scholarly journals Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment

2018 ◽  
Vol 14 (9) ◽  
pp. 4928-4937 ◽  
Author(s):  
Hima Bindu Kolli ◽  
Antonio de Nicola ◽  
Sigbjørn Løland Bore ◽  
Ken Schäfer ◽  
Gregor Diezemann ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Aqueous Environment ◽  
Particle Field ◽  
Hybrid Particle ◽  
Dynamics Simulations

scholarly journals Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in Aqueous Environment

2018 ◽  
Author(s):  
Hima Bindu Kolli ◽  
Antonio de Nicola ◽  
Sigbjørn Løland Bore ◽  
Ken Schäfer ◽  
Gregor Diezemann ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sodium Dodecyl ◽  
Intermolecular Forces ◽  
Coarse Grained ◽  
Qualitative Behavior ◽  
Aqueous Environment ◽  
Particle Field ◽  
Hybrid Particle ◽  
Dynamics Simulations

<p>We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoyl phosphatidylglycerol (POPG) lipid bilayer, and sodium dodecyl sulphate (SDS) surfactant in aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolyte soft-matter systems. The intramolecular interactions are treated by a standard molecular Hamiltonian and the non-electrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of dielectric values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. </p>

scholarly journals Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in Aqueous Environment

2018 ◽  
Author(s):  
Hima Bindu Kolli ◽  
Antonio de Nicola ◽  
Sigbjørn Løland Bore ◽  
Ken Schäfer ◽  
Gregor Diezemann ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sodium Dodecyl ◽  
Intermolecular Forces ◽  
Coarse Grained ◽  
Qualitative Behavior ◽  
Aqueous Environment ◽  
Particle Field ◽  
Hybrid Particle ◽  
Dynamics Simulations

<p>We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoyl phosphatidylglycerol (POPG) lipid bilayer, and sodium dodecyl sulphate (SDS) surfactant in aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolyte soft-matter systems. The intramolecular interactions are treated by a standard molecular Hamiltonian and the non-electrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of dielectric values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. </p>

Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks

2012 ◽  
Vol 33 (8) ◽  
pp. 868-880 ◽  
Author(s):  
Ying Zhao ◽  
Antonio De Nicola ◽  
Toshihiro Kawakatsu ◽  
Giuseppe Milano
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Particle Field ◽  
Hybrid Particle ◽  
Dynamics Simulations

scholarly journals The structure and dynamics of chitin nanofibrils in an aqueous environment revealed by molecular dynamics simulations

RSC Advances ◽  
2016 ◽  
Vol 6 (36) ◽  
pp. 30710-30721 ◽  
Author(s):  
Zora Střelcová ◽  
Petr Kulhánek ◽  
Martin Friák ◽  
Helge-Otto Fabritius ◽  
Michal Petrov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Aqueous Environment ◽  
Structure Property ◽  
Typical Size ◽  
Natural Systems ◽  
Property Relations ◽  
Structure And Dynamics ◽  
Dynamics Simulations

The structure–property relations reveal the typical size of chitin nanofibrils observed in natural systems.

Density Functional Theory Calculations and Molecular Dynamics Simulations of the Interaction of Bio-molecules with Hydroxyapatite Surfaces in an Aqueous Environment

2008 ◽  
Vol 1131 ◽  
Author(s):  
Neyvis Almora-Barrios ◽  
Nora H de Leeuw
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Density Functional Theory ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Water Environment ◽  
Aqueous Environment ◽  
Functional Theory ◽  
Natural Bone ◽  
Dynamics Simulations

AbstractIn view of the importance of the hydroxyapatite/collagen composite of both natural bone tissue and synthetic biomaterials for hard tissue replacement, we have employed a combination of electronic structure calculations based on the Density Functional Theory and molecular dynamics simulations to investigate the adsorption of three major collagen I amino acids, as well as a complete peptide strand, at two hydroxyapatite surfaces, both in vacuo and in a liquid water environment. The free amino acids as well as the peptide form multiple interactions with the surfaces and bind more strongly to the (01.0) surface than the (0001) surface, in agreement with experiment, which has found that in natural bone the (01.0) surface grows preferentially from a collagen matrix.

Sign in / Sign up

Export Citation Format

Share Document