Bottom-up coarse-graining: Principles and perspectives

J Jin, 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 …

Chemically specific coarse‐graining of polymers: Methods and prospects

S Dhamankar, MA Webb - Journal of Polymer Science, 2021 - Wiley Online Library
Coarse‐grained (CG) modeling is an invaluable tool for the study of polymers and other soft
matter systems due to the span of spatiotemporal scales that typify their physics and …

Modeling and simulations of polymers: a roadmap

TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

PWJM Frederix, I Patmanidis, SJ Marrink - Chemical Society Reviews, 2018 - pubs.rsc.org
In bionanotechnology, the field of creating functional materials consisting of bio-inspired
molecules, the function and shape of a nanostructure only appear through the assembly of …

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 …

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 DNA molecule in salt solution

J Zavadlav, R Podgornik… - Journal of chemical theory …, 2015 - ACS Publications
We present a multiscale simulation of a DNA molecule in 1 M NaCl salt solution
environment, employing the adaptive resolution simulation approach that allows the solvent …

Molecular modeling of water interfaces: From molecular spectroscopy to thermodynamics

Y Nagata, T Ohto, EHG Backus… - The Journal of Physical …, 2016 - ACS Publications
Understanding aqueous interfaces at the molecular level is not only fundamentally
important, but also highly relevant for a variety of disciplines. For instance, electrode–water …