Bottom-up derived flexible water model with dipole and quadrupole moments for coarse-grained molecular simulations

2020 ◽  
Vol 22 (46) ◽  
pp. 27394-27412
Author(s):  
Chen Li ◽  
Zhongyuan Qin ◽  
Wei Han
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained ◽  
Water Model ◽  
Quadrupole Moments ◽  
Bottom Up ◽  
Structural Correlation

A bottom-up CG water model is developed to capture the electrostatic multipoles, structural correlation and thermodynamics of water.

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.

scholarly journals Temperature and Phase Transferable Bottom-up Coarse-Grained Models

2020 ◽  
Vol 16 (11) ◽  
pp. 6823-6842 ◽  
Author(s):  
Jaehyeok Jin ◽  
Alvin Yu ◽  
Gregory A. Voth
Keyword(s):  
Coarse Grained ◽  
Bottom Up

scholarly journals A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model

2019 ◽  
Vol 151 (4) ◽  
pp. 044111 ◽  
Author(s):  
Tanmoy Sanyal ◽  
Jeetain Mittal ◽  
M. Scott Shell
Keyword(s):  
Coarse Grained ◽  
Bottom Up ◽  
Protein Model
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