Perspective: Advances, challenges, and insight for predictive coarse-grained models

WG Noid - The Journal of Physical Chemistry B, 2023 - ACS Publications
By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …

Simulation strategies for ReaxFF molecular dynamics in coal pyrolysis applications: A review

S Liu, L Wei, Q Zhou, T Yang, S Li, Q Zhou - Journal of Analytical and …, 2023 - Elsevier
Research on pyrolysis mechanisms has attracted significant attention as they can efficiently
assist in coal resource utilization. Although experimental techniques have significant …

LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

AP Thompson, HM Aktulga, R Berger… - Computer physics …, 2022 - Elsevier
Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …

Electrocatalytic synthesis of adipic acid coupled with H2 production enhanced by a ligand modification strategy

Z Li, X Li, H Zhou, Y Xu, SM Xu, Y Ren, Y Yan… - Nature …, 2022 - nature.com
Adipic acid is an important building block of polymers, and is commercially produced by
thermo-catalytic oxidation of ketone-alcohol oil (a mixture of cyclohexanol and …

Structural analysis of molecular materials using the pair distribution function

MW Terban, SJL Billinge - Chemical Reviews, 2021 - ACS Publications
This is a review of atomic pair distribution function (PDF) analysis as applied to the study of
molecular materials. The PDF method is a powerful approach to study short-and …

Supramolecular polymers in aqueous media

E Krieg, MMC Bastings, P Besenius… - Chemical …, 2016 - ACS Publications
This review discusses one-dimensional supramolecular polymers that form in aqueous
media. First, naturally occurring supramolecular polymers are described, in particular …

Pragmatic coarse-graining of proteins: models and applications

L Borges-Araújo, I Patmanidis, AP Singh… - Journal of Chemical …, 2023 - ACS Publications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

Perspective on the Martini model

SJ Marrink, DP Tieleman - Chemical Society Reviews, 2013 - pubs.rsc.org
The Martini model, a coarse-grained force field for biomolecular simulations, has found a
broad range of applications since its release a decade ago. Based on a building block …

Improved parameters for the martini coarse-grained protein force field

DH De Jong, G Singh, WFD Bennett… - Journal of chemical …, 2013 - ACS Publications
The Martini coarse-grained force field has been successfully used for simulating a wide
range of (bio) molecular systems. Recent progress in our ability to test the model against …

Martini 3 coarse‐grained force field: small molecules

R Alessandri, J Barnoud, AS Gertsen… - Advanced Theory …, 2022 - Wiley Online Library
The recent re‐parametrization of the Martini coarse‐grained force field, Martini 3, improved
the accuracy of the model in predicting molecular packing and interactions in molecular …