Literature DB >> 17677593

Data-based parameter estimation of generalized multidimensional Langevin processes.

Illia Horenko1, Carsten Hartmann, Christof Schütte, Frank Noe.   

Abstract

The generalized Langevin equation is useful for modeling a wide range of physical processes. Unfortunately its parameters, especially the memory function, are difficult to determine for nontrivial processes. We establish relations between a time-discrete generalized Langevin model and discrete multivariate autoregressive (AR) or autoregressive moving average models (ARMA). This allows a wide range of discrete linear methods known from time series analysis to be applied. In particular, the determination of the memory function via the order of the respective AR or ARMA model is addressed. The method is illustrated on a one-dimensional test system and subsequently applied to the molecular dynamics time series of a biomolecule that exhibits an interesting relationship between the solvent method used, the respective molecular conformation, and the depth of the memory.

Year:  2007        PMID: 17677593     DOI: 10.1103/PhysRevE.76.016706

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  6 in total

Review 1.  Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems.

Authors:  Paraskevi Gkeka; Gabriel Stoltz; Amir Barati Farimani; Zineb Belkacemi; Michele Ceriotti; John D Chodera; Aaron R Dinner; Andrew L Ferguson; Jean-Bernard Maillet; Hervé Minoux; Christine Peter; Fabio Pietrucci; Ana Silveira; Alexandre Tkatchenko; Zofia Trstanova; Rafal Wiewiora; Tony Lelièvre
Journal:  J Chem Theory Comput       Date:  2020-07-16       Impact factor: 6.006

2.  Quantifying multiscale noise sources in single-molecule time series.

Authors:  Christopher P Calderon; Nolan C Harris; Ching-Hwa Kiang; Dennis D Cox
Journal:  J Phys Chem B       Date:  2009-01-08       Impact factor: 2.991

3.  Extracting Kinetic and Stationary Distribution Information from Short MD Trajectories via a Collection of Surrogate Diffusion Models.

Authors:  Christopher P Calderon; Karunesh Arora
Journal:  J Chem Theory Comput       Date:  2009-01-01       Impact factor: 6.006

4.  VAMPnets for deep learning of molecular kinetics.

Authors:  Andreas Mardt; Luca Pasquali; Hao Wu; Frank Noé
Journal:  Nat Commun       Date:  2018-01-02       Impact factor: 14.919

5.  Time-Dependent Friction Effects on Vibrational Infrared Frequencies and Line Shapes of Liquid Water.

Authors:  Florian N Brünig; Otto Geburtig; Alexander von Canal; Julian Kappler; Roland R Netz
Journal:  J Phys Chem B       Date:  2022-02-15       Impact factor: 2.991

6.  Non-Markovian modeling of protein folding.

Authors:  Cihan Ayaz; Lucas Tepper; Florian N Brünig; Julian Kappler; Jan O Daldrop; Roland R Netz
Journal:  Proc Natl Acad Sci U S A       Date:  2021-08-03       Impact factor: 11.205

  6 in total

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