A review of multiscale computational methods in polymeric materials

A Gooneie, S Schuschnigg, C Holzer - Polymers, 2017 - mdpi.com
Polymeric materials display distinguished characteristics which stem from the interplay of
phenomena at various length and time scales. Further development of polymer systems …

From system modeling to system analysis: The impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules

M Giulini, M Rigoli, G Mattiotti, R Menichetti… - Frontiers in Molecular …, 2021 - frontiersin.org
The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …

[HTML][HTML] Molecular systems with open boundaries: Theory and simulation

L Delle Site, M Praprotnik - Physics Reports, 2017 - Elsevier
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 …

From adaptive resolution to molecular dynamics of open systems

R Cortes-Huerto, M Praprotnik, K Kremer… - The European Physical …, 2021 - Springer
We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on
discussing its basic principles and presenting its current numerical and theoretical …

Molecular dynamics of open systems: construction of a mean‐field particle reservoir

L Delle Site, C Krekeler, J Whittaker… - Advanced Theory …, 2019 - Wiley Online Library
The simulation of open molecular systems requires explicit or implicit reservoirs of energy
and particles. Whereas full atomistic resolution is desired in the region of interest, there is …

ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation

HV Guzman, N Tretyakov, H Kobayashi… - Computer Physics …, 2019 - Elsevier
Molecular simulation is a scientific tool used in many fields including material science and
biology. This requires constant development and enhancement of algorithms within …

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

AC Fogarty, R Potestio, K Kremer - The Journal of chemical physics, 2015 - pubs.aip.org
A fully atomistic modelling of many biophysical and biochemical processes at biologically
relevant length-and time scales is beyond our reach with current computational resources …

Open boundary molecular dynamics of sheared star-polymer melts

J Sablić, M Praprotnik, R Delgado-Buscalioni - Soft Matter, 2016 - pubs.rsc.org
Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt
under isothermal conditions are performed to study the rheology and molecular structure of …

Spatially resolved thermodynamic integration: an efficient method to compute chemical potentials of dense fluids

M Heidari, K Kremer, R Cortes-Huerto… - Journal of chemical …, 2018 - ACS Publications
Many popular methods for the calculation of chemical potentials rely on the insertion of test
particles into the target system. In the case of liquids and liquid mixtures, this procedure …

A multi‐resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand‐binding site

AC Fogarty, R Potestio, K Kremer - Proteins: Structure, Function …, 2016 - Wiley Online Library
In multi‐resolution simulations, different system components are simultaneously modeled at
different levels of resolution, these being smoothly coupled together. In the case of enzyme …