Yang Cao

Associate Professor

2160L Torgersen Hall
Blacksburg, VA 24061

ycao@vt.edu

(540) 231-1417

About

Dr. Cao's research interests are in computational science and engineering. He has worked in the field of numerical solution of differential-algebraic equations (DAEs), sensitivity analysisfor DAEs and ordinary differential equations (ODEs), error estimation and control for linear systems and ODEs, and stochastic simulation for biochemical systems. He has made significant contribution in the stochastic algorithms related to multi-scale problems. The implicit tau-leapingmethod and the slow-scale SSA method proposed by him and his collaborators have become a hot topic in this area.

Labs

Computational Biology Lab

URL: http://people.cs.vt.edu/~ycao
Contact: Yang Cao

Our group focuses on the development of multiscale, multiphysics modeling and simulation methods and tools that help biologists build, simulate and analyze complex biological systems, simulate their dynamics and analyze their functions. Typical biological models include gene expression models, protein interaction networks, and cell cycle models. We are paricularly interested in applications where multiple scales and multiple physics are presented, and has to be modeled in a hybrid way that include both discrete and continuous variables, deterministic and stochastic equations.

We work at the interface of mathematics, computer science, biology and other related subjects. Due to the interdisciplinary feature, we collaborate with other groups with different background.

Laboratory for Advanced Scientific Computing and Applications

URL: http://research.cs.vt.edu/~lasca/
Contact: Layne Watson

The goal of the Laboratory for Advanced Scientific Computing and Applications (LASCA) is to provide expertise and leadership in high-end scientific computing research and education at Virginia Tech. Located in Torgersen Hall, the laboratory is a visible and strategic center of activity in applied high-computation and assist scientists and engineers in applying high-end computing resources to their problems. By bringing together experts in scientific cp\omputing and its applications, LASCA helps build the kind of multidisciplinary teams needed to address today's most challenging computational science problems.

Multiscale Modeling and Computation

Contact: Yang Cao

Publications

2014

Cao, Y., and R. Erban, "Stochastic Turing Patterns: Analysis of Compartment-Based Approaches", Bulletin of Mathematical Biology: Springer US, pp. 1-19, 2014.

Ahn, T., A. Sandu, L. T. Watson, C. A. Shaffer, Y. Cao, and W. T. Baumann, "A framework to analyze the performance of load balancing schemes for ensembles of stochastic simulations", International Journal of Parallel Programming, 04/2014.

2013

Pu, Y., S. Lee, D. C. Samuels, L. T. Watson, and Y. Cao, "The effect of unhealthy beta-cells on insulin secretion in pancreatic islets", BMC MEDICAL GENOMICS}, vol. 6, no. 3, {236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND}, {BIOMED CENTRAL LTD}, NOV 11, 2013.

Li, F., and Y. Cao, "Multigrid Discretization Method for PopZ Polarization in Caulobacter Cell Cycle", The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013), Shanghai, China, 12/2013.

Jin, F., E. Dougherty, P. Saraf, Y. Cao, and N. Ramakrishnan, "Modeling of News and Rumors on Twitter", The 7thWorkshop on Social Network Mining and Analysis (SNA KDD), Chicago, IL, 08/2013.

Pu, Y., S. Lee, D. C. Samuels, L. T. Watson, and Y. Cao, "The effect of unhealthy β-cells on insulin secretion in pancreatic islets", BMC Medical Genomics, vol. 6, Suppl. 3, issue Suppl 3, no. Article S6, pp. 1--13, 2013.

2012

2012

Kang, P., N. Selvarasu, N. Ramakrishnan, C. J. Ribbens, D. Tafti, Y. Cao, and S. Varadarajan, "Implementing modular adaptation of scientific software", Jnl. of Computational Science, vol. 3, pp. 28-45, 2012.

Pu, Y., S. Lee, L. T. Watson, and Y. Cao, "The effect of unhealthy-cells in synchronized insulin secretion", 2012 IEEE Internat. Conf. on Bioinformatics and Biomedicine, Philadelphia, PA, pp. 416--419, 2012.

Liu, Z., Y. Pu, F. Li, C. A. Shaffer, S. Hoops, J. J. Tyson, and Y. Cao, "Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle", {JOURNAL OF CHEMICAL PHYSICS}, vol. {136}, no. {3}, {CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}, {AMER INST PHYSICS}, {JAN 21}, 2012. Abstract

Arendt, D., and Y. Cao, "EFFECTIVE GPU ACCELERATION OF LARGE SCALE, ASYNCHRONOUS SIMULATIONS ON GRAPHS", {ADVANCES IN COMPLEX SYSTEMS}, vol. {15}, no. {8}, {5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE}, {WORLD SCIENTIFIC PUBL CO PTE LTD}, {DEC}, 2012. Abstract

Arendt, D., and Y. Cao, "EVOLUTIONARY MOTIFS FOR THE AUTOMATED DISCOVERY OF SELF-ORGANIZING DIMER AUTOMATA", {ADVANCES IN COMPLEX SYSTEMS}, vol. {15}, no. {8}, {5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE}, {WORLD SCIENTIFIC PUBL CO PTE LTD}, {DEC}, 2012. Abstract

Wang, S., and Y. Cao, "Efficient Implementation of the Hybrid Method for Stochastic Simulation of Biochemical Systems", 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), Orlando, Florida, 2012.

2011

Ball, D. A., T. - H. Ahn, P. Wang, K. C. Chen, Y. Cao, J. J. Tyson, J. Peccoud, and W. T. Baumann, "Stochastic exit from mitosis in budding yeast Model predictions and experimental observations", CELL CYCLE, vol. 10, no. 6, 1806 RIO GRANDE ST, AUSTIN, TX 78702 USA, LANDES BIOSCIENCE, pp. 999-1009, MAR 15, 2011. Abstract

Pu, Y., L. T. Watson, and Y. Cao, "Stiffness detection and reduction in discrete stochastic simulation of biochemical systems", JOURNAL OF CHEMICAL PHYSICS, vol. 134, no. 5, CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA, AMER INST PHYSICS, FEB 7, 2011. Abstract

Wu, S., J. Fu, Y. Cao, and L. Petzold, "Michaelis-Menten speeds up tau-leaping under a wide range of conditions", JOURNAL OF CHEMICAL PHYSICS, vol. 134, no. 13, CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA, AMER INST PHYSICS, APR 7, 2011. Abstract

Song, Z., Y. Cao, and D. C. Samuels, "Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study", PLoS Comput Biol, vol. 7, no. 11: Public Library of Science, pp. e1002287, 11, 2011.

Song, Z., Y. Cao, and D. C. Samuels, "Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study", PLOS COMPUTATIONAL BIOLOGY, vol. 7, no. 11, 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA, PUBLIC LIBRARY SCIENCE, NOV, 2011. Abstract

2010

Zhang, J., L. T. Watson, C. A. Beattie, and Y. Cao, "Radial basis function collocation for the chemical master equation", Internat. J. Comput. Methods, vol. 7, pp. 477-498, 2010.

Pu, Y., L. T. Watson, and Y. Cao, "Stiffness detection and reduction in discrete stochastic simulation of biochemical systems", 2010 Spring Simulation Multiconference, High Performance Computing Symp., Vista, CA, Soc. for Modelling and Simulation Internat., pp. 41-48, 2010.

Pu, Y., S. Lee, D. C. Samuels, L. T. Watson, and Y. Cao, "Hybrid modeling and simulation of insulin secretion pathway in pancreatic islets", 10th IEEE Internat. Conf. on Bioinformatics and Bioengineering, Philadelphia, PA, pp. 156-161, 2010.

Liu, Z., C. A. Shaffer, U. J. Mobassera, L. T. Watson, and Y. Cao, "Multistate modeling and simulation for regulatory networks", 2010 Winter Simulation Conference, pp. 631-642, 2010.

Zhang, J., L. T. Watson, C. A. Beattie, and Y. Cao, "RADIAL BASIS FUNCTION COLLOCATION FOR THE CHEMICAL MASTER EQUATION", INTERNATIONAL JOURNAL OF COMPUTATIONAL METHODS, vol. 7, no. 3, 5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE, WORLD SCIENTIFIC PUBL CO PTE LTD, pp. 477-498, SEP, 2010. Abstract

Zhang, J., L. T. Watson, and Y. Cao, "A modified uniformization method for the solution of the chemical master equation", COMPUTERS & MATHEMATICS WITH APPLICATIONS, vol. 59, no. 1, THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND, PERGAMON-ELSEVIER SCIENCE LTD, pp. 573-584, JAN, 2010. Abstract

2009

Gillespie, D., Y. Cao, K. Sanft, and L. Petzold, "The subtle business of model reduction for stochastic chemical kinetics", J. Chem. Phys. , 2009.

Kang, P., Y. Cao, N. Ramakrishnan, C. J. Ribbens, and S. Varadarajan, "Modular Implementation of Adaptive Decisions in Stochastic Simulations", Proceedings of the 24th Annual ACM Symposium on Applied Computing (SAC'09): ACM, New York, pp. 995-1001, 2009.

Ahn, T. - H., P. Wang, L. T. Watson, Y. Cao, C. A. Shaffer, and W. T. Baumann, "Stochastic cell cycle modeling for budding yeast", Proceedings of 2009 Spring Simulation Multiconference: HPC, G. Wainer, M. Chinni, P. Roman, H. Rajaei, B. Zeigler, and C. Ribbens (eds.), Soc. for Modeling Simulation Internat., San Diego, CA, SCS, pp. 569-574, 03/2009.

Ahn, T. - H., L. T. Watson, Y. Cao, C. A. Shaffer, and W. T. Baumann, "Cell cycle modeling for budding yeast with stochastic simulation algorithms", Computer Modeling in Engineering and Sciences, vol. 51, pp. 27--52, 2009.

Zhang, J., L. T. Watson, and Y. Cao, "Adaptive aggregation method for the Chemical Master Equation", International Journal of Computational Biology and Drug Design, vol. Volume 2, pp. 134 - 148, 2009.

Liu, Z., and Y. Cao, "Stochastic Simulation Methods for Biochemical Models with Multi-State Species", Proceedings to 2009 IEEE Toronto International Conference Science and Technology for Humanity, pp. 363-368, 09/2009.

Pu, Y., S. Lee, Z. Liu, D. Samuels, L. T. Watson, and Y. Cao, "Medeling of Metabolic Oscillations in Mitochondria and their Coupling in a Cell", Medeling of Metabolic Oscillations in Mitochondria and their Coupling in a Cell, Las Vegas, Nevada, pp. 620 625, 07/2009.

Liu, Z., Y. Pu, and Y. Cao, "A Hybrid Method Combining Improved StochSim with SSA for Solving Systems with Multi-State Species", Proceedings of the 2009 International Conference on Bioinformatics & Computational Biology, Las Vegas, Nevada, pp. 626 631, 07/2009.

Zhang, J., L. T. Watson, and Y. Cao, "Radial basis function collocation for the chemical master equation", Conf. on Bioinformatics and Computational Biology, pp. 295–300, 2009.

Zhang, J., M. Sosonkina, L. T. Watson, and Y. Cao, "Parallel solution of the chemical master equation", Proc. 2009 Spring Simulation Multiconference: HPC, San Diego, CA, pp. 563–567, 2009.

Gillespie, D. T., Y. Cao, K. R. Sanft, and L. R. Petzold, "The subtle business of model reduction for stochastic chemical kinetics", JOURNAL OF CHEMICAL PHYSICS, vol. 130, no. 6, CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA, AMER INST PHYSICS, FEB 14, 2009. Abstract

Wendelsdorf, K. V., Z. Song, Y. Cao, and D. C. Samuels, "An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors", PLOS COMPUTATIONAL BIOLOGY, vol. 5, no. 1, 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA, PUBLIC LIBRARY SCIENCE, JAN, 2009. Abstract

Cao, Y., and D. C. Samuels, "DISCRETE STOCHASTIC SIMULATION METHODS FOR CHEMICALLY REACTING SYSTEMS", METHODS IN ENZYMOLOGY: COMPUTER METHODS, VOL 454, PT A, vol. 454, no. Part A, 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA, ELSEVIER ACADEMIC PRESS INC, pp. 115-140, 2009. Abstract

Cao, Y., and D. C. Samuels, Methods in EnzymologyComputer Methods, Part AChapter 5 Discrete Stochastic Simulation Methods for Chemically Reacting Systems, , vol. 454: Elsevier, pp. 115 - 140, 2009.

2008

Wang, P., R. Randhawa, C. A. Shaffer, Y. Cao, and W. T. Baumann, "Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation", Proceedings of High Performance Computing and Simulation 2008 (HPCS 2008), pp. 385–392, April, 2008.

Z. Ruscio, J., D. Kumar, M. Shukla, M. G. Prisant, T. M. Murali, and A. Onufriev, "Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin", Proceedings of the National Academy of Sciences, vol. 105, no. 27, pp. 9204-9209, 2008. Abstract

Cho, Y. J., N. Ramakrishnan, and Y. Cao, "Reconstructing Chemical Reaction Networks: Data Mining meets System Identification", 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'08), Feb, 2008.

Cao, Y., and L. Petzold, "Slow Scale Tau-leaping Method", Computer Methods in Applied Mechanics and Engineering, 2008.

Li, H., Y. Cao, L. Petzold, and D. Gillespie, "Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems", Biotechnology Progress, vol. 24, no. 1, 2008.

Barik, D., M. Paul, W. Baumann, Y. Cao, and J. Tyson, "Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Time Scales", Biophysics Journal, vol. 95, 2008.

Cao, Y., and L. Petzold, "Slow-scale tau-leaping method", COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, vol. 197, no. 43-44, PO BOX 564, 1001 LAUSANNE, SWITZERLAND, ELSEVIER SCIENCE SA, pp. 3472-3479, 2008. Abstract

Li, H., Y. Cao, L. R. Petzold, and D. T. Gillespie, "Algorithms and software for stochastic simulation of biochemical reacting systems", BIOTECHNOLOGY PROGRESS, vol. 24, no. 1, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA, AMER CHEMICAL SOC, pp. 56-61, JAN-FEB, 2008. Abstract

Barik, D., M. R. Paul, W. T. Baumann, Y. Cao, and J. J. Tyson, "Stochastic simulation of enzyme-catalyzed reactions with disparate timescales", BIOPHYSICAL JOURNAL, vol. 95, no. 8, 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA, CELL PRESS, pp. 3563-3574, OCT 15, 2008. Abstract

Liu, Z., and Y. Cao, "Detailed comparison between StochSim and SSA", IET Systems Biology, vol. 2, issue 5, pp. 334, 2008.

2007/2006

2007

Cao, Y., D. Gillespie, and L. Petzold, "The adaptive explicit-implicit tau-leaping method with automatic tau selection", J. Chem. Phys., 2007.

Gillespie, D. T., L. R. Petzold, and Y. Cao, "Comment on Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates", J. Chem. Phys, 2007.

Cao, Y., and Z. Liu, "The detailed comparison between StochSim and SSA", The first q-bio conference on cellular information processing, Santa Fe, New Mexico, August, 2007.

Cao, Y., "The adaptive explicit-implicit tau-leap method", SCICADE (International Conference on SCIentic Computation And Dierential Equations), Santa Malo, France, July, 2007.

Cao, Y., D. T. Gillespie, and L. R. Petzold, "Adaptive explicit-implicit tau-leaping method with automatic tau selection", JOURNAL OF CHEMICAL PHYSICS, vol. 126, no. 22, CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA, AMER INST PHYSICS, JUN 14, 2007. Abstract

2006

Petzold, L., S. T. Li, Y. Cao, and R. Serban, "Sensitivity analysis of dierential-algebraic equations and partial dierential equations", COMPUTERS & CHEMICAL ENGINEERING, 2006.

Cao, Y., D. Gillespie, and L. Petzold, "Efficient Stepsize Selection for the Tau-Leaping Method", J. Chem. Phys., 2006.

Cao, Y., and L. Petzold, "Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems", J. Comput. Phys., 2006.

Cao, Y., L. Petzold, and D. Gillespie, "Adaptive tau-leaping method for biochemical systems", minisymposium talk in SIAM Annual Meeting 2006, Boston, Massachusetts, July, 2006.

2005/2004

2005

Cao, Y., D. Gillespie, and L. Petzold, "Avoiding Negative Populations in Explicit Tau Leaping", J. Chem. Phys., 2005.

Cao, Y., D. Gillespie, and L. Petzold, "Accelerated Stochastic Simulation of the Sti Enzyme-Substrate Reaction", J. Chem. Phys., 2005.

Gunawan, R., Y. Cao, L. Petzold, and D. F. III, "Sensitivity analysis of discrete stochastic systems", Biophys. J., 2005.

Cao, Y., L. Petzold, and D. Gillespie, "Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems", J. Comput. Phys., 2005.

Cao, Y., D. Gillespie, and L. Petzold, "The slow-scale stochastic simulation algorithm", J. Chem. Phys., 2005.

Rathinam, M., L. Petzold, Y. Cao, and D. Gillespie, "Consistency and stability of tau leaping schemes for chemical reaction systems", SIAM Multiscale Modeling and Simulation, 2005.

Cao, Y., A. Hall, L. H, and L. Petzold, "StochKit, a new stochastic simulation toolkit", Sixth International Conference on Systems Biology, Boston, Massachusetts, October, 2005.

Cao, Y., and L. Petzold, "Trapezoidal tau-lepaing formula for the stochastic simulation of biochemical systems", Proceedings of Foundations of Systems Biology in Engineering (FOSBE 2005), pp. pp 149- 152, August, 2005.

Cao, Y., and L. Petzold, "Measurement of error in stochastic simulation: when the mean and the variance are not enough", 4th SIAM conference on Computational Science and Engineering, February, 2005.

Cao, Y., S. Lampoudi, H. Li, and L. Petzold, "A software package for discrete stochastic simulation of chemically reacting systems", 4th SIAM conference on Computational Science and Engineering, February, 2005.

2004

Cao, Y., L. Petzold, M. Rathinam, and D. Gillespie, "The numerical stability of leaping methods for stochastic simulation of chemically reacting systems", J. Chem. Phys., 2004.

Cao, Y., H. Li, and L. Petzold, "Efficient formulation of the stochastic simulation algorithm for chemically reacting systems", J. Chem. Phys., 2004.

Cao, Y., and L. Petzold, "A posteriori error estimation and global error control for rrdinary dierential equations by the adjoint method", SIAM J. Scientic Computing, 2004.

Cao, Y., and L. Petzold, "An error estimate for matrix equations", Applied Numerical Mathematics, 2004.

Cao, Y., H. Li, and L. Petzold, "Efficient formulation of the stochastic simulation algorithm for chemically reacting systems", the 5th International Conference on Systems Biology, October, 2004.

Gunawan, R., Y. Cao, S. Lampoudi, L. Petzold, and D. F. III, "Stochastic sensitivity analysis of a circadian gene network", the 5th International Conference on Systems Biology, Heidelberg, Germany, October, 2004.

2003/2002

2003

Rathinam, M., L. Petzold, Y. Cao, and D. Gillespie, "Stiness in stochastic chemically reacting systems: The implicit tau-leaping method", J. Chem. Phys., 2003.

Cao, Y., and L. Petzold, "A subspace error estimate for linear systems", SIAM J. Mat. Anal. Appl., 2003.

Cao, Y., L. Petzold, and D. Gillespie, "Towards the multiscale simulation of biochemical systems", the workshop of U.S. Army Research Oce, Institute for Collaborative Biotechnologies site visit, UCSB, July, 2003.

Petzold, L., Y. Cao, S. Li, and R. Serban, "Adaptive numerical methods for sensitivity analysis of dierential-algebraic equations and partial dierential equations", Proceedings,Workshop on Modeling and Simulation in Chemical Engineering, Coimbra, Portugal, 2003.

2002

Cao, Y., S. Li, L. Petzold, and R. Serban, "Adjoint sensitivity analysis for dierential-algebraic equations: the adjoint DAE system and its numerical solution", SIAM J. Sci. Comput., 2002.

Cao, Y., S. Li, and L. Petzold, "Adjoint sensitivity analysis for dierential-algebraic equations: algorithms and software", J. Comp. Appl. Math., 2002.

2001/2000

2001

Petzold, L., R. Serban, S. Li, S. Raha, and Y. Cao, "sensitivity analysis and design optimization of dierential-algebraic equation systems", NATO Advanced Research Workshop on Computational Aspects of Nonlinear Structural Systems with Large Rigid Body Motion, 2001.

2000

Cao, Y., and Q. Li, "Multistep discretization of index 3 DAEs", ICMSEC Chinese Acd. Sci, 2000.

Cao, Y., S. Li, and L. Petzold, "Adjoint sensitivity analysis for DAE systems", NSF-KDI/IGPP W orkshop 2000 on Accurate Simulation and Modelling of Physical Systems, San Diego, 2000.