Yaohang Li Publications

Publications

Journal Papers:

· Yaohang Li, C. E. M. Strauss, A. Gorin, “Hybrid Parallel Tempering and Simulated Annealing Method – an Efficient Sampling Method in ab initio Protein Folding,” in Press, Bioinformatics and Computational Biology for International Journal of Computational Science, 2008.

· Yaohang Li, M. Mascagni, A. Gorin “A Decentralized Parallel Implementation for Parallel Tempering Algorithm,” submitted to Parallel Computing, 2008.

· Yaohang Li, Y. D. Song, “An Adaptive and Trustworthy Software Testing Framework on the Grid,” in Press, Journal of SupterComputing, 2008.

· Yaohang Li, D. Chen, X. Yuan, “Trustworthy Remote Compiling Service for Grid-based Scientific Applications,” Journal of SuperComputing, 41(2):119-131, 2007.

· Yaohang Li, “A Bio-inspired Adaptive Job Scheduling Mechanism on the Grid,” International Journal of Computer Science and Network Security, 6(3B): 1-7, 2006.

· Yaohang Li, V. A. Protopopescu, N. Arnold, X. Zhang, A. Gorin, “Hybrid Parallel Tempering/Simulated Annealing Method,” submitted to Physics Review E., 2006.

· Yaohang Li, M. Mascagni, “Optimizing Dynamic Grid-based Resources for Large Scale Monte Carlo Applications,” submitted for publication in Mathematics and Computers in Simulation, 2005.

· Yaohang Li, M. Mirugi, M. Mascagni, “Test the Rule 30 Cellular Automata Random Number Generator,” submitted for publication in Mathematics and Computers in Simulation, 2005.

· Yaohang Li, M. Mascagni, “Grid-based Quasi-Monte Carlo Applications,” Monte Carlo Methods and Applications, 11: 39-55, 2005.

· Yaohang Li, V. A. Protopopescu, A. Gorin, “Accelerated Simulated Tempering,” Physics Letters A, 328(4): 274-283, 2004.

· Yaohang Li, M. Mascagni, R. van Engelen, Q. Cai, “A Grid Workflow-Based Monte Carlo Simulation Environment,” Journal of Neural Parallel and Scientific Computations (NPSC), 12:439-455, 2004.

· Yaohang Li, M. Mascagni, “Analysis of Large-scale Grid-based Monte Carlo Applications,” International Journal of High Performance Computing Applications (IJHPCA), 17(4): 369-382, 2003. (Jan. 2006, one of the 50 Most-Frequently-Read Articles in International Journal of High Performance Computing Applications. http://hpc.sagepub.com/reports/mfr7.dtl)

· Y. Zhang, Yaohang Li, M. H. Peters, “Nonequilibrium, Multiple-Time Scale Simulations of Ligand-Receptor Interactions in Structured Protein Systems,” Proteins: Structure, Function, and Genetics, 52(3): 339-348, 2003.

M. Mascagni, A. Karaivanova, Yaohang Li, “Quasi-Monte Carlo method for elliptic boundary value problems”, Monte Carlo Methods and Applications, 7: 283-294, 2001.

Book Chapter:

· Yaohang Li, M. Mascagni, “An Overview of Grid-based Monte Carlo Computing,” Grid Technologies, Emerging from Distributed Architectures to Virtual Organizations, WIT Press, ISBN: 978-1-84564-055-2, 2006.

Conference Proceedings:

· Yaohang Li, A. J. Bordner, Y. Tian, X. Tao, A. Gorin, “Extensive Exploration of the Conformational Space Improves Rosetta Results for Short Protein Domains”, accepted in 7th Annual International Conference on Computational Systems Bioinformatics (CSB08), Stanford, 2008.

· Yaohang Li, A. Esterline, C. Baber, K. Fuller, M. Burns, T. L. Hanson, T. LeFebvre, M. Schultz, M. Govett, P. Hamer, A. Mysore, “A Sensor Information Framework for Integrating and Orchestrating Distributed Sensor Services,” accepted in PDPTA’08, Las Vegas, 2008.

· A. Frazier, S. Hudson, Yaohang Li, X. Yuan, “Developing Software System Security Modules,” accepted in 12th Colloquium for Information Systems Security Education, Dallas, 2008.

· Yaohang Li, M. Mascagni, A. Gorin “Decentralized Replica Exchange Parallel Tempering: An Efficient Implementation of Parallel Tempering using MPI and SPRNG,” Proceedings of International Conference on Computational Science and Its Applications (ICCSA), Kuala Lumpur, 2007.

· Yaohang Li, J. Clark, K. Williams, Y. Song, “Efficient Parallel Implementation of Evolutionary Markov Chain Monte Carlo,” Proceedings of PDPTA’07, Las Vegas, 2007.

· Yaohang Li, T. Dong, Y. Song, “Using Grid Computing for Distributed Software Testing,” Proceedings of PDPTA’06, Las Vegas, 2006.

· Yaohang Li, T. Dong, X. Zhang, Y. Song, X. Yuan, “Large-Scale Software Unit Testing on the Grid,” Proceedings of IEEE International Conference on Granular Computing, Atlanta, 2006.

· Yaohang Li, J. Clark, X. Zhang, “Parallel Implementation of the Accelerated Simulated Tempering Method,” Proceedings of 3^rd NPSC Conference, Atlanta, 2006.

· X. Zhang, Yaohang Li, A. Myklebust, “Hybrid Optimization of Geometrically Trimmed NURBS Surfaces,” Proceedings of ASME IMECE, Orlando, 2005.

· Yaohang Li, D. Chen, X. Yuan, Y. Yu, A. Esterline, “Secure Remote Compiling Service on the Grid,” Proceedings of PDPTA’05, Las Vegas, 2005.

· Yaohang Li, M. Mascagni, “A Bio-inspired Job Scheduling Algorithm for Monte Carlo Applications on a Computational Grid,” proceedings of 17^th IMACS World Congress, Scientific Computation, Applied Mathematics, and Simulation, Paris, France, 2005.

· Yaohang Li, T. Dong, M. Bikdash, Y. Song, “Path Planning for Unmanned Vehicles using Ant Colony Optimization on a Dynamic Voronoi Diagram,” Proceedings of International Conference on Artificial Intelligence, ICAI’05, Las Vegas, 2005.

· X. Yuan, P. Vega, H. Yu, Yaohang Li, “A Personal Software Process Tool for Eclipse Environment”, Proceedings of International Conference on Software Engineering Research and Practice (SERP'05), Las Vegas, 2005.

· Yaohang Li, C. E. M. Strauss, A. Gorin, “Parallel Tempering in Rosetta Practice,” Proceedings of International Conference on Bioinformatics and its Applications, (ICBA’04), Fort Lauderdale, Florida, 2004.

· Yaohang Li, M. Mascagni, “E-Science on the Grid: Toward a Dynamic E-Scienc Automation with XML and Workflow Techniques,” Proceedings of the 8^th World Multi-Conference on Systemics, Cybernetics, and Informatics, SCI’04, Orlando, 2004.

· Yaohang Li, Y. Song, “Bio-inspired Fault Tolerant and Adaptive System Modeling and Simulation on the Grid,” Proceedings of the International Conference on Computing, Communications and Control Technologies, CCCT’04, Austin, 2004.

· Yaohang Li, M. Mascagni, “e-Science Workflow on the Grid,” Proceedings of the IADIS International Conference, e-Society 2004, Avila, Spain, 2004.

· Yaohang Li, Q. Cai, Y. Li, “Toward a Dynamic E-Commerce Automation with XML and Workflow Techniques on the Grid,” Proceedings of IEEE SoutheastCon, 2004.

· Yaohang Li, M. Mascagni, M. H. Peters, “Grid-based Nonequilibrium Multiple-Time Scale Molecula Dynamics/Brownian Dynamics Simulations of Ligand-Receptor Interactions in Structured Protein Systems,” Proceedings of the First BioGrid Workshop at the 3rd IEEE/ACM Symposium Cluster Computing and the Grid, Tokyo, 2003.

· M. Mascagni, Yaohang Li, “Computational Infrastructure for Parallel, Distributed, and Grid-based Monte Carlo Computations,” Proceedings of the Fourth International Conference on Large-Scale Scientific Computations (LSSC'03), Sozopol, Bulgaria, Lecture Notes in Computer Sciences, 2907: 39-52, 2003.

· Yaohang Li, M. Mascagni, R. van Engelen “GCIMCA: A Globus and SPRNG Implementation of a Grid Computing Infrastructure for Monte Carlo Applications,” Proceeding of the International Multiconference in Computer Science and Computer Engineering, PDPTA’03, 2003.

· Yaohang Li, M. Mascagni, “Improving Performance via Computational Replication on a Large-Scale Computational Grid,” proceedings of the GP2PC at the IEEE/ACM International Symposium on Cluster Computing and the Grid, IEEE/ACM CCGRID2003, Tokyo, 2003.

· Yaohang Li, M. Mascagni, “Grid-based Monte Carlo Applications,” Lecture Notes in Computer Science, 2536:13-24, GRID2002, Grid Computing Third International Workshop/Conference, Baltimore, 2002.

· Yaohang Li, A. Ali, “Neural Network in Business Application”, Proceedings of IEMS’99 International Conference, Cocoa Beach, FL, 1999.

· Yaohang Li, M. Mascagni, “A Distributed Monte Carlo Integration Tool”, Proceedings of the First Southern Symposium on Computing, Hattiesburg, MS, 1998.