Yongchang Ji

Ad hoc grids: communication and computing in a power constrained environment

We introduce ad hoc grids as a hierarchy of mobile devices with different computing and communication capabilities. An ad hoc grid allows a group of individuals to accomplish a mission, often in a hostile environment; examples of applications of ad hoc grids are disaster management, wild-fire prevention, and peacekeeping operations. We are concerned with the interplay between computing and communication in the power-constrained environment of an ad hoc grid.

A computational framework for the 3D structure determination of viruses with unknown symmetry

The protein shell of all virus structures resolved to this date exhibit some form of symmetry, most of them are spherical viruses with icosahedral symmetry; the study of viruses whose symmetry is not known, of structures which do not exhibit any symmetry, as well as the study of the genetic material of a virus are considerably more challenging. Increasing the resolution of the structure determination and solving structures with no symmetry represents a quantum leap in virus structure determination based upon electron microscopy. Computing is a major component of the structure determination process. Nowadays it is not feasible to increase the resolution of the structure determination of large macromolecules like viruses or to solve structures with no symmetry without novel parallel algorithms and environments enabling structural biologists to use parallel systems, clusters of workstations, or providing access to grid computing.

A routing protocol for power constrained networks with asymmetric links

In many instances, an ad hoc network consists of nodes with different hardware and software capabilities as well as power limitations. This is the case of ad hoc grids where devices such as desktops, laptops, robots, palmtops, sensors, and actuators collaborate to solve computational problems. In such a heterogeneous environment, the nodes have various degrees of mobility and range and the communication links are asymmetric: node i may be able to reach node j, but j may not be able to reach i. A4LP, is a Location-Aware and Power-Aware routing protocol designed primarily for heterogeneous Ad hoc networks with Asymmetric links.

Orientation refinement of virus structures with unknown symmetry

Structural biology, in particular the structure determination of viruses and other large macromolecular complexes lead to data- and compute-intensive problems that require resources well beyond those available on a single system. Thus, there is an imperative need to develop parallel algorithms and programs for clusters and computational grids. We present one of the most challenging computational problems posed by the three-dimensional structure determination of viruses, the orientation refinement.

Improving routing performance through m-limited forwarding in power-constrained wireless ad hoc networks

We present m-limited forwarding, a technique to reduce the cost of disseminating information in a power-constrained environment by limiting the cardinality of the subset of nodes which retransmit a packet. We show how this technique can be used to improve the performance of ad hoc routing protocols. m-AODV applies m-limited forwarding to the AODV routing protocol, and is used for networks with symmetric connections. We implemented m-A^4LP, a protocol which can take advantage of the asymmetric links found in heterogeneous networks consisting of nodes with different transmission ranges. We quantify the benefits of the enhanced routing protocols and report the results of a simulation study regarding the power consumption of the nodes and the packet loss ratio. We conclude that m-AODV outperforms plain AODV and LAR in general scenarios, and m-A^4LP shows a significantly lower packet loss ratio than AODV in heterogeneous networks.

Coordination in Intelligent Grid Environments

A computational grid is a complex system. The state space of a complex system is very large and it is infeasible to create a rigid infrastructure implementing optimal policies and strategies which take into account the current state of the system. An alternative to a rigid infrastructure is to base the systems reactions on logical inference, planning, and learning, the quintessential elements of an intelligent system. An intelligent grid is one where societal services exhibit intelligent behavior. A coordination service acting as a proxy on behalf of end users reacts to unforeseen events, plans how to carry out complex tasks, and learns from the history of the system. Various policies implemented by the societal services of an intelligent grid, such as brokerage and matchmaking, are based upon rules and facts gathered with the aid of a monitoring service. The question we address is how to construct intelligent computational grids which are truly scalable and could respond to the needs of a diverse user community. We present a prototype of a system used for a virtual laboratory in computational biology.

A simulation study of a MAC layer protocol for wireless networks with asymmetric links

Asymmetric links are common in wireless networks for a variety of physical, logical, operational, and legal considerations. An asymmetric link supports uni-directional communication between a pair of mobile stations and requires a set of relay stations for the transmission of packets in the other direction. We introduce a MAC layer protocol for wireless networks with Asymmetric links (AMAC). The MAC layer protocol requires fewer nodes to maintain silence during a transmission exchange than the protocols proposed in [1, 2]. We present a set of concepts and metrics characterizing the ability of a medium access control protocol to silence nodes which could cause collisions.

Software Engineering Challenges for Mutable Agent Systems

Reconfigurability and mutability are features frequently found in agents operating in heterogeneous computing environment. At the same time, they pose major challenges to the software engineering process. In this paper we review these challenges and discuss their implications towards the agent oriented software engineering methodologies. We propose a set of extensions to the Gaia agent-oriented design and analysis methodology. These extensions allow the methodology to handle certain important classes of mutable systems. These results are presented in the context of the Bond system, a FIPA compliant agent framework, with support for reconfigurability and mutability.

Metainformation and workflow management for solving complex problems in grid environments

Summary form only given. We discuss the semantics of process and case description necessary for the workflow management on a grid used for scientific applications and outline the structure of basic ontologies supporting the coordinated execution of complex tasks. We survey the core services provided by our environment and discuss in some detail the planning service.

A parallel 3D piecewise constant reconstruction algorithm for asymmetric virus structures

In this paper we present an improved method for computing the electron density of virus structures; it uses O(N2) less work and is based on piecewise constant approximation of the Discrete Fourier Transform of the electron density. In these algorithms, the computations to determine the values of the 3D Discrete Fourier Transforms of the density of an asymmetric object can be naturally distributed over the nodes of a parallel system. Some computational results, pertaining to the accuracy, are also given.