Potentials of Mean Force and Escape Times of Surfactants from Micelles and Hydrophobic Surfaces Using Molecular Dynamics Simulations

Langmuir ◽  
2015 ◽  
Vol 31 (4) ◽  
pp. 1336-1343 ◽  
Author(s):  
Fang Yuan ◽  
Shihu Wang ◽  
Ronald G. Larson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Surfaces ◽  
Potentials Of Mean Force ◽  
Dynamics Simulations

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 Bulk Ionic Screening Lengths from Extremely Large-Scale Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Johannes Zeman ◽  
Svyatoslav Kondrat ◽  
Christian Holm
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Scaling Relations ◽  
Bulk Properties ◽  
Charged Surfaces ◽  
Ionic Systems ◽  
Concentrated Electrolytes ◽  
Potentials Of Mean Force ◽  
Dynamics Simulations

Recent experiments have reported anomalously large screening lengths of interactions between charged surfaces confining concentrated electrolytes and ionic liquids. Termed underscreening, this effect was ascribed to bulk properties of dense ionic systems. Herein, we study bulk ionic screening with extremely large-scale molecular dynamics simulations, allowing us to assess the range of distances relevant to the experiments. Our results yield two screening lengths satisfying distinct scaling relations. However, with an accuracy of 10^-5 kT in interionic potentials of mean force, we find no signs of underscreening, suggesting that other than bulk effects might be at play in the experiments.

Molecular dynamics simulations of urea–water binary droplets on flat and pillared hydrophobic surfaces

2010 ◽  
Vol 146 ◽  
pp. 185 ◽  
Author(s):  
Takahiro Koishi ◽  
Kenji Yasuoka ◽  
Xiao Cheng Zeng ◽  
Shigenori Fujikawa
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Surfaces ◽  
Dynamics Simulations
Sign in / Sign up

Export Citation Format

Share Document