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.

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...

Multipolar Expansion Methods for Coarse Grained Force Fields [PowerPoint Submission]

2006 ◽  
Vol 978 ◽  
Author(s):  
Sheng D. Chao
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemistry ◽  
Large Scale ◽  
Force Fields ◽  
Coarse Graining ◽  
Expansion Method ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Quantum Chemistry Calculations ◽  
Multipolar Expansion

AbstractCurrent large scale atomistic simulations remain too computationally demanding to be generally applicable to industrial and bioengineering materials. It is desirable to develop multiscale modeling algorithms to perform efficient and informative mesoscopic simulations. Here we present a multipolar expansion method to construct coarse grained force fields (CGFF) for polymer nanostructures and nanocomposites. This model can effectively capture the stereochemical response to anisotropic long-range interactions and can be systematically improved upon adding higher order terms. The coarse-graining procedure forms the basis to perform a hierarchy of multiscale simulations starting with the quantum chemistry calculations to coarse grained molecular dynamics, hopefully toward continuum modeling. We have applied this procedure to molecular clusters such as alkane, benzene, and fullerene. For liquid alkane, molecular dynamics simulations using the CGFF can reproduce the pair distribution functions using atomistic force fields. Molecular mechanics simulations using the CGFF can well reproduce the energetics of benzene clusters from quantum chemistry electronic structure calculations. Subtle anisotropy in the interaction potentials of the fullerene dimer using the Brenner force field can also be well represented by the model. It is promising this procedure can be standardized and further extended.

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

2021 ◽  
Author(s):  
Rakesh Vaiwala ◽  
K. Ganapathy Ayappa
Keyword(s):  
Phase Space ◽  
Force Field ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Secondary Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Radius Of Gyration ◽  
Protein Secondary Structures

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 mapping the bonds and angles for 20 amino acids onto target distributions obtained from fully atomistic simulations in explicit solvent. A dual-basin potential is introduced for stabilizing backbone angles, to cover a wide spectrum of protein secondary structures. The backbone dihedral potential enables folding of the protein from an unfolded initial state to the folded native structure. The proposed force field is validated by evaluating structural properties of several model peptides and proteins including the SARS-CoV-2 fusion peptide, consisting of α-helices, β-sheets, loops and turns. Detailed comparisons with fully atomistic simulations are carried out to assess the ability of the proposed force field to stabilize the different secondary structures present in proteins. The compact conformations of the native states were evident from the radius of gyration as well as the high intensity peaks of the root mean square deviation histograms, which were found to lie below 0.4 nm. The Ramachandran-like energy landscape on the phase space of backbone angles (θ) and dihedrals (ϕ) effectively captured the conformational phase space of α-helices at ~(ϕ=50°, θ=90°) and β-strands at ~(ϕ=±180°, θ=90°-120°). Furthermore, the residue-residue native contacts are also well reproduced by the proposed DPD model. The applicability of the model to multidomain complexes is assessed using lysozyme as well as a large α helical bacterial pore-forming toxin, cytolysin A. Our studies illustrate that the proposed force field is generic, and can potentially be extended for efficient in-silico investigations of membrane bound polypeptides and proteins using DPD simulations.

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.

A molecular modeling study for miscibility of polyimide/polythene mixing systems with/without compatibilizer

2018 ◽  
Vol 38 (9) ◽  
pp. 891-898 ◽  
Author(s):  
Song Chen ◽  
Jian Li ◽  
Lei Wei ◽  
Yongliang Jin ◽  
Tushar Khosla ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Phase Separation ◽  
Molecular Modeling ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Distribution Functions ◽  
Radial Distribution Functions ◽  
Molecular Models ◽  
Promising Technique ◽  
Dynamics Simulations

AbstractMolecular models were established to predict the miscibility of polyimide/polythene mixing systems and the enhancing effects of compatibilizer addition of maleic anhydride grafted polythene (MAH-g-PE). Molecular dynamics simulations were applied to investigate radial distribution functions and Flory-Huggins parameters of the mixing systems. Results show that polyimide/polythene is miscible to a certain degree, and the miscibility gets better after adding MAH-g-PE. Dissipative particle dynamics (DPD) simulations display that micro-phase separation occurs in the polyimide/polythene mixing systems, however, effective interfaces appear between polyimide and polythene phases after adding MAH-g-PE. The results of molecular mechanics simulations indicate that the ability of mixing systems to resist stretch, compression and shear deformation increases after adding MAH-g-PE. This work offers a promising technique to predict miscibility properties for polyimide/polythene system prior to actual production and attempt to find a suitable compatibilizer for that system.

Three-dimensional line edge roughness in pre- and post-dry etch line and space patterns of block copolymer lithography

2020 ◽  
Vol 22 (2) ◽  
pp. 478-488
Author(s):  
Shubham Pinge ◽  
Yufeng Qiu ◽  
Victor Monreal ◽  
Durairaj Baskaran ◽  
Abhaiguru Ravirajan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Block Copolymer ◽  
Large Scale ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Line Edge Roughness ◽  
Edge Roughness ◽  
Dry Etch ◽  
Block Copolymer Lithography ◽  
Symmetric Block

In this work, we employ large-scale coarse-grained molecular dynamics (CGMD) simulations to study the three-dimensional line edge roughness associated with line and space patterns of chemo-epitaxially directed symmetric block copolymers.

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.

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