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 …

The power of coarse graining in biomolecular simulations

HI Ingólfsson, CA Lopez, JJ Uusitalo… - Wiley …, 2014 - Wiley Online Library
Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

Perspective: Coarse-grained models for biomolecular systems

WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

The MARTINI force field: coarse grained model for biomolecular simulations

SJ Marrink, HJ Risselada, S Yefimov… - The journal of …, 2007 - ACS Publications
We present an improved and extended version of our coarse grained lipid model. The new
version, coined the MARTINI force field, is parametrized in a systematic way, based on the …

The MARTINI coarse-grained force field: extension to proteins

L Monticelli, SK Kandasamy, X Periole… - Journal of chemical …, 2008 - ACS Publications
Many biologically interesting phenomena occur on a time scale that is too long to be studied
by atomistic simulations. These phenomena include the dynamics of large proteins and self …

Aggregation and vesiculation of membrane proteins by curvature-mediated interactions

BJ Reynwar, G Illya, VA Harmandaris, MM Müller… - Nature, 2007 - nature.com
Abstract Membrane remodelling,,,, plays an important role in cellular tasks such as
endocytosis, vesiculation and protein sorting, and in the biogenesis of organelles such as …

Nanoporous graphene as a reverse osmosis membrane: recent insights from theory and simulation

D Cohen-Tanugi, JC Grossman - Desalination, 2015 - Elsevier
In this review, we examine the potential and the challenges of designing an ultrathin reverse
osmosis (RO) membrane from graphene, focusing on the role of computational methods in …

[BUCH][B] Coarse-graining of condensed phase and biomolecular systems

GA Voth - 2008 - taylorfrancis.com
Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

Multiscale simulation of soft matter systems–from the atomistic to the coarse-grained level and back

C Peter, K Kremer - Soft Matter, 2009 - pubs.rsc.org
Many physical phenomena and properties of soft matter systems such as synthetic or
biological materials are governed by interactions and processes on a wide range of length …

[HTML][HTML] Lipids on the move: simulations of membrane pores, domains, stalks and curves

SJ Marrink, AH De Vries, DP Tieleman - Biochimica et Biophysica Acta …, 2009 - Elsevier
In this review we describe the state-of-the-art of computer simulations studies of lipid
membranes. We focus on collective lipid–lipid and lipid–protein interactions that trigger …