scholarly journals Efficient Hybrid Particle-Field Coarse-Grained Model of Polymer Filler Interactions: Multiscale Hierarchical Structure of Carbon Black Particles in Contact with Polyethylene

2021 ◽  
Author(s):  
Stefano Caputo ◽  
Velichko Hristov ◽  
Antonio De Nicola ◽  
Harald Herbst ◽  
Antonio Pizzirusso ◽  
...  
Keyword(s):  
Carbon Black ◽  
Hierarchical Structure ◽  
Coarse Grained ◽  
Particle Field ◽  
Hybrid Particle ◽  
Coarse Grained Model ◽  
Polymer Filler

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

Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids

2011 ◽  
Vol 7 (9) ◽  
pp. 2947-2962 ◽  
Author(s):  
Antonio De Nicola ◽  
Ying Zhao ◽  
Toshihiro Kawakatsu ◽  
Danilo Roccatano ◽  
Giuseppe Milano
Keyword(s):  
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

A Hybrid Particle-Field Coarse-Grained Molecular Model for Pluronics Water Mixtures

2013 ◽  
Vol 214 (17) ◽  
pp. 1940-1950 ◽  
Author(s):  
Antonio De Nicola ◽  
Toshihiro Kawakatsu ◽  
Giuseppe Milano
Keyword(s):  
Molecular Model ◽  
Coarse Grained ◽  
Particle Field ◽  
Hybrid Particle

scholarly journals Aggregation of Lipid A Variants: a Hybrid Particle-Field Model

2019 ◽  
Author(s):  
Antonio De Nicola ◽  
Thereza A. Soares ◽  
Sigbjørn Løland Bore ◽  
G. J. Agur Sevink ◽  
Michele Cascella ◽  
...  
Keyword(s):  
Self Assembly ◽  
Electrostatic Interactions ◽  
Lipid A ◽  
Md Simulations ◽  
Coarse Grained ◽  
Water Mixture ◽  
Particle Field ◽  
Hybrid Particle ◽  
Acyl Chains ◽  
The Stability

<p>Lipid A is one of three components of bacterial lipopolysaccharides (constituting the outer membrane of Gram-negative bacteria) and is recognized to have an important biological role in inflammatory response of the immune system. Its biological activity is modulated by the number of acyl-chains and from the electrostatic interactions with the different counter-ions. In this paper we report a coarse-grained model of poly-acyl Lipid A based on the hybrid particle field molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayer with two different acyl-chains, hexa- and tetra-. We find a good agreement of the particle distribution along the cross-section of bilayer by comparing the density profiles calculated from hPF-MD simulations with respect to reference all-atom. Moreover, we validate the model simulating the self-assembly of lamellar phase from an initial random distribution of Lipid A/N<sup>2+</sup>molecules in water. Finally, we test the stability of a vesicle composed of hexa-acylated Lipid A in water. The proposed model is able to maintain stable bilayer aggregates and spherical vesicle, and to correctly reproduce the phase behavior of Lipid A/Ca<sup>2+</sup>/Water mixture.</p>

scholarly journals HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multi-Scale Simulations of Soft Matter

2021 ◽  
Author(s):  
Morten Ledum ◽  
Samiran Sen ◽  
Xinmeng Li ◽  
Manuel Carrer ◽  
Yu Feng ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Self Assembly ◽  
Soft Matter ◽  
Time Integration ◽  
Hamiltonian Formulation ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Physical Force ◽  
Particle Field ◽  
Hybrid Particle

We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics (hPF). The methodology is based on tunable, grid-independent length-scale of coarse graining, obtained by filtering particle densities in reciprocal space. This enables systematic convergence of energies and forces by grid refinement, also eliminating non-physical force aliasing. Separating the time integration of fast modes associated with internal molecular motion, from slow modes associated with their density fields, we implement the first time-reversible hPF simulations. HyMD comprises the optional use of explicit electrostatics, which, in this formalism, corresponds to the long-range potential in Particle-Mesh Ewald. We demonstrate the ability of HhPF to perform simulations in the microcanonical and canonical ensembles with a series of test cases, comprising lipid bilayers and vesicles, surfactant micelles, and polypeptide chains, comparing our results to established literature. An on-the-fly increase of the characteristic coarse graining length significantly speeds up dynamics, accelerating self-diffusion and leading to expedited aggregation. Exploiting this acceleration, we find that the time scales involved in the self-assembly of polymeric structures can lie in the tens to hundreds of picoseconds instead of the multi microsecond regime observed with comparable coarse-grained models.

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>

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