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ycao's picture

Yang Cao Blacksburg

Assistant Professor

Office: 2160D Torgersen
Email: ycao@cs.vt.edu
Phone: (540) 231-1417
Website: http://people.cs.vt.edu/~ycao/
Office Hours: MW: 11:00 a.m. - 12:00 p.m.
  • About
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Research Interests
  • Cell Cycle Modeling
  • Computational Biology and Bioinformatics
  • Mathematical Foundations
  • Scientific Computing

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.

Mitochondrion

Computational Biology Lab

URL: 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.

lab-LASCA.jpg

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

2009
Cao Y., Song Z., Cao Y., Samuels D., " An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Polymerase-gamma Inhibition by Nucleoside Reverse Transcriptase Inhibitor", PLos Computational Biology, vol. 5, Jan 2009. Tagged BibTex xml
Gillespie D., Cao Y., Sanft K., Petzold L., " The subtle business of model reduction for stochastic chemical kinetics ", J. Chem. Phys. , 2009. Tagged BibTex xml
Kang P., Cao Y., Ramakrishnan N., Ribbens C.J., Varadarajan S., "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. Tagged BibTex xml
2008
Wang P., Randhawa R., Shaffer C.A., Cao Y., Baumann W.T., "Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation", Proceedings of High Performance Computing and Simulation 2008 (HPCS 2008), pp. 385–392, April, 2008. Tagged BibTex xml
Cao Y., Petzold L., "Slow Scale Tau-leaping Method", Computer Methods in Applied Mechanics and Engineering, 2008. Tagged BibTex xml
Li H., Cao Y., Petzold L., Gillespie D., "Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems", Biotechnology Progress, vol. 24, no. 1, 2008. Tagged BibTex xml
Wang P., Randhawa R., Sha er C., Cao Y., Baumann W., "Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation", High Performance Computing and Simulation Symposium (HPCS 2008), 2008. Tagged BibTex xml
Barik D., Paul M., Baumann W., Cao Y., Tyson J., "Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Time Scales", Biophysics Journal, vol. 95, 2008. Tagged BibTex xml
2007
Y C., D. G., L. P., "The adaptive explicit-implicit tau-leaping method with automatic tau selection", J. Chem. Phys., 2007. Tagged BibTex xml
Gillespie D T., Petzold L R., Cao Y., "Comment on Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates", J. Chem. Phys, 2007. Tagged BibTex xml
Cao Y., Liu Z., "The detailed comparison between StochSim and SSA", The first q-bio conference on cellular information processing, Santa Fe, New Mexico, August, 2007. Tagged BibTex xml
Cao Y., "The adaptive explicit-implicit tau-leap method", SCICADE (International Conference on SCIenti c Computation And Di erential Equations), Santa Malo, France, July, 2007. Tagged BibTex xml
2006
L P., ST L., Y C., Serban R, "Sensitivity analysis of di erential-algebraic equations and partial di erential equations", COMPUTERS & CHEMICAL ENGINEERING, 2006. Tagged BibTex xml
Cao Y., Gillespie D., Petzold L., "Efficient Stepsize Selection for the Tau-Leaping Method", J. Chem. Phys., 2006. Tagged BibTex xml
Cao Y., Petzold L., "Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems", J. Comput. Phys., 2006. Tagged BibTex xml
Cao Y., Petzold L., Gillespie D., "Adaptive tau-leaping method for biochemical systems", minisymposium talk in SIAM Annual Meeting 2006, Boston, Massachusetts, July, 2006. Tagged BibTex xml
2005
Cao Y., Gillespie D., Petzold L., "Avoiding Negative Populations in Explicit Tau Leaping", J. Chem. Phys., 2005. Tagged BibTex xml
Cao Y., Gillespie D., Petzold L., "Accelerated Stochastic Simulation of the Sti Enzyme-Substrate Reaction", J. Chem. Phys., 2005. Tagged BibTex xml
Gunawan R., Cao Y., Petzold L., III D.F., "Sensitivity analysis of discrete stochastic systems", Biophys. J., 2005. Tagged BibTex xml
Cao Y., Petzold L., Gillespie D., "Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems", J. Comput. Phys., 2005. Tagged BibTex xml
Cao Y., Gillespie D., Petzold L., "The slow-scale stochastic simulation algorithm", J. Chem. Phys., 2005. Tagged BibTex xml
Rathinam M., Petzold L., Cao Y., Gillespie D., "Consistency and stability of tau leaping schemes for chemical reaction systems", SIAM Multiscale Modeling and Simulation, 2005. Tagged BibTex xml
Cao Y., Hall A., H L., Petzold L., "StochKit, a new stochastic simulation toolkit", Sixth International Conference on Systems Biology, Boston, Massachusetts, October, 2005. Tagged BibTex xml
Cao Y., Petzold L., "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. Tagged BibTex xml
Cao Y., Petzold L., "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. Tagged BibTex xml
Cao Y., Lampoudi S., Li H., Petzold L., "A software package for discrete stochastic simulation of chemically reacting systems", 4th SIAM conference on Computational Science and Engineering, February, 2005. Tagged BibTex xml
2004
Cao Y., Petzold L., Rathinam M., Gillespie D., "The numerical stability of leaping methods for stochastic simulation of chemically reacting systems", J. Chem. Phys., 2004. Tagged BibTex xml
Cao Y., Li H., Petzold L., "Efficient formulation of the stochastic simulation algorithm for chemically reacting systems", J. Chem. Phys., 2004. Tagged BibTex xml
Cao Y., Petzold L., "A posteriori error estimation and global error control for rrdinary di erential equations by the adjoint method", SIAM J. Scienti c Computing, 2004. Tagged BibTex xml
Cao Y., Petzold L., "An error estimate for matrix equations", Applied Numerical Mathematics, 2004. Tagged BibTex xml
Cao Y., Li H., Petzold L., "Efficient formulation of the stochastic simulation algorithm for chemically reacting systems", the 5th International Conference on Systems Biology, October, 2004. Tagged BibTex xml
Gunawan R., Cao Y., Lampoudi S., Petzold L., III D.F., "Stochastic sensitivity analysis of a circadian gene network", the 5th International Conference on Systems Biology, Heidelberg, Germany, October, 2004. Tagged BibTex xml
2003
Rathinam M., Petzold L., Cao Y., Gillespie D., "Sti ness in stochastic chemically reacting systems: The implicit tau-leaping method", J. Chem. Phys., 2003. Tagged BibTex xml
Cao Y., Petzold L., "A subspace error estimate for linear systems", SIAM J. Mat. Anal. Appl., 2003. Tagged BibTex xml
Cao Y., Petzold L., Gillespie D., "Towards the multiscale simulation of biochemical systems", the workshop of U.S. Army Research Oce, Institute for Collaborative Biotechnologies site visit, UCSB, July, 2003. Tagged BibTex xml
Petzold L., Cao Y., Li S., Serban R., "Adaptive numerical methods for sensitivity analysis of di erential-algebraic equations and partial di erential equations", Proceedings,Workshop on Modeling and Simulation in Chemical Engineering, Coimbra, Portugal, 2003. Tagged BibTex xml
2002
Cao Y., Li S., Petzold L., Serban R., "Adjoint sensitivity analysis for di erential-algebraic equations: the adjoint DAE system and its numerical solution", SIAM J. Sci. Comput., 2002. Tagged BibTex xml
Cao Y., Li S., Petzold L., "Adjoint sensitivity analysis for di erential-algebraic equations: algorithms and software", J. Comp. Appl. Math., 2002. Tagged BibTex xml
2001
Petzold L., Serban R., Li S., Raha S., Cao Y., "sensitivity analysis and design optimization of di erential-algebraic equation systems", NATO Advanced Research Workshop on Computational Aspects of Nonlinear Structural Systems with Large Rigid Body Motion, 2001. Tagged BibTex xml
2000
Cao Y., Li Q., "Multistep discretization of index 3 DAEs", ICMSEC Chinese Acd. Sci, 2000. Tagged BibTex xml
Cao Y., Li S., Petzold L., "Adjoint sensitivity analysis for DAE systems", NSF-KDI/IGPP W orkshop 2000 on Accurate Simulation and Modelling of Physical Systems, San Diego, 2000. Tagged BibTex xml
1999
Cao Y., Li Q., "Predictor-corrector formula for solving index-2 di erential-algebraic equations", Mathematica Numerica Sinica,, 1999. Tagged BibTex xml
1998
Cao Y., Li Q., "A-stable explicit nonlinear Runge-Kutta methods", Tsinghua Science & Technoloty, 1998. Tagged BibTex xml
Cao Y., Li Q., "Nonlinear Runge-Kutta methods for solving di erential-algebraic equations", Chinese J. Numer. Math., April, 1998. Tagged BibTex xml

3000 Level Courses

  • CS/Math3414: Numerical Methods

5000 Level Courses

  • CS5424: Computational Cell Biology
  • CS/Math5485: Numerical Analysis and Software
  • CS5984: Special Study

6000 Level Courses

  • CS6404: Advanced Topics in Mathematical Software

Mitochondrial Deoxynucleotide Metabloism And Disease

Granting Institution: National Institute for General Medial Sciences
Amount: $30,252

Multiscale Modeling Simulation And Sensitivity Analysis of Biochemical Systems Motivated By Pulsatile Insulin Secretion

Granting Institution: National Science Foundation
Amount: $131,568

Stochasitic Models Of Cell Cycle Regulation In Eukaryotes

Granting Institution: National Institute of General Medical Sciences
Amount: $216,240

 
 
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