Benchmarking the Performance of Irregular Computations in AutoDock-GPU Molecular Docking [0.03%]
AutoDock-GPU分子对接中的不规则计算性能基准测试
Leonardo Solis-Vasquez,Andreas F Tillack,Diogo Santos-Martins et al.
Leonardo Solis-Vasquez et al.
Irregular applications can be found in different scientific fields. In computer-aided drug design, molecular docking simulations play an important role in finding promising drug candidates. AutoDock is a software application widely used for...
Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales [0.03%]
从电子到细胞尺度的光能转换过程的多尺度建模和影视化展示
Melih Sener,Stuart Levy,John E Stone et al.
Melih Sener et al.
Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. A visualization depicting this process, based on multiscale computational models from electronic to cell scales, is presented...
Qianqian Tong,Guannan Liang,Xingyu Cai et al.
Qianqian Tong et al.
Although first-order stochastic algorithms, such as stochastic gradient descent, have been the main force to scale up machine learning models, such as deep neural nets, the second-order quasi-Newton methods start to draw attention due to th...
William M Putman,Lesley Ott,Anton Darmenov et al.
William M Putman et al.
A high-resolution (7 km) non-hydrostatic global mesoscale simulation using the Goddard Earth Observing System (GEOS-5) model is used to visualize the flow and fluxes of carbon dioxide throughout the year. Carbon dioxide (CO2) is the most im...
Visualizing multiphysics, fluid-structure interaction phenomena in intracranial aneurysms [0.03%]
颅内动脉瘤多物理场流固耦合现象的可视化研究
Paris Perdikaris,Joseph A Insley,Leopold Grinberg et al.
Paris Perdikaris et al.
This work presents recent advances in visualizing multi-physics, fluid-structure interaction (FSI) phenomena in cerebral aneurysms. Realistic FSI simulations produce very large and complex data sets, yielding the need for parallel data proc...
Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing [0.03%]
基于GPU加速的光线追踪的光合作用膜原子细节可视化技术研究
John E Stone,Melih Sener,Kirby L Vandivort et al.
John E Stone et al.
The cellular process responsible for providing energy for most life on Earth, namely photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several or...
Zhihao Lou,John Reinitz
Zhihao Lou
This paper presents a parallel simulated annealing algorithm that is able to achieve 90% parallel efficiency in iteration on up to 192 processors and up to 40% parallel efficiency in time when applied to a 5000-dimension Rastrigin function....
Region Templates: Data Representation and Management for High-Throughput Image Analysis [0.03%]
区域模板：高通量图像分析的数据表示与管理
George Teodoro,Tony Pan,Tahsin Kurc et al.
George Teodoro et al.
We introduce a region template abstraction and framework for the efficient storage, management and processing of common data types in analysis of large datasets of high resolution images on clusters of hybrid computing nodes. The region tem...
Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations [0.03%]
使用多GPU工作站仿真生物学相关的时间和空间尺度上的反应扩散过程
Michael J Hallock,John E Stone,Elijah Roberts et al.
Michael J Hallock et al.
Simulation of in vivo cellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time...
Efficient Irregular Wavefront Propagation Algorithms on Hybrid CPU-GPU Machines [0.03%]
高效的混合CPU-GPU机器上的不规则波前传播算法
George Teodoro,Tony Pan,Tahsin Kurc et al.
George Teodoro et al.
We address the problem of efficient execution of a computation pattern, referred to here as the irregular wavefront propagation pattern (IWPP), on hybrid systems with multiple CPUs and GPUs. The IWPP is common in several image processing op...