Coarse-grained simulation of the translational and rotational diffusion of globular proteins by dissipative particle dynamics

2020 ◽  
Vol 153 (23) ◽  
pp. 234902
Author(s):  
Jiachen Wei ◽  
Yawei Liu ◽  
Fan Song
Keyword(s):  
Rotational Diffusion ◽  
Dissipative Particle Dynamics ◽  
Globular Proteins ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Translational And Rotational Diffusion

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.

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...

Four-to-one coarse-grained polarisable water model for dissipative particle dynamics

2017 ◽  
Vol 44 (7) ◽  
pp. 540-550 ◽  
Author(s):  
Rakesh Vaiwala ◽  
Sameer Jadhav ◽  
Rochish Thaokar
Keyword(s):  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Water Model

How the Antimicrobial Peptides Kill Bacteria: Computational Physics Insights

2012 ◽  
Vol 11 (3) ◽  
pp. 709-725 ◽  
Author(s):  
Licui Chen ◽  
Lianghui Gao ◽  
Weihai Fang ◽  
Leonardo Golubovic
Keyword(s):  
Electrostatic Interactions ◽  
Constant Pressure ◽  
Membrane Lipids ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Hydrophobic Domain ◽  
Vital Functions ◽  
Dissipative Particle Dynamics Simulation

AbstractIn the present article, coarse grained Dissipative Particle Dynamics simulation with implementation of electrostatic interactions is developed in constant pressure and surface tension ensemble to elucidate how the antimicrobial peptide molecules affect bilayer cell membrane structure and kill bacteria. We find that peptides with different chemical-physical properties exhibit different membrane obstructing mechanisms. Peptide molecules can destroy vital functions of the affected bacteria by translocating across their membranes via worm-holes, or by associating with membrane lipids to form hydrophilic cores trapped inside the hydrophobic domain of the membranes. In the latter model, the affected membranes are strongly buckled, in accord with very recent experimental observations [G. E. Fantner et al., Nat. Nanotech., 5 (2010), pp. 280-285].

Dissipative Particle Dynamics Studies on the Self-Assembling Dynamics of the Peptide Amphiphiles

2008 ◽  
Vol 1135 ◽  
Author(s):  
Taiga Seki ◽  
Noriyoshi Arai ◽  
Taku Ozawa ◽  
Tomoko Shimada ◽  
Kenji Yasuoka ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
The Self ◽  
Peptide Amphiphiles ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Self Assembling ◽  
Micro Structures ◽  
Good Agreement

ABSTRACTA coarse-grained model of peptide amphiphiles (PA) dissolved in aqueous solution was presented, where the effects of PA concentration, temperature and shear stress upon the self-assembly of PA were numerically studied by dissipative particle dynamics (DPD) simulation. We technically investigate the repulsion parameter aHW which indicates the repulsion force between the hydrophilic head of PA and water molecules, hence, at the same time, indicating the change in temperature. It was found that aHW played an important role in the self-assembly dynamics and in the resulting micro-structures of PA. By imposing shear strain on the simulation system, the formation of wormlike PA micelles was accelerated. The simulation results were in good agreement with our previous experimental results and the mechanism of shear-induced transition was proposed.

scholarly journals Forced Convection Heat Transfer Simulation Using Dissipative Particle Dynamics With Energy Conservation

2011 ◽  
Author(s):  
Toru Yamada ◽  
Anurag Kumar ◽  
Yutaka Asako ◽  
Mohammad Faghri
Keyword(s):  
Heat Flux ◽  
Energy Conservation ◽  
Boundary Conditions ◽  
Forced Convection ◽  
Flow Direction ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Channel Cross Section ◽  
Difference Approximation

Dissipative particle dynamics (DPD) with energy conservation was applied to simulate forced convection in parallel-plate channels with boundary conditions of constant wall temperature (CWT) and constant wall heat flux (CHF). DPD is a coarse-grained version of molecular dynamics. An additional governing equation for energy conservation was solved along with conventional DPD equations where inter-particle heat flux accounts for changes in mechanical and internal energies when particles interact with surrounding particles. The solution domain was considered to be two-dimensional with periodic boundary condition in the flow direction. Additional layers of particles on top and bottom of the channel were utilized to apply no-slip velocity and temperature boundary conditions. The governing equations for energy conservation were modified based on periodic fully developed velocity and temperature conditions. The results were shown via velocity and temperature profiles across the channel cross section. The Nusselt numbers were calculated from the temperature gradient at the wall using a second order accurate forward difference approximation. The results agreed well with the exact solutions to within 2.3%.

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