Moon Jung Chung

Multiple sequence alignment using simulated annealing.

Multiple sequence alignment is a useful technique for studying molecular evolution and analyzing structure-sequence relationships. Dynamic programming of multiple sequence alignment has been widely used to find an optimal alignment. However, dynamic programming does not allow for certain types of gap costs, and it limits the number of sequences that can be aligned due to its high computational complexity. The focus of this paper is to use simulated annealing as the basis for developing an efficient multiple sequence alignment algorithm. An algorithm called Multiple Sequence Alignment using Simulated Annealing (MSASA) has been developed. The computational complexity of MSASA is significantly reduced by replacing the high-temperature phase of the annealing process by a fast heuristic algorithm. This heuristic algorithm facilitates in minimizing the solution set of the low-temperature phase of the annealing process. Compared to the dynamic programming approach, MSASA can (i) use natural gap costs which can generate better solution, (ii) align more sequences and (iii) take less computation time.

Generalized Fibonacci cubes are mostly Hamiltonian

The Hamiltonian problem is to determine whether a graph contains a spanning (Hamiltonian) path or cycle. Here we study the Hamiltonian problem for the generalized Fibonacci cubes, which are a new family of graphs that have applications in interconnection topologies [J. Liuand W.-J. Hsu, „Distributed Algorithms for Shortest-Path, Deadlock-Free Routing and Broadcasting in a Class of Interconnection Topologies,” International Parallel Processing Symposium (1992)]. We show that each member of this family contains a Hamiltonian path. Furthermore, we also characterize the members of this family that contain a Hamiltonian cycle.

An object-oriented VHDL design environment

This paper presents a System-level Design Environment(SDE) for VHDL. The object-oriented approach is used for modeling the VHDL entities, design constraints and even design patterns. We suggest the data model and its internal schema, which is suitable for the VHDL semantics. SDE allows a designer to reconfigure the designed schematic by binding its generic components to technology-specific ones. It is effectively used for version control. SDE verifies the design by dynamically checking the constraints. The standard VHDL is extended in order to represent the constraints properly.

Making process visible: A grammatical approach to managing design processes

This paper presents a novel framework for managing design processes using a formal grammar as the theoretical foundation to represent, manipulate and execute design processes. The grammatical approach allows designers to represent a complex activity concisely with a small number of higher-level tasks and to explore alternative processes within a space of feasible alternatives. These capabilities allow the engineers to visualize the design process so that they can fully understand the alternative methods before making any design decisions. The framework, called MIDAS, includes separate layers for process specification and execution. Using the process specification layer, designers can capture the overall design process and each designer can understand his or her task with respect to the whole design process. In the process execution layer, design tasks are executed according to the information in specification layer so that designers can be informed of the current design status, alternative design methods, and their impacts in a whole design process. The framework has the potential to improve design productivity by accessing, reusing, and revising previous processes for a similar design. We use a gearbox design process to demonstrate the framework.

A formal approach to managing design processes

To capture market opportunities, competition within the microelectronics industry demands ever-faster product development, which means ever-shorter design cycles. Shorter design cycles can be achieved by carefully managing the design process during rapid prototyping. Careful management is important because the design process must be (1) adjusted to accommodate constraints such as product performance and design time, and (2) frequently updated to take advantage of new design tools and methodologies. Traditionally, designers have used whatever tools seemed convenient to them at the time, which has made it virtually impossible to determine what methodology was used to produce a given design. These problems can be avoided through design methodology management, which ensures that appropriate tools are selected and executed in the appropriate sequence. Effective design management requires an environment equipped with a formal representation of supported design processes and tools, and an execution environment that helps designers select and execute an appropriate design process. We propose a methodology management system that provides this functionality. >

WSCPC: an architecture using semantic web services for collaborative product commerce

In collaborative product commerce (CPC), design activities need to be carried out concurrently with the identification of potential manufacturing partners based on the design requirements and manufacturing constraints. This paper presents a web service based CPC framework, WSCPC (web services for CPC). WSCPC integrates design process, business plan, and assembly operations using web services in which a task is regarded as a service that an organization can provide and is outsourced to other companies on the fly. In addition, we propose a service-oriented process model that enables a machine to locate actively a CPC service, to check service capabilities, and to execute collaborative service: into an optimized process workflow. Our service-oriented process model is a general drawing to realize functionalities, such as defining CPC service, enacting CPC service, and monitoring the executing status of CPC service. CPC, therefore, can utilize web services to not only discover diverse services of design, manufacturing and logistics, but configure collaborative process design, supporting service oriented CPC within WSCPC framework.

Managing engineering data for complex products

In this article we propose a design framework that integrates many application programs and manages the enormous quantity and variety of data generated while designing a complex product. Our discipline-independent framework provides data management services, such as version control and configuration management, needed by many engineering disciplines. This discipline-independent framework may be extended to satisfy the particular needs of specific engineering disciplines. The framework supports a message passing system and a flexible formula language, which facilitate the integration of design data from multiple disciplines.Our framework also includes powerful features for designing products with customer selectable options. First, we provide constructs, called option variables and option restrictions, for indicating what options are to be offered. Then, our option language allows designers to specify the product parametrically as a function of the option variables. Finally, we provide features for verifying that the design satisfies specified constraints for all combinations of options to be offered.

Generalized Fibonacci Cubes

We present a new class of interconnection topolo gies called the generalized Fibonacci cubes (GFCs, for short) that encompass a range of networks such as the popular Boolean cube (hypercube) and the recent second-order Fibonacci cube in [5]. We show that each GFC has a recursive and self-similar structure and hence exhibits fault tolerant features. We also show that each GFC admits simple embedding of other useful net works such as cycles, trees, and meshes. The GFCs may find applications in fault-tolerant com puting.

A framework for collaborative product commerce using Web services

This paper presents a novel Web-based service-oriented framework to support collaborative product commerce. The framework coordinates processes to design and manufacture a product in a loosely coupled environment using Web services. We have developed a service model using OWL. It provides facilities for companies to discover services that other companies provide. Choreography of Web services is achieved using the process grammar. Usage of process grammar helps to configure processes dynamically, facilitating collaboration among companies. The framework, therefore, provides a truly distributed architecture for management of service composition and interoperation, lending a unique functionality to the framework.

Linear recursive networks and their applications in distributed systems

We present a new class of interconnection topologies called the Linear Recursive Networks (LRNs) and examine their possible applications in distributed systems. Each LRN is characterized by a recursive pattern of interconnection which can be specified by simple parameters. Basic properties such as node degree, diameter, and the performance of routing algorithms for all LRNs are then collectively analyzed in terms of these parameters. By choosing appropriate values for the parameters, our results can assist a network designer in selecting a topology with required routing performance and cost of interconnection. A subclass of LRNs, called Congruent LRNs (CLRNs), is also identified here and shown to possess desirable properties for more tightly coupled systems. It is shown that the CLRNs include existing networks such as hypercube and generalized Fibonacci cubes. These results suggest that the linear recursive networks potentially have applications in interconnecting distributed systems.