Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space.
Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space.
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DOI：
10.1039/c3fd00159h
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发表时间：
2014-10
影响因子：
3.4
通讯作者：
E. Pavlov;M. Taiji;A. Scukins;A. Markesteijn;S. Karabasov;D. Nerukh
中科院分区：
文献类型：
--
作者：
E. Pavlov;M. Taiji;A. Scukins;A. Markesteijn;S. Karabasov;D. Nerukh
描述了一种同时在空间和时间的多尺度上对生物分子系统进行建模的新框架。原子分子动力学表示与统计连续流体动力学描述平滑地连接。该系统的行为正确的纯分子动力学（流体动力学）的限制，并在中间政权时，原子部分原子粒子的运动，并在同一时间遵循流体动力学流动。相应的贡献由一个参数控制，该参数被定义为空间和时间的任意函数，因此，允许原子的“核心”和连续体的“环境”的有效分离。为了填补原子和连续表示之间的规模差距，我们的专用计算机分子动力学，MDGRAPE-4，以及基于GPU的计算用于开发的框架。这些硬件开发还包括交互式分子动力学模拟，允许通过力反馈装置干预建模。
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.