφαρμόζουμε τη μέθοδο μας σε προβλήματα τα οποία εμφανίζονται στο πεδίο των μοριακών δυναμικών, όπου το προτει- νόμενο σχήμα το οποίο διατηρεί τη δομή της αρχικής εξίσωσης προσεγγίζει αποτελεσματικά κάποιες ΣΔΕ οι οποίες προκύπτουν έπειτα από μια διαδικασία απλοποίησης (coarse graining ). Θεωρούμε επίσης την περίπτωση Στοχαστικών Διαφορικών Εξισώσεων με Υστέρηση με μη-αρνητικές λύσεις. Ξανά στόχος μας είναι άμεσα αριθμητικά σχήματα τα οποία διατηρούν τη θετικότητα. Επεκτείνουμε την Ημι-Διακριτή μέθοδο από το πλαίσιο των Συνήθων ΣΔΕ στην περίπτωση με σταθερή υστέρηση, όπου και αποδεικνύουμε ισχυρή σύγκλιση (μοντέλο DGBM). Αριθμητικά πειράματα υποστηρίζουν τα θεωρητικά μας αποτελέσματα.


Author(s):  
Eike H. Müller ◽  
Rob Scheichl ◽  
Tony Shardlow

This paper applies several well-known tricks from the numerical treatment of deterministic differential equations to improve the efficiency of the multilevel Monte Carlo (MLMC) method for stochastic differential equations (SDEs) and especially the Langevin equation. We use modified equations analysis as an alternative to strong-approximation theory for the integrator, and we apply this to introduce MLMC for Langevin-type equations with integrators based on operator splitting. We combine this with extrapolation and investigate the use of discrete random variables in place of the Gaussian increments, which is a well-known technique for the weak approximation of SDEs. We show that, for small-noise problems, discrete random variables can lead to an increase in efficiency of almost two orders of magnitude for practical levels of accuracy.


Nanoscale ◽  
2019 ◽  
Vol 11 (29) ◽  
pp. 14042-14049 ◽  
Author(s):  
Guoqing Wang ◽  
Bo Xu ◽  
Jing Shi ◽  
Musheng Wu ◽  
Haibin Su ◽  
...  

The effect of Si microstructures on Li diffusion in Li–Si alloys was studied by using first-principles molecular dynamics calculations. The relationship between aggregation degree of Si and Li diffusion coefficients is established.


Sign in / Sign up

Export Citation Format

Share Document