Coarse-Grained and Atomistic Simulations for theG = 4 PAMAM-EDA Dendrimer

2015 ◽  
Vol 24 (5) ◽  
pp. 432-441 ◽  
Author(s):  
Juan J. Freire ◽  
Ana M. Rubio ◽  
Carl McBride
Keyword(s):  
Coarse Grained ◽  
Atomistic Simulations

scholarly journals Coarse-Grained and Atomistic Simulations of the Mature HIV Capsid and Related Restriction Factors

2019 ◽  
Vol 116 (3) ◽  
pp. 459a
Author(s):  
Alvin Yu ◽  
Barbie K. Ganser-Pornillos ◽  
Owen Pornillos ◽  
Gregory A. Voth
Keyword(s):  
Coarse Grained ◽  
Atomistic Simulations ◽  
Restriction Factors

scholarly journals A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

Polymers ◽  
2014 ◽  
Vol 6 (6) ◽  
pp. 1655-1675 ◽  
Author(s):  
Nikolay Korolev ◽  
Di Luo ◽  
Alexander Lyubartsev ◽  
Lars Nordenskiöld
Keyword(s):  
Monte Carlo ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Inverse Monte Carlo

Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations

2007 ◽  
Vol 69 (1) ◽  
pp. 5-13 ◽  
Author(s):  
Chia-En A. Chang ◽  
Joanna Trylska ◽  
Valentina Tozzini ◽  
J. Andrew McCammon
Keyword(s):  
Coarse Grained ◽  
Atomistic Simulations ◽  
Hiv 1

scholarly journals A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

2020 ◽  
Author(s):  
Alvin Yu ◽  
Alexander J. Pak ◽  
Peng He ◽  
Viviana Monje-Galvan ◽  
Lorenzo Casalino ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Model ◽  
Structural Data ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Current Status ◽  
Multiscale Approach ◽  
X Ray Crystallography ◽  
Coarse Grained Model ◽  
Viral Particles

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely “bottom-up” coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.Significance StatementThis study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions.

Coarse-grained simulation: a high-throughput computational approach to membrane proteins

2008 ◽  
Vol 36 (1) ◽  
pp. 27-32 ◽  
Author(s):  
Mark S.P. Sansom ◽  
Kathryn A. Scott ◽  
Peter J. Bond
Keyword(s):  
Membrane Proteins ◽  
Lipid Bilayer ◽  
High Throughput ◽  
Protein Interactions ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Lactose Permease ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations ◽  
Good Agreement

An understanding of the interactions of membrane proteins with a lipid bilayer environment is central to relating their structure to their function and stability. A high-throughput approach to prediction of membrane protein interactions with a lipid bilayer based on coarse-grained Molecular Dynamics simulations is described. This method has been used to develop a database of CG simulations (coarse-grained simulations) of membrane proteins (http://sbcb.bioch.ox.ac.uk/cgdb). Comparison of CG simulations and AT simulations (atomistic simulations) of lactose permease reveals good agreement between the two methods in terms of predicted lipid headgroup contacts. Both CG and AT simulations predict considerable local bilayer deformation by the voltage sensor domain of the potassium channel KvAP.

scholarly journals Self-Assembly of Nanoparticles Decorated by Liquid Crystalline Groups: Computer Simulations

2020 ◽  
Author(s):  
Jaroslav Ilnytskyi
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulations ◽  
Self Assembly ◽  
Surface Density ◽  
Liquid Crystalline ◽  
Terminal Group ◽  
The Self ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Group Attachment

We present the results of the computer simulations for the self-assembly of decorated nanoparticles. The models are rather generic and comprise a central core and a shell of ligands containing terminal liquid crystalline group, including the case of the azobenzene chromophores. The simulations are performed using the coarse-grained molecular dynamics with the effective soft-core interparticle interaction potentials obtained from the atomistic simulations. The discussion is centred around the set of the self-assembled morphologies in a melt of 100–200 of such decorated nanoparticles obtained upon the change of the temperature, surface density of ligands, the type of the terminal group attachment, as well as the prediction of the possibility of photo-assisted self-assembly of the nanoparticles decorated by the azobenzene chromophores.

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