A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)-block-poly(ε-caprolactone) (PEG-b-PCL) micelles

2020 ◽  
Vol 22 (41) ◽  
pp. 24028-24040
Author(s):  
Maryam S. Sadeghi ◽  
Mohammad Reza Moghbeli ◽  
William A. Goddard
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Force Field ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Coarse Grain ◽  
The Novel ◽  
Poly Ethylene Glycol ◽  
P Application ◽  
Poly Ethylene

Application of the novel quantum based coarse grained force field (CGq FF) for formation of a micelle from 250 chains of 2000 Dalton CG-MePEG23-b-PCL9 block copolymer in water at 310.15 K.

Mesoscale Simulation of the Structure of Star Acrylated Poly(ethylene glycol-co-lactide) Hydrogels

2012 ◽  
Vol 1418 ◽  
Author(s):  
Seyed Sina Moeinzadeh ◽  
Esmaiel Jabbari
Keyword(s):  
Ethylene Glycol ◽  
Volume Fraction ◽  
Equations Of Motion ◽  
Dissipative Particle Dynamics ◽  
Random Force ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Poly Ethylene Glycol ◽  
The Core ◽  
Poly Ethylene

ABSTRACTIn this work the microstructures of star acrylated poly(ethylene glycol-co-lactide) (SPELA) with different LA:EG ratios in the aqueous solution have been simulated via Dissipative Particle Dynamics (DPD) approach at the mesoscale. The system components were coarse-grained into different beads (set of atoms) which moved according to the Newton’s equations of motion integrated via a modified Velocity-Verlet algorithm. The force acting on each bead, in a specific cutoff distance (rc), was divided into a conservative force (FC), random force (FR), dissipative force (FD), bond force (FS) and bond angle force (FE). The repulsion parameters of the conservative force (αij) were calculated from the solubility parameter of the beads, each of which were extracted from an atomistic molecular dynamics simulation (MD). Simulations showed the formation of micelles with lactide and acrylate beads occupied the core and hydrophilic ethylene oxide segments extending through the water to form the corona. The micelles showed an increasing trend in size and decreasing trend in number density with increase in LA:EG ratio. Results showed that the acrylate density decreased from the center of the micelles to the core surface although the overall amount of acrylates increased due to the increase in volume. Furthermore, the running integration number of acrylate-water beads showed decreasing accessibility of acrylates to water with increasing PLA volume fraction.

scholarly journals Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

2017 ◽  
Author(s):  
Ronald D Hills, Jr
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interfacial Behavior ◽  
Potentials Of Mean Force ◽  
Arginine Residues ◽  
Dynamics Simulations

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.

scholarly journals Molecular dynamics simulation of imidazolium CnMIM-BF4 ionic liquids using a coarse grained force-field

2020 ◽  
Vol 22 (3) ◽  
pp. 1682-1692 ◽  
Author(s):  
Oscar Y. Fajardo ◽  
Silvia Di Lecce ◽  
Fernando Bresme
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Interfacial Properties ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Structure Dynamics

A Coarse Grained (CG) model to investigate the structure, dynamics and interfacial properties of the [C2–8MIM][BF4] family of ionic liquids is proposed.

scholarly journals Coarse-grained molecular dynamics study of the self-assembly of polyphilic bolaamphiphiles using the SAFT-γ Mie force field

2021 ◽  
Author(s):  
Maziar Fayaz-Torshizi ◽  
Erich A. Müller
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystals ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Molecular Models ◽  
Coarse Grained Molecular Dynamics

A methodology is outlined to parametrize coarse grained molecular models for the molecular dynamics simulation of liquid crystals.

scholarly journals Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

2017 ◽  
Author(s):  
Ronald D Hills, Jr
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interfacial Behavior ◽  
Potentials Of Mean Force ◽  
Arginine Residues ◽  
Dynamics Simulations

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.

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