Bottom-up coarse-graining: Principles and perspectives

J **, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

[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 …

Rotational dynamics of a protein under shear flow studied by the Eckart frame formalism

P Papež, F Merzel, M Praprotnik - The Journal of Physical …, 2023 - ACS Publications
Proteins are natural polymers that play an essential role in both living organisms and
biotechnological applications. During certain bioprocessing steps, they can be exposed to …

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 …

Adaptive resolution molecular dynamics technique: Down to the essential

C Krekeler, A Agarwal, C Junghans… - The Journal of …, 2018 - pubs.aip.org
We investigate the role of the thermodynamic (TD) force as an essential and sufficient
technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force …

Simulation of a particle domain in a continuum, fluctuating hydrodynamics reservoir

A Gholami, R Klein, L Delle Site - Physical Review Letters, 2022 - APS
In molecular simulation and fluid mechanics, the coupling of a particle domain with a
continuum representation of its embedding environment is an ongoing challenge. In this …

Passing waves from atomistic to continuum

X Chen, A Diaz, L **ong, DL McDowell… - Journal of Computational …, 2018 - Elsevier
Progress in the development of coupled atomistic–continuum methods for simulations of
critical dynamic material behavior has been hampered by a spurious wave reflection …

Single-layer and double-layer filtration materials based on polyvinylidene fluoride-co-hexafluoropropylene nanofibers coated on melamine microfibers

T Potisk, M Remškar, L Pirker, G Filipič… - ACS applied nano …, 2023 - ACS Publications
In this work, we demonstrate selected optimization changes in the simple design of filtration
masks to increase particle removal efficiency (PRE) and filter quality factor by combining …

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 …

Multiscale simulation of fluids: coupling molecular and continuum

ER Smith, PE Theodorakis - Physical Chemistry Chemical Physics, 2024 - pubs.rsc.org
Computer simulation is an important tool for scientific progress, especially when lab
experiments are either extremely costly and difficult or lack the required resolution. However …