scholarly journals Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space

2014 ◽  
Vol 169 ◽  
pp. 285-302 ◽  
Author(s):  
Evgen Pavlov ◽  
Makoto Taiji ◽  
Arturs Scukins ◽  
Anton Markesteijn ◽  
Sergey Karabasov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Feedback ◽  
Multiple Scales ◽  
Biomolecular Systems ◽  
Space And Time ◽  
Statistical Continuum ◽  
Dynamics Simulations ◽  
Purpose Computer ◽  
Special Purpose Computer ◽  
The Continuum

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.

scholarly journals MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations

2014 ◽  
Vol 372 (2021) ◽  
pp. 20130387 ◽  
Author(s):  
Itta Ohmura ◽  
Gentaro Morimoto ◽  
Yousuke Ohno ◽  
Aki Hasegawa ◽  
Makoto Taiji
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computer System ◽  
Three Dimensional ◽  
Md Simulations ◽  
Particle Simulation ◽  
Peak Performance ◽  
Dynamics Simulations ◽  
Purpose Computer ◽  
Special Purpose Computer

We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s −1 for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.

scholarly journals A Special-purpose Computer for Molecular Dynamics Simulations: MDM

2003 ◽  
Vol 208 ◽  
pp. 349-358
Author(s):  
Tetsu Narumi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Real Space ◽  
Host Computer ◽  
Peak Performance ◽  
Dynamics Simulations ◽  
Force Calculation ◽  
Purpose Computer ◽  
Special Purpose Computer

We developed a special-purpose computer for molecular dynamics simulations, which we call Molecular Dynamics Machine (MDM). MDM accelerates the Coulomb and van der Waals force calculation with the Ewald method. It is composed of three parts: MDGRAPE-2, WINE-2 and a host computer. MDGRAPE-2 accelerates the real-space part of the Coulomb and van der Waals forces. WINE-2 accelerates wavenumber-space part of the Coulomb force. The host computer performs other calculations. The peak performance is 78 Tflop/s. It can also be used for cosmological, Smoothed Particle Hydrodynamics, and vortex dynamics simulations.

Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations

1999 ◽  
Vol 21 (5-6) ◽  
pp. 401-415 ◽  
Author(s):  
Tetsu Narumi ◽  
Ryutaro Susukita ◽  
Toshikazu Ebisuzaki ◽  
Geoffrey McNiven ◽  
Bruce Elmegreen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Purpose Computer ◽  
Special Purpose Computer

Molecular Dynamics Simulations of Interfacial Heat and Mass Transfer at Nanostructured Surface

2007 ◽  
Author(s):  
Gyoko Nagayama ◽  
Masako Kawagoe ◽  
Takaharu Tsuruta
Keyword(s):  
Heat Transfer ◽  
Molecular Dynamics ◽  
Boundary Condition ◽  
Thermal Resistance ◽  
Hydrodynamic Resistance ◽  
Hydrophilic Surface ◽  
Dynamics Simulations ◽  
Solid Liquid Interface ◽  
Solid Liquid ◽  
The Continuum

The nanoscale heat and mass transport phenomena play important roles on the applications of nanotechnologies with great attention to its differences from the continuum mechanics. In this paper, the breakdown of the continuum assumption for nanoscale flows has been verified based on the molecular dynamics simulations and the heat transfer mechanism at the nanostructured solid-liquid interface in the nanochannels is studied from the microscopic point of view. Simple Lennard-Jones (LJ) fluids are simulated for thermal energy transfer in a nanochannel using nonequilibrium molecular dynamics techniques. Multi-layers of platinum atoms are utilized to simulate the solid walls with arranged nanostructures and argon atoms are employed as the LJ fluid. The results show that the interface structure (i.e. the solid-like structure formed by the adsorption layers of liquid molecules) between solid and liquid are affected by the nanostructures. It is found that the hydrodynamic resistance and thermal resistance dependents on the surface wettability and for the nanoscale heat and fluid flows, the interface resistance cannot be neglected but can be reduced by the nanostructures. For the hydrodynamic boundary condition at the solid-liquid interface, the no-slip boundary condition holds good at the super-hydrophilic surface with large hydrodynamic resistance. However, apparent slip is observed at the low hydrodynamic resistance surface when the driving force overcomes the interfacial resistance. For the thermal boundary condition, it is found that the thermal resistance at the interface depends on the interface wettability and the hydrophilic surface has lower thermal resistance than that of the hydrophobic surfaces. The interface thermal resistance decreases at the nanostructed surface and significant heat transfer enhancement has been achieved at the hydrophilic nanostructured surfaces. Although the surface with nanostrutures has larger surface area than the flat surface, the rate of heat flux increase caused by the nanostructures is remarkable.

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