Parallel Particle-In-Cell Plasma Simulations on GPU, Vector, and Scalar Systems

The calculation performance of two types of moment calculation algorithms are evaluated on a GPU system with nVIDIA C2070 board and vector-type system on the Earth Simulator for one of the particle-in-cell plasma simulations. Those are WORK and SORT algorithms. The performances are compared with the scalar system (Intel Xeon) performance. We use 8 byte double precision variables for physical memory on both CPU and GPU chips. The used simulation algorithm is three-dimensional Hybrid code for ion-ion beam instability with periodic boundary system.OS6-9; 31st JSST Annual Conference (September 27-28, 2012, Kobe University, Japan) / Authors from proceedings TO

Nonlinearity of Mechanochemical Motions in Motor Proteins

The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are traditionally analyzed in terms of normal modes and experimental data on thermal fluctuations in such macromolecules is also usually interpreted in terms of the excitation of normal modes. We have chosen two important protein motors - myosin V and kinesin KIF1A - and performed numerical investigations of their conformational relaxation properties within the coarse-grained elastic network approximation. We have found that the linearity assumption is deficient for ligand-induced conformational motions and can even be violated for characteristic thermal fluctuations. The deficiency is particularly pronounced in KIF1A where the normal mode description fails completely in describing functional mechanochemical motions. These results indicate that important assumptions of the theory of protein dynamics may need to be reconsidered. Neither a single normal mode, nor a superposition of such modes yield an approximation of strongly nonlinear dynamics.Comment: 10 pages, 6 figure

ヒューリスティックモデルによる群集シミュレーション

1H1-2 / 2017年度（第31回）人工知能学会全国大会（2017年5月23日-5月26日、名古屋市ウィンクあいち