• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.228-233
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• 2005

The protein side-chain packing problem (SCPP) is known to be NP-complete. Various graph theoretic based side-chain packing algorithms have been proposed. However as the size of the protein becomes larger, the sampling space increases exponentially. Hence, one approach to cope with the time complexity is to decompose the graph of the protein into smaller subgraphs. Some existing approaches decompose the graph into biconnected components at an articulation point (resulting in an at-most 21-residue subgraph) or solve the SCPP by tree decomposition (4-, 5-residue subgraph). In this regard, we had also presented a deterministic based approach called as SPWCQ using the notion of maximum edge weight clique in which we reduce SCPP to a graph and then obtain the maximum edge-weight clique of the obtained graph. This algorithm performs well for a protein of less than 500 residues. However, it fails to produce a feasible solution for larger proteins because of the size of the search space. In this paper, we present a new heuristic approach for the side-chain packing problem based on the maximum edge-weight clique finding algorithm that enables us to compute the side-chain packing of much larger proteins. Our new approach can compute side-chain packing of a protein of 874 residues with an RMSD of 1.423${\AA}$.

• ETRI Journal
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• v.37 no.5
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• pp.888-897
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• 2015

Group scheduling is an operation whereby control packets arriving in a time slot schedule their bursts simultaneously. Normally, those bursts that are of the same wavelength are scheduled on the same channel. In cases where the support of full wavelength converters is available, such scheduling can be performed on multiple channels for those bursts that are of an arbitrary wavelength. This paper presents a new algorithm for group scheduling on multiple channels. In our approach, to reach a near-optimal schedule, a maximum-weight clique needs to be determined; thus, we propose an additional algorithm for this purpose. Analysis and simulation results indicate that an optimal schedule is almost attainable, while the complexity of computation and that of implementation are reduced.

• Journal of Communications and Networks
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• v.18 no.5
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• pp.846-856
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• 2016

Wireless sensor networks (WSNs) are widely applied in monitoring and control of environment parameters. It is sometimes necessary to disseminate data through wireless links after they are deployed in order to adjust configuration parameters of sensors or distribute management commands and queries to sensors. Several approaches have been proposed recently for data dissemination in WSNs. However, none of these approaches achieves both high efficiency and low complexity simultaneously. To address this problem, cluster-tree based network architecture, which divides a WSN into hierarchies and clusters is proposed. Upon this architecture, data is delivered from base station to all sensors in clusters hierarchy by hierarchy. In each cluster, father broadcasts data to all his children with instantly decodable network coding (IDNC), and a novel scheme targeting to maximize total transmission gain (MTTG) is proposed. This scheme employs a new packet scheduling algorithm to select IDNC packets, which uses weight status feedback matrix (WSFM) directly. Analysis and simulation results indicate that the transmission efficiency approximate to the best existing approach maximum weight clique, but with much lower computational overhead. Hence, the energy efficiency achieves both in data transmission and processing.