Coarse-grained models of protein folding: toy models or predictive tools?
C Clementi - Current opinion in structural biology, 2008 - Elsevier
Coarse-grained models are emerging as a practical alternative to all-atom simulations for
the characterization of protein folding mechanisms over long time scales. While a decade …
the characterization of protein folding mechanisms over long time scales. While a decade …
Recent progress in adaptive multiscale molecular dynamics simulations of soft matter
SO Nielsen, RE Bulo, PB Moore… - Physical Chemistry …, 2010 - pubs.rsc.org
Understanding mesoscopic phenomena in terms of the fundamental motions of atoms and
electrons poses a severe challenge for molecular simulation. This challenge is being met by …
electrons poses a severe challenge for molecular simulation. This challenge is being met by …
A Coste, E Slejko, J Zavadlav… - Journal of chemical …, 2023 - ACS Publications
Molecular dynamics (MD) simulations of biophysical systems require accurate modeling of
their native environment, ie, aqueous ionic solution, as it critically impacts the structure and …
their native environment, ie, aqueous ionic solution, as it critically impacts the structure and …
Adaptive resolution simulation of liquid water
Water plays a central role in biological systems and processes, and is equally relevant in a
large range of industrial and technological applications. Being the most important natural …
large range of industrial and technological applications. Being the most important natural …
[HTML][HTML] Molecular systems with open boundaries: Theory and simulation
Typical experimental setups for molecular systems must deal with a certain coupling to the
external environment, that is, the system is open and exchanges mass, momentum, and …
external environment, that is, the system is open and exchanges mass, momentum, and …
Thermostats and thermostat strategies for molecular dynamics simulations of nanofluidics
The thermostats in molecular dynamics (MD) simulations of highly confined channel flow
may have significant influences on the fidelity of transport phenomena. In this study, we …
may have significant influences on the fidelity of transport phenomena. In this study, we …
Concurrent triple-scale simulation of molecular liquids
We present a triple-scale simulation of a molecular liquid, in which the atomistic, coarse-
grained, and continuum descriptions of the liquid are concurrently coupled. The presented …
grained, and continuum descriptions of the liquid are concurrently coupled. The presented …
A review of current progress in multiscale simulations for fluid flow and heat transfer problems: The frameworks, coupling techniques and future perspectives
Many heat transfer and fluid flow problems are multiscale in nature, and the multiscale
numerical methods are needed to solve the problems by considering the phenomena in all …
numerical methods are needed to solve the problems by considering the phenomena in all …
From adaptive resolution to molecular dynamics of open systems
We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on
discussing its basic principles and presenting its current numerical and theoretical …
discussing its basic principles and presenting its current numerical and theoretical …