CALIBRATION AND RANKING OF COARSE-GRAINED MODELS IN MOLECULAR SIMULATIONS USING BAYESIAN FORMALISM

2017 ◽  
Vol 7 (2) ◽  
pp. 99-115 ◽  
Author(s):  
Hadi Meidani ◽  
Justin B. Hooper ◽  
Dmitry Bedrov ◽  
Robert M. Kirby
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained

scholarly journals Introducing Memory in Coarse-Grained Molecular Simulations

2021 ◽  
Author(s):  
Viktor Klippenstein ◽  
Madhusmita Tripathy ◽  
Gerhard Jung ◽  
Friederike Schmid ◽  
Nico F. A. van der Vegt
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained

scholarly journals How proteins open fusion pores: insights from molecular simulations

2020 ◽  
Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller
Keyword(s):  
Free Energy ◽  
Fusion Proteins ◽  
Graphics Processing Units ◽  
Fusion Reaction ◽  
Molecular Simulations ◽  
Minimum Free Energy ◽  
Free Energy Calculations ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Graphics Processing

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.

Correlation between morphology and anisotropic transport properties of diblock copolymers melts

Soft Matter ◽  
2019 ◽  
Vol 15 (5) ◽  
pp. 851-859 ◽  
Author(s):  
Mohammed Suliman Alshammasi ◽  
Fernando A. Escobedo
Keyword(s):  
Transport Properties ◽  
Diblock Copolymers ◽  
Molecular Simulations ◽  
Coarse Grained ◽  
Anisotropic Transport

Molecular simulations of coarse-grained diblock copolymers (DBP) were conducted to study the effect of segregation strength and morphology on transport properties.

Coarse-Grained Molecular Simulations to Investigate Asphaltenes at the Oil–Water Interface

2015 ◽  
Vol 29 (3) ◽  
pp. 1597-1609 ◽  
Author(s):  
Yosadara Ruiz-Morales ◽  
Oliver C. Mullins
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained ◽  
Water Interface ◽  
Oil Water

Molecular Simulations of Thermoset Polymers Implementing Theoretical Kinetics with Top-Down Coarse-Grained Models

2020 ◽  
Vol 53 (7) ◽  
pp. 2310-2322 ◽  
Author(s):  
Amulya K. Pervaje ◽  
Joseph C. Tilly ◽  
Andrew T. Detwiler ◽  
Richard J. Spontak ◽  
Saad A. Khan ◽  
...  
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained ◽  
Top Down ◽  
Thermoset Polymers

scholarly journals Atomistic and Coarse-Grained Molecular Simulations of Mixed Lamellar/Nonlamellar Lipid Membranes

2016 ◽  
Vol 110 (3) ◽  
pp. 572a
Author(s):  
Wei Ding ◽  
Michail Palaiokostas ◽  
Wen Wang ◽  
Mario Orsi
Keyword(s):  
Lipid Membranes ◽  
Molecular Simulations ◽  
Coarse Grained
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