☆ 4.7 Article

Generalized Langevin equation with a nonlinear potential of mean force and nonlinear memory friction from a hybrid projection scheme

PHYSICAL REVIEW E (2022)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Chemistry, Physical

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

Florian N. Bruenig et al.

Summary: In this study, ab initio simulations were performed to investigate the friction functions and effective bond potentials for the OH stretch and HOH bend vibrations in liquid water. The results showed that intermolecular interactions resulted in the softening of the stretch and bend potentials, leading to a red-shift of the vibrational bands. However, nonadiabatic friction contributions caused a blue shift in the spectra. The observed line broadening in liquid water was found to be approximately equal due to adiabatic and nonadiabatic friction contributions for both the stretch and bend modes.

JOURNAL OF PHYSICAL CHEMISTRY B (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Likelihood-based non-Markovian models from molecular dynamics

Hadrien Vroylandt et al.

Summary: We introduce a method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. By using a parametrization based on hidden auxiliary variables, this method recovers both the memory kernel and random noise, providing a reduced dynamical model for multidimensional collective variables. It allows for the accurate sampling of their long-time dynamical properties at a lower computational cost, and conveniently provides other observables beyond the memory kernel or velocity-autocorrelation function.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

添加到收藏夹

Article Physics, Multidisciplinary

The interplay between memory and potentials of mean force: A discussion on the structure of equations of motion for coarse-grained observables

Fabian Glatzel et al.

Summary: The underdamped, non-linear, generalized Langevin equation is widely used in modeling coarse-grained dynamics of soft and biological materials. This study highlights the importance of approximations in obtaining the equation from microscopic dynamics and discusses the implications on memory terms and fluctuation-dissipation relations. It shows that the commonly used structure with a potential of mean force, a linear memory term, and a related fluctuating force is not exact and cannot always be derived as a controlled approximation.

EPL (2021)

添加到收藏夹

Article Chemistry, Physical

Cross-correlation corrected friction in (generalized) Langevin models

Viktor Klippenstein et al.

Summary: In this study, a new approach is proposed to correct the dynamics of coarse-grained models by including memory effects, leading to more accurate simulation results and revealing previously neglected important factors in simulations.

JOURNAL OF CHEMICAL PHYSICS (2021)

添加到收藏夹

Review Chemistry, Physical

Introducing Memory in Coarse-Grained Molecular Simulations

Viktor Klippenstein et al.

Summary: Preserving the correct dynamics at the coarse-grained (CG) level is crucial in soft matter simulation, with efforts focused on establishing a connection between CG and fine-grained (FG) dynamics based on statistical mechanics approaches. Successful attempts include CG models based on the Mori-Zwanzig (MZ) theory, resulting in generalized Langevin equations (GLE) that closely preserve FG dynamics. This review discusses recent studies in constructing and simulating systematic CG models based on GLE, while also exploring physical effects of memory and highlighting future challenges and directions.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Non-Markovian modeling of protein folding

Cihan Ayaz et al.

Summary: By extracting the folding free energy landscape and time-dependent friction function using explicit-water MD simulations, the study demonstrates the robustness of a non-Markovian model based on the generalized Langevin equation (GLE). In contrast, Markovian models fail to accurately describe peptide kinetics, highlighting the importance of memory friction effects predicted by the Grote-Hynes theory in speeding up peptide folding and unfolding kinetics and causing anomalous diffusion in configuration space. The methods presented are applicable to various reaction coordinates and potentially to experimental trajectories from single-molecule experiments, emphasizing the necessity of considering memory friction effects in a consistent description of protein-folding dynamics.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

添加到收藏夹

Article Chemistry, Physical

Use the force! Reduced variance estimators for densities, radial distribution functions, and local mobilities in molecular simulations

Benjamin Rotenberg

JOURNAL OF CHEMICAL PHYSICS (2020)

添加到收藏夹

Article Physics, Multidisciplinary

Cyclization and Relaxation Dynamics of Finite-Length Collapsed Self-Avoiding Polymers

Julian Kappler et al.

PHYSICAL REVIEW LETTERS (2019)

添加到收藏夹

Article Chemistry, Physical

The multi-dimensional generalized Langevin equation for conformational motion of proteins

Hee Sun Lee et al.

JOURNAL OF CHEMICAL PHYSICS (2019)

添加到收藏夹

Article Chemistry, Physical

Mass-Dependent Solvent Friction of a Hydrophobic Molecule

Jan O. Daldrop et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

添加到收藏夹

Article Chemistry, Physical

Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular Folding

Rohit Satija et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

添加到收藏夹

Article Physics, Fluids & Plasmas

Memory-kernel extraction for different molecular solutes in solvents of varying viscosity in confinement

Bartosz Kowalik et al.

PHYSICAL REVIEW E (2019)

添加到收藏夹

Article Multidisciplinary Sciences

Butane dihedral angle dynamics in water is dominated by internal friction

Jan O. Daldrop et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

添加到收藏夹

Article Chemistry, Physical

Transition Path Times in Non-Markovian Activated Rate Processes

Eduardo Medina et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

添加到收藏夹

Article Chemistry, Physical

On the non-stationary generalized Langevin equation

Hugues Meyer et al.

JOURNAL OF CHEMICAL PHYSICS (2017)

添加到收藏夹

Article Chemistry, Physical

Iterative Reconstruction of Memory Kernels

Gerhard Jung et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

添加到收藏夹

Article Chemistry, Physical

Applicability of the Caldeira-Leggett Model to Vibrational Spectroscopy in Solution

Fabian Gottwald et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2015)

添加到收藏夹

Article Multidisciplinary Sciences

Structural origin of slow diffusion in protein folding

Hoi Sung Chung et al.

SCIENCE (2015)

添加到收藏夹

Article Chemistry, Physical

Two algorithms to compute projected correlation functions in molecular dynamics simulations

Antoine Carof et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

添加到收藏夹

Article Biochemical Research Methods

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Sander Pronk et al.

BIOINFORMATICS (2013)

添加到收藏夹

Article Multidisciplinary Sciences

Native contacts determine protein folding mechanisms in atomistic simulations

Robert B. Best et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

添加到收藏夹

Article Multidisciplinary Sciences

Resonances arising from hydrodynamic memory in Brownian motion

Thomas Franosch et al.

NATURE (2011)

添加到收藏夹

Article Multidisciplinary Sciences

How Fast-Folding Proteins Fold

Kresten Lindorff-Larsen et al.

SCIENCE (2011)

添加到收藏夹

Article Chemistry, Physical

Mori-Zwanzig formalism as a practical computational tool

Carmen Hijon et al.

FARADAY DISCUSSIONS (2010)

添加到收藏夹

Article Multidisciplinary Sciences

Computing generalized Langevin equations and generalized Fokker-Planck equations

Eric Darve et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

添加到收藏夹

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

添加到收藏夹

Article Multidisciplinary Sciences

Ultrafast carbon-carbon single-bond rotational isomerization in room-temperature solution

Junrong Zheng et al.

SCIENCE (2006)

添加到收藏夹

Article Chemistry, Physical

Collective Langevin dynamics of conformational motions in proteins

Oliver F. Lange et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

添加到收藏夹

Article Chemistry, Physical

A general purpose model for the condensed phases of water: TIP4P/2005

JLF Abascal et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

添加到收藏夹

Article Chemistry, Multidisciplinary

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6

C Oostenbrink et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

添加到收藏夹

Review Chemistry, Physical

A new approach to calculating the memory kernel of the generalized quantum master equation for an arbitrary system-bath coupling

Q Shi et al.

JOURNAL OF CHEMICAL PHYSICS (2003)

添加到收藏夹

Article Multidisciplinary Sciences

Optimal prediction and the Mori-Zwanzig representation of irreversible processes

AJ Chorin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.