Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
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 …
broad range of applications since its release a decade ago. Based on a building block …
LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
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 …
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
[BOOK][B] Monte Carlo simulation in statistical physics
K Binder, DW Heermann, K Binder - 1992 - Springer
Roughly at the time (1987) when the manuscript for the first three chapters of the present
book was completed, several breakthroughs occurred. They had a profound influence on the …
book was completed, several breakthroughs occurred. They had a profound influence on the …
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 …
range of (bio) molecular systems. Recent progress in our ability to test the model against …
Machine learning of coarse-grained molecular dynamics force fields
Atomistic or ab initio molecular dynamics simulations are widely used to predict
thermodynamics and kinetics and relate them to molecular structure. A common approach to …
thermodynamics and kinetics and relate them to molecular structure. A common approach to …
Perspective: Dissipative particle dynamics
Dissipative particle dynamics (DPD) belongs to a class of models and computational
algorithms developed to address mesoscale problems in complex fluids and soft matter in …
algorithms developed to address mesoscale problems in complex fluids and soft matter in …
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 …
grained (CG) models provide significant computational and conceptual advantages with …
Airborne transmission of COVID-19: aerosol dispersion, lung deposition, and virus-receptor interactions
Coronavirus disease 2019 (COVID-19), due to infection by the severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), is now causing a global pandemic. Aerosol …
syndrome coronavirus 2 (SARS-CoV-2), is now causing a global pandemic. Aerosol …
Polarizable water model for the coarse-grained MARTINI force field
Coarse-grained (CG) simulations have become an essential tool to study a large variety of
biomolecular processes, exploring temporal and spatial scales inaccessible to traditional …
biomolecular processes, exploring temporal and spatial scales inaccessible to traditional …