Graphics Processing Unit Accelerated Coarse-Grained Protein-Protein Docking

Graphics processing unit (GPU) architectures are increasingly used for general purpose computing, providing the means to migrate algorithms from the SISD paradigm, synonymous with CPU architectures, to the SIMD paradigm. Generally programmable commodity multi-core hardware can result in significant speed-ups for migrated codes. Because of their computational complexity, molecular simulations in particular stand to benefit from GPU acceleration. Coarse-grained molecular models provide reduced complexity when compared to the traditional, computationally expensive, all-atom models. However, while coarse-grained models are much less computationally expensive than the all-atom approach, the pairwise energy calculations required at each iteration of the algorithm continue to cause a computational bottleneck for a serial implementation. In this work, we describe a GPU implementation of the Kim-Hummer coarse-grained model for protein docking simulations, using a Replica Exchange Monte-Carlo (REMC) method. Our highly parallel implementation vastly increases the size- and time scales accessible to molecular simulation. We describe in detail the complex process of migrating the algorithm to a GPU as well as the effect of various GPU approaches and optimisations on algorithm speed-up. Our benchmarking and profiling shows that the GPU implementation scales very favourably compared to a CPU implementation. Small reference simulations benefit from a modest speedup of between 4 to 10 times. However, large simulations, containing many thousands of residues, benefit from asynchronous GPU acceleration to a far greater degree and exhibit speed-ups of up to 1400 times. We demonstrate the utility of our system on some model problems. We investigate the effects of macromolecular crowding, using a repulsive crowder model, finding our results to agree with those predicted by scaled particle theory. We also perform initial studies into the simulation of viral capsids assembly, demonstrating the crude assembly of capsid pieces into a small fragment. This is the first implementation of REMC docking on a GPU, and the effectuate speed-ups alter the tractability of large scale simulations: simulations that otherwise require months or years can be performed in days or weeks using a GPU

Coarse-grained Algorithms and Implementations of Structural Indexing-based Object Recognition on Intel Touchstone Delta

In this paper, we present efficient parallel solutions for structural indexing-based object recognition on coarse-grained parallel machines. Based on the analysis using the C 3 -model, the parallel algorithm proposed in this paper takes O(Sk=p) computation units and O(p 3=2 ) communication units on a p processor coarse-grained machine such that 1 p S, whereas the sequential solution takes O(Sk). The proposed solution is implemented on the Intel Touchstone Delta and performance results are shown. For a scene consisting of 160 feature points, the recognition phase takes 258 ms on a 64 processor Delta when the model database contains 256 models. The sequential algorithm takes approximately 4 seconds on a single node of the Delta. 1 Introduction Object recognition is a key step in a high level vision task. In a model-based recognition system, a set of models is given and the task is to find instances of these these in a given scene. The models are represented as sets of geometric ..

Proceedings of the NASA Conference on Space Telerobotics, volume 5

Papers presented at the NASA Conference on Space Telerobotics are compiled. The theme of the conference was man-machine collaboration in space. The conference provided a forum for researchers and engineers to exchange ideas on the research and development required for the application of telerobotics technology to the space systems planned for the 1990's and beyond. Volume 5 contains papers related to the following subject areas: robot arm modeling and control, special topics in telerobotics, telerobotic space operations, manipulator control, flight experiment concepts, manipulator coordination, issues in artificial intelligence systems, and research activities at the Johnson Space Center

The 1993 Goddard Conference on Space Applications of Artificial Intelligence

This publication comprises the papers presented at the 1993 Goddard Conference on Space Applications of Artificial Intelligence held at the NASA/Goddard Space Flight Center, Greenbelt, MD on May 10-13, 1993. The purpose of this annual conference is to provide a forum in which current research and development directed at space applications of artificial intelligence can be presented and discussed

An evaluation of the challenges of Multilingualism in Data Warehouse development

In this paper we discuss Business Intelligence and define what is meant by support for Multilingualism in a Business Intelligence reporting context. We identify support for Multilingualism as a challenging issue which has implications for data warehouse design and reporting performance. Data warehouses are a core component of most Business Intelligence systems and the star schema is the approach most widely used to develop data warehouses and dimensional Data Marts. We discuss the way in which Multilingualism can be supported in the Star Schema and identify that current approaches have serious limitations which include data redundancy and data manipulation, performance and maintenance issues. We propose a new approach to enable the optimal application of multilingualism in Business Intelligence. The proposed approach was found to produce satisfactory results when used in a proof-of-concept environment. Future work will include testing the approach in an enterprise environmen