High Throughput Virtual Screening with Data Level Parallelism in Multi-core Processors

Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements, the world might find cures for incurable diseases like HIV disease and Cancer sooner. Our approach presented in this paper is to utilize a multi-core environment to introduce Data Level Parallelism (DLP) to the Autodock Vina software, which is a widely used for molecular docking software. Autodock Vina already exploits Instruction Level Parallelism (ILP) in multi-core environments and therefore optimized for such environments. However, with the results we have obtained, it can be clearly seen that our approach has enhanced the throughput of the already optimized software by more than six times. This will dramatically reduce the time consumed for the lead identification phase in drug designing along with the shift in the processor technology from multi-core to many-core of the current era. Therefore, we believe that the contribution of this project will effectively make it possible to expand the number of small molecules docked against a drug target and improving the chances to design drugs for incurable diseases.Comment: Information and Automation for Sustainability (ICIAfS), 2012 IEEE 6th International Conference o

Performance evaluation of multi-core multi-cluster architecture

A multi-core cluster is a cluster composed of numbers of nodes where each node has a number of processors, each with more than one core within each single chip. Cluster nodes are connected via an interconnection network. Multi-cored processors are able to achieve higher performance without driving up power consumption and heat, which is the main concern in a single-core processor. A general problem in the network arises from the fact that multiple messages can be in transit at the same time on the same network links. This paper considers the communication latencies of a multi-core multi-cluster architecture will be investigated using simulation experiments and measurements under various working conditions

The Design of a System Architecture for Mobile Multimedia Computers

This chapter discusses the system architecture of a portable computer, called Mobile Digital Companion, which provides support for handling multimedia applications energy efficiently. Because battery life is limited and battery weight is an important factor for the size and the weight of the Mobile Digital Companion, energy management plays a crucial role in the architecture. As the Companion must remain usable in a variety of environments, it has to be flexible and adaptable to various operating conditions. The Mobile Digital Companion has an unconventional architecture that saves energy by using system decomposition at different levels of the architecture and exploits locality of reference with dedicated, optimised modules. The approach is based on dedicated functionality and the extensive use of energy reduction techniques at all levels of system design. The system has an architecture with a general-purpose processor accompanied by a set of heterogeneous autonomous programmable modules, each providing an energy efficient implementation of dedicated tasks. A reconfigurable internal communication network switch exploits locality of reference and eliminates wasteful data copies

Design as conversation with digital materials

This paper explores Donald Schön's concept of design as a conversation with materials, in the context of designing digital systems. It proposes material utterance as a central event in designing. A material utterance is a situated communication act that depends on the particularities of speaker, audience, material and genre. The paper argues that, if digital designing differs from other forms of designing, then accounts for such differences must be sought by understanding the material properties of digital systems and the genres of practice that surround their use. Perspectives from human-computer interaction (HCI) and the psychology of programming are used to examine how such an understanding might be constructed.</p