5 research outputs found
From Quantity to Quality: Massive Molecular Dynamics Simulation of Nanostructures under Plastic Deformation in Desktop and Service Grid Distributed Computing Infrastructure
The distributed computing infrastructure (DCI) on the basis of BOINC and
EDGeS-bridge technologies for high-performance distributed computing is used
for porting the sequential molecular dynamics (MD) application to its parallel
version for DCI with Desktop Grids (DGs) and Service Grids (SGs). The actual
metrics of the working DG-SG DCI were measured, and the normal distribution of
host performances, and signs of log-normal distributions of other
characteristics (CPUs, RAM, and HDD per host) were found. The practical
feasibility and high efficiency of the MD simulations on the basis of DG-SG DCI
were demonstrated during the experiment with the massive MD simulations for the
large quantity of aluminum nanocrystals (-). Statistical
analysis (Kolmogorov-Smirnov test, moment analysis, and bootstrapping analysis)
of the defect density distribution over the ensemble of nanocrystals had shown
that change of plastic deformation mode is followed by the qualitative change
of defect density distribution type over ensemble of nanocrystals. Some
limitations (fluctuating performance, unpredictable availability of resources,
etc.) of the typical DG-SG DCI were outlined, and some advantages (high
efficiency, high speedup, and low cost) were demonstrated. Deploying on DG DCI
allows to get new scientific from the simulated
of numerous configurations by harnessing sufficient computational power to
undertake MD simulations in a wider range of physical parameters
(configurations) in a much shorter timeframe.Comment: 13 pages, 11 pages (http://journals.agh.edu.pl/csci/article/view/106
Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space
A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices
Mathematical Modeling of Polymer Loading Process in Extruders
Based on the state of the problem related to highquality
and reliable insulation coating of high-voltage cables, the
problems of mathematical modeling of pro-cesses in the loading
zone and the delay of the polymer mixture in a single-screw
extruder are formulated, which is crucial in terms of providing a
high-quality insulation coating. An iterative numerical-analytical
method for solving the corresponding nonlinear boundary value
problems is proposed, based on the use of finite integral
transformations in the spatial and temporal domains and their
implementation
A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time
A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported
Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model
Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics