Combination of Hybrid Particle-Field Molecular Dynamics and Slip-Springs for the Efficient Simulation of Coarse-Grained Polymer Models: Static and Dynamic Properties of Polystyrene Melts

2020 ◽  
Author(s):  
Zhenghao Wu ◽  
Giuseppe Milano ◽  
Florian Müller-Plathe
Keyword(s):  
Molecular Dynamics ◽  
Dynamic Properties ◽  
Coarse Grained ◽  
Particle Field ◽  
Hybrid Particle ◽  
Efficient Simulation ◽  
Polymer Models

A hybrid particle–field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes

2013 ◽  
Vol 10 (4) ◽  
pp. 045007 ◽  
Author(s):  
Giuseppe Milano ◽  
Toshihiro Kawakatsu ◽  
Antonio De Nicola
Keyword(s):  
Molecular Dynamics ◽  
Coarse Grained ◽  
Particle Field ◽  
Hybrid Particle

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 Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

2014 ◽  
Vol 595-596 ◽  
pp. 156-166 ◽  
Author(s):  
Edita Sarukhanyan ◽  
Antonio De Nicola ◽  
Danilo Roccatano ◽  
Toshihiro Kawakatsu ◽  
Giuseppe Milano
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Coarse Grained ◽  
Particle Field ◽  
Hybrid Particle ◽  
Nanotube Bundles ◽  
Coarse Grained Molecular Dynamics

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>

Self-assembly of carbon nanotubes in polymer melts: simulation of structural and electrical behaviour by hybrid particle-field molecular dynamics

Nanoscale ◽  
2016 ◽  
Vol 8 (34) ◽  
pp. 15538-15552 ◽  
Author(s):  
Ying Zhao ◽  
Maksym Byshkin ◽  
Yue Cong ◽  
Toshihiro Kawakatsu ◽  
Liberata Guadagno ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Self Assembly ◽  
Polymer Melts ◽  
Electrical Behaviour ◽  
Particle Field ◽  
Hybrid Particle

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 Energy renormalization for coarse-graining polymers having different segmental structures

2019 ◽  
Vol 5 (4) ◽  
pp. eaav4683 ◽  
Author(s):  
Wenjie Xia ◽  
Nitin K. Hansoge ◽  
Wen-Sheng Xu ◽  
Frederick R. Phelan ◽  
Sinan Keten ◽  
...  
Keyword(s):  
Dynamic Properties ◽  
Interaction Strength ◽  
Configurational Entropy ◽  
Coarse Graining ◽  
Soft Materials ◽  
Polymer Materials ◽  
Coarse Grained ◽  
Art Form ◽  
Polymer Models ◽  
Energy Renormalization

Multiscale coarse-grained (CG) modeling of soft materials, such as polymers, is currently an art form because CG models normally have significantly altered dynamics and thermodynamic properties compared to their atomistic counterparts. We address this problem by exploiting concepts derived from the generalized entropy theory (GET), emphasizing the central role of configurational entropy sc in the dynamics of complex fluids. Our energy renormalization (ER) method involves varying the cohesive interaction strength in the CG models in such a way that dynamic properties related to sc are preserved. We test this ER method by applying it to coarse-graining polymer melts (i.e., polybutadiene, polystyrene, and polycarbonate), representing polymer materials having a relatively low, intermediate, and high degree of glass “fragility”. We find that the ER method allows the dynamics of the atomistic polymer models to be faithfully described to a good approximation by CG models over a wide temperature range.

scholarly journals Generation of well relaxed all atom models of stereoregular polymers: a validation of hybrid particle-field molecular dynamics for polypropylene melts of different tacticities

2020 ◽  
Vol 18 (2-3) ◽  
pp. 228-241
Author(s):  
Antonio De Nicola ◽  
Gianmarco Munaò ◽  
Nino Grizzuti ◽  
Finizia Auriemma ◽  
Claudio De Rosa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Particle Field ◽  
Hybrid Particle ◽  
Stereoregular Polymers
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