The influence of temperature and density on the microscopic structure and dynamics of long polymer chains: Molecular dynamics and dissipative particle dynamics modeling

2017 ◽  
Vol 06 (03) ◽  
pp. 1750023
Author(s):  
M. Lemaalem ◽  
A. Derouiche ◽  
S. EL Fassi ◽  
H. Ridouane
Keyword(s):  
Molecular Dynamics ◽  
Dynamic Properties ◽  
Dissipative Particle Dynamics ◽  
Simulation Method ◽  
Particle Dynamics ◽  
Polymer Physics ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Dynamics Modeling ◽  
Polymer Simulation

Long polymer chains that mainly exhibit thermoplastic properties are recognized to demonstrate excellent thermal and mechanical features at the molecular level. For the purpose of facilitating its study, we present the results of a coarse-grained Molecular Dynamics (MD) and Dissipative Particle Dynamics (DPD) simulations under the Canonical ensemble (NVT) conditions. For each simulation method, the structure, static and dynamic properties were analyzed, with particular emphasis on the influence of density and temperature on the equilibrium of the polymer. We find, after correcting the Soft Repulsive Potential (SRP) parameters used in DPD method, that both simulation methods describe the polymer physics with the same accuracy. This proves that the DPD method can simplify the polymer simulation and can reproduce with the same precision the equilibrium obtained in the MD simulation.

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

scholarly journals Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
P. M. Pieczywek ◽  
W. Płaziński ◽  
A. Zdunek
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Large Scale ◽  
Dissipative Particle Dynamics ◽  
Three Dimensional ◽  
Structural Features ◽  
Particle Dynamics ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Dynamics Model

Abstract In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.

MORPHOLOGICAL PROPERTIES OF PYRROLE AND PHENYLENE ROD–COIL DIBLOCK COPOLYMERS BY DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (01) ◽  
pp. 1250100 ◽  
Author(s):  
EROL YILDIRIM ◽  
MINE YURTSEVER
Keyword(s):  
Diblock Copolymers ◽  
Dissipative Particle Dynamics ◽  
Atomic Charge ◽  
Simulation Method ◽  
Particle Dynamics ◽  
Industrial Applications ◽  
Coarse Grained ◽  
Morphological Properties ◽  
Dynamics Simulations ◽  
Phase Behaviors

Poly (para-phenylene)s (PPP) and polypyrroles (PPy) are important members of the conducting polymers. Rod–coil type diblock copolymers formed by coupling of PPP and PPy rigid blocks with polycaprolactone (PCL), polystyrene (PS) and polymethylmethacrylate (PMMA) coil blocks were modeled and morphological properties have been studied by a coarse grained simulation method at the mesoscale. Geometry optimizations and the atomic charge calculations were done quantum mechanically to obtain the input parameters for the mesoscale dynamics simulations. The accurate mixing energies and the Flory–Huggins interaction parameters between the monomers of polymers were calculated and used to study the phase behaviors and the morphologies of the copolymers as a function of type and weight percentages of the blocks by Dissipative Particle Dynamics (DPD) simulations. We showed that the methodology employed took into account not only the interaction parameter and chain length of the blocks but also the chemical structure of the polymers and it could be used to produce the phase diagram of the copolymers which has importance for the industrial applications of such materials. Among the studied copolymers, the most suitable one for thin layer applications was predicted to be PPP–b–PCL in which PPP forms lamellar and cylindrical phases in the PCL matrix if amount of PPP rod block is below 50 wt%.

scholarly journals Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields

2019 ◽  
Author(s):  
James McDonagh ◽  
Ardita Shkurti ◽  
David J. Bray ◽  
Richard L. Anderson ◽  
Edward O. Pyzer-Knapp
Keyword(s):  
Machine Learning ◽  
Force Field ◽  
Dissipative Particle Dynamics ◽  
Simulation Method ◽  
Particle Dynamics ◽  
Bayesian Optimization ◽  
Coarse Grained ◽  
Proof Of Concept ◽  
Novel Approach ◽  
Molecular Force

This work demonstrates the use of open literature data to force field paramterization via a novel approach applying Bayesian optimization. We have selected Dissipative Particle Dynamics (DPD) as the simulation method in this proof-of-concept work.

Multiscale Modeling of Flow Induced Thrombogenicity Using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics

2013 ◽  
Author(s):  
Peng Zhang ◽  
Jawaad Sheriff ◽  
João S. Soares ◽  
Chao Gao ◽  
Seetha Pothapragada ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Blood Flow ◽  
Red Blood Cells ◽  
Platelet Activation ◽  
Blood Cells ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Activated Platelets ◽  
Coarse Grained Molecular Dynamics

The coagulation cascade of blood may be initiated by flow induced platelet activation, which prompts clot formation in prosthetic cardiovascular devices and arterial disease processes. While platelet activation may be induced by biochemical agonists, shear stresses arising from pathological flow patterns enhance the propensity of platelets to activate and initiate the intrinsic pathway of coagulation, leading to thrombosis. Upon activation platelets undergo complex biochemical and morphological changes: organelles are centralized, membrane glycoproteins undergo conformational changes, and adhesive pseudopods are extended. Activated platelets polymerize fibrinogen into a fibrin network that enmeshes red blood cells. Activated platelets also cross-talk and aggregate to form thrombi. Current numerical simulations to model this complex process mostly treat blood as a continuum and solve the Navier-Stokes equations governing blood flow, coupled with diffusion-convection-reaction equations. It requires various complex constitutive relations or simplifying assumptions, and is limited to μm level scales. However, molecular mechanisms governing platelet shape change upon activation and their effect on rheological properties can be in the nm level scales. To address this challenge, a multiscale approach which departs from continuum approaches, may offer an effective means to bridge the gap between macroscopic flow and cellular scales. Coarse Grained Molecular dynamics (CGMD) and discrete/dissipative particle dynamics (DPD) methods have been employed in recent years to simulate complex processes at the molecular scales, and various viscous fluids at low-to-high Reynolds numbers at mesoscopic scales. Such particle methods possess important properties at the mesoscopic scale: complex fluids with heterogeneous particles can be modeled, allowing the simulation of processes which are otherwise very difficult to solve by continuum approaches. It is becoming a powerful tool for simulating complex blood flow, red blood cells interactions, and platelet-mediated thrombosis involving platelet activation, aggregation, and adhesion.

scholarly journals Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields

2019 ◽  
Author(s):  
James McDonagh ◽  
Ardita Shkurti ◽  
David J. Bray ◽  
Richard L. Anderson ◽  
Edward O. Pyzer-Knapp
Keyword(s):  
Machine Learning ◽  
Force Field ◽  
Dissipative Particle Dynamics ◽  
Simulation Method ◽  
Particle Dynamics ◽  
Bayesian Optimization ◽  
Coarse Grained ◽  
Proof Of Concept ◽  
Novel Approach ◽  
Molecular Force

This work demonstrates the use of open literature data to force field paramterization via a novel approach applying Bayesian optimization. We have selected Dissipative Particle Dynamics (DPD) as the simulation method in this proof-of-concept work.

THE SIMULATION OF POLYSTYRENE/NANOPARTICLES COMPOSITE MICROSPHERES USING DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (02) ◽  
pp. 1250111 ◽  
Author(s):  
HAILONG XU ◽  
QIUYU ZHANG ◽  
HEPENG ZHANG ◽  
BAOLIANG ZHANG ◽  
CHANGJIE YIN
Keyword(s):  
Dissipative Particle Dynamics ◽  
Sodium Dodecyl ◽  
Coarse Graining ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Polystyrene Nanoparticles ◽  
Coarse Grained Model ◽  
Composite Microspheres ◽  
Polystyrene Matrix ◽  
Materials Studio

Dissipative particle dynamics (DPD) was initially used to simulate the polystyrene/nanoparticle composite microspheres (PNCM) in this paper. The coarse graining model of PNCM was established. And the DPD parameterization of the model was represented in detail. The DPD repulsion parameters were calculated from the cohesive energy density which could be calculated by amorphous modules in Materials Studio. The equilibrium configuration of the simulated PNCM shows that the nanoparticles were actually "modified" with oleic acid and the modified nanoparticles were embedded in the bulk of polystyrene. As sodium dodecyl sulfate (SDS) was located in the interface between water and polystyrene, the hydrophilic head of SDS stretched into water while the hydrophobic tailed into polystyrene. All simulated phenomena were consistent with the experimental results in preparation of polystyrene/nanoparticles composite microspheres. The effect of surface modification of nanoparticles on its dispersion in polystyrene matrix was also studied by adjusting the interaction parameters between the OA and NP beads. The final results indicated that the nanoparticles removed from the core of composite microsphere to the surface with increase of a OA-NP . All the simulated results demonstrated that our coarse–grained model was reasonable.

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