Scientific Computing
|
|
Scientific computing concerns the interface between computer science, mathematics, statistics, and science and engineering applications requiring high performance computing. The area is also known as "computational science and engineering" and is truly interdisciplinary. Many computer science faculty are involved with scientific computing to some degree, most notably those in high end computing and computational biology and bioinformatics. Scientific computing activity on campus is focussed by the 
Yang Cao
Associate Professor
| Office: | 2160L Torgersen |
|---|---|
| Email: | ycao@cs.vt.edu |
| Phone: | (540) 231-1417 |
| Website: | http://people.cs.vt.edu/~ycao/ |
| Office Hours: | TR: 9:30 to 10:30 a.m. |
|---|
Wu Feng
Elizabeth and James E. Turner Jr. '56 Faculty Fellowship and Professor
| Office: | 2209 KWII |
|---|---|
| Email: | feng@cs.vt.edu |
| Phone: | 540-231-1192 |
| Website: | http://www.cs.vt.edu/~feng |
| Office Hours: | McBryde 122-B, TR 1:45 - 3:15 pm |
|---|
Alexey V Onufriev
Associate Professor, Computer Science and Physics
| Office: | 2160C Torgersen |
|---|---|
| Email: | alexey@vt.edu |
| Phone: | (540) 231-4237 |
| Website: | http://people.cs.vt.edu/~onufriev/ |
| Office Hours: | by appointment |
|---|
Calvin J. Ribbens
Professor and Associate Department Head for Undergraduate Studies
| Office: | 1108 KWII |
|---|---|
| Email: | ribbens@vt.edu |
| Phone: | (540) 231-6262 |
| Website: | http://people.cs.vt.edu/~ribbens/ |
| Office Hours: | By appointment |
|---|
Adrian Sandu
Professor
| Office: | 2204 KW-II |
|---|---|
| Email: | asandu7@vt.edu |
| Phone: | 231-2193 |
| Website: | http://www.cs.vt.edu/~asandu |
| Office Hours: | McBryde 122-A: Thursday 12:45 - 1:45 pm |
|---|
Layne T. Watson
Professor, Computer Science, Mathematics, and Aerospace and Ocean Engineering
| Office: | 2000B Torgersen |
|---|---|
| Email: | ltw@vt.edu |
| Phone: | (540) 231-7540 |
| Website: | http://people.cs.vt.edu/~ltw/shortvita.html |
| Office Hours: | McBryde 122-A: MWF: 10:00 to 11:00 am |
|---|
2013
Gao, D. Y., L. T. Watson, D. R. Easterling, and W. I. Thacker,
"Solving the canonical dual of box- and integer-constrained nonconvex quadratic programs via a deterministic direct search algorithm",
Optim. Methods Software, vol. 28, pp. 313--326, 2013.
Radcliffe, N. R., L. T. Watson, M. Sosonkina, and R. T. Haftka,
"Adjusting process count on demand for petascale global optimization",
Parallel Comput., vol. 39, pp. 21--35, 2013.
Setareh, M., F. Bacim, B. D. Jones, N. F. Polys, T. Geng, and B. Orsa,
"Integrating Web-based Visualization with Structural System Understanding to Improve the Technical Education of Architects",
Journal of Online Engineering Education, vol. 3, no. 2, 2013.
2012
Polys, N., and A. Wood,
"New Platforms for Health Hypermedia",
Issues in Information Systems, vol. 13, no. 1, pp. 40-50, 2012.
Phillips, R. D., L. T. Watson, R. H. Wynne, and N. Ramakrishnan,
"Continuous iterative guided spectral class rejection classification algorithm",
IEEE Trans. Geoscience Remote Sensing, vol. 50, pp. 2303--2317, 2012.
Viana, F. A. C., R. T. Haftka, and L. T. Watson,
"Sequential sampling for contour estimation with concurrent function evaluations",
Structural Multidisciplinary Optim., vol. 45, pp. 615--618, 2012.
Ghommem, M., M. R. Hajj, D. T. Mook, and L. T. Watson,
"Global optimization of actively morphing flapping wings",
Journal of Fluids and Structures, vol. 33, pp. 210--228, 2012.
Ghommem, M., M. R. Hajj, B. K. Stanford, and L. T. Watson,
"Global and local optimization of flapping kinematics",
53rd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conf., Honolulu, HI, AIAA, pp. 15 pages, 2012.
Allison, D. L., C. C. Morris, J. A. Schetz, and L. T. Watson,
"A multidisciplinary design optimization framework for design studies of an efficient supersonic air vehicle",
14th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conf., Indianapolis, IN, AIAA, pp. 22 pages, 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.
2011
Kang, P., E. Tilevich, S. Varadarajan, and N. Ramakrishnan,
"Maintainable and Reusable Scientific Software Adaptation",
10th International Conference on Aspect-Oriented Software Development (AOSD’11), Porto de Galinhas, Brazil, 03/2011.
Shu, J., L. T. Watson, N. Ramakrishnan, and F. A. Kamke,
"Computational steering in the problem solving environment WBCSim",
Engrg. Comput., vol. 28, pp. 888--911, 2011.
Penninger, C. L., A. Tovar, L. T. Watson, and J. E. Renaud,
"KKT conditions satisfied using adaptive neighboring in hybrid cellular automata for topology optimization",
Internat. J. Pure Appl. Math., vol. 66, pp. 245--262, 2011.
Deshpande, S., L. T. Watson, J. Shu, and F. A. Kamke,
"Data driven surrogate-based optimization in the problem solving environment WBCSim",
Engrg. with Computers, vol. 27, pp. 211--223, 2011.
Radcliffe, N., L. Watson, and M. Sosonkina,
"A comparison of alternatives for communicating with spawned processes",
49th ACM Southeast Conf., Kennesaw, GA, pp. 132--137, 2011.
Akhtar, I., M. Ghommem, L. T. Watson, and A. Mehmood,
"Optimization of lift suppression over a circular cylinder undergoing inline vibrations",
52nd AIAA/\-ASME/\-ASCE/\-AHS/\-ASC Structures, Structural Dynamics, and Materials Conf., Denver, CO, AIAA Paper 2011-1996, pp. 9 pages, 2011.
Mehmood, A., I. Akhtar, M. Ghommem, and L. T. Watson,
"Optimization of drag reduction on a cylinder undergoing rotary oscillations",
52nd AIAA/\-ASME/\-ASCE/\-AHS/\-ASC Structures, Structural Dynamics, and Materials Conf., Denver, CO, AIAA Paper 2011-1997, 2011.
Easterling, D. R., L. T. Watson, and M. Madigan,
"Direct search versus simulated annealing on two high dimensional problems",
2011 Spring Simulation Multiconference, High Performance Computing Symp., Vista, CA, Soc. for Modelling and Simulation Internat., pp. 89--95, 2011.
Radcliffe, N., M. Sosonkina, and L. T. Watson,
"Communication with spawned processes",
2011 Spring Simulation Multiconference, High Performance Computing Symp., Vista, CA, Soc. for Modelling and Simulation Internat., pp. 126--133, 2011.
Phillips, R. D., L. T. Watson, and R. H. Wynne,
"An SMP soft classification algorithm for remote sensing",
2011 Spring Simulation Multiconference, High Performance Computing Symp., Vista, CA, Soc. for Modelling and Simulation Internat., 2011.
Ghommem, M., M. R. Hajj, D. T. Mook, and L. T. Watson,
"Global optimization of flapping kinematics for micro air vehicles",
Internat. Forum of Aeroelasticity and Structural Dynamics, Paris, France, Paper IFASD-2011-150, 2011.
Deshpande, S. G., L. T. Watson, R. A. Canfield, and M. Blair,
"XML schema for aircraft conceptual model representation",
2011 Internat. Conf. on Information and Knowledge Engineering, Las Vegas, NV, CSREA Press, 2011.
Watson, L. T., G. Howell, W. I. Thacker, and S. Seidel,
Proceedings of the 2011 Spring Simulation Multiconference, High Performance Computing Symposium 2011 (HPC 2011),
, vol. 6, Vista, CA, Society for Modeling and Simulation International, pp. iv + 174, 2011.
2010
Belgin, M., G. Back, and C. J. Ribbens,
"Applicability of pattern-based sparse matrix representation for real applications",
International Conference on Computational Science (ICCS 2010), Amsterdam, Elsevier, pp. 203-211, 2010.
Kang, P., N. Selvarasu, N. Ramakrishnan, C. J. Ribbens, D. Tafti, and S. Varadarajan,
"Dynamic tuning of algorithmic parameters of parallel scientific codes",
International Conference on Computational Science (ICCS 2010), Amsterdam, Elsevier, pp. 145-153, 2010.
Randhawa, R., C. A. Shaffer, and J. J. Tyson,
"Model Composition for Macromolecular Regulatory Networks",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 278-287, 2010.
Ramakrishnan, N., S. Tadepalli, L. T. Watson, R. F. Helm, M. Antoniotti, and B. Mishra,
"Reverse engineering dynamic temporal models of biological processes and their relationships",
Proc. National Academy of Sciences, vol. 107, pp. 12511-12516, 2010.
Newkirk, J. T., L. T. Watson, and M. M. Stanisic,
"Determining the number of inverse kinematic solutions of a constrained parallel mechanism using a homotopy algorithm",
ASME J. Mechanisms Robotics, vol. 2, 2010.
Thacker, W. I., J. Zhang, L. T. Watson, J. B. Birch, M. A. Iyer, and M. W. Berry,
"Algorithm 905: SHEPPACK: modified Shepard algorithm for interpolation of scattered multivariate data",
ACM Trans. Math. Software, vol. 37, pp. 1-20, 2010.
Cao, Z., D. R. Easterling, L. T. Watson, D. Li, K. W. Cameron, and W. C. Feng,
"Power saving experiments for large-scale global optimization",
Internat J. Parallel Emergent Distrib. Systems, vol. 25, pp. 381-400, 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.
Viana, F. A. C., R. T. Haftka, and L. T. Watson,
"Why not run the efficient global optimization algorithm with multiple surrogates?",
Structural Dynamics, and Materials Conf., Orlando, FL, 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.
Deshpande, S. G., and L. T. Watson,
"Sequential approximate optimization in the problem solving environment WBCSim",
2010 Spring Simulation Multiconference, High Performance Computing Symp., Vista, CA, Soc. for Modelling and Simulation Internat., pp. 49-56, 2010.
Radcliffe, N. R., D. R. Easterling, L. T. Watson, M. L. Madigan, and K. A. Bieryla,
"Results of two global optimization algorithms applied to a problem in biomechanics",
2010 Spring Simulation Multiconference, High Performance Computing Symp., Vista, CA, Soc. for Modelling and Simulation Internat., pp. 117-123, 2010.
Zhang, L., and L. T. Watson,
"The expected fitness cost of a mutation fixation under the one-dimensional Fisher model",
6th Internat. Symp. on Bioinformatics Research and Appl., vol. LNBI 6053/2010, Springer-Verlag, Berlin, pp. 241-252, 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.
Cao, Y., S. I. Park, and L. T. Watson,
"A novel computation-to-core mapping scheme for robust facet image modeling on GPUs",
2010 Internat. Conf. on Parallel and Distributed Processing Techniques and Appl., vol. 1, Las Vegas, NV, CSREA Press, pp. 189-195, 2010.
Easterling, D. R., L. T. Watson, and M. Madigan,
"The DIRECT algorithm applied to a problem in biomechanics with conformal mapping",
2010 Internat. Conf. on Scientific Computing, Las Vegas, NV, CSREA Press, pp. 128-133, 2010.
Hossain, M. S., S. Tadepalli, L. T. Watson, I. Davidson, R. F. Helm, and N. Ramakrishnan,
"Unifying dependent clustering and disparate clustering for nonhomogeneous data",
16th ACM SIGKDD Conf. on Knowledge Discovery and Data Mining, Washington, DC, pp. 593-602, 2010.
Ghommem, M., M. R. Hajj, L. T. Watson, D. T. Mook, R. D. Snyder, and P. S. Beran,
"Deterministic global optimization of flapping wing motions for micro air vehicles",
13th AIAA/ISSMO Multidisciplinary Analysis Optimization conf., Fort Worth, TX, 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.
Sandu, A., L. Watson, and W. Thacker,
Proceedings of the 2010 Spring Simulation Multiconference, High Performance Computing Symposium (HPC 2010),
, vol. 6, Vista, CA, Society for Modeling and Simulation International, pp. iv + 145, 2010.
2009
Akhtar, I., A. H. Nayfeh, and C. J. Ribbens,
"On the stability and extension of reduced-order galerkin models in incompressible flows: a numerical study of vortex shedding",
Theoretical & Computational Fluid Dynamics, vol. 23, pp. 213-237, 2009.
Sudarsan, R., C. J. Ribbens, and D. Farkas,
"Dynamic Resizing of Parallel Scientific Simulations: A Case Study Using LAMMPS",
International Conference on Computational Science (ICCS 2009): Springer, Heidelberg, pp. 175-184, 2009.
Abstract
Kim, D. K., M. Song, E. Tilevich, C. J. Ribbens, and S. A. Bohner,
"Dynamic Software Updates for Accelerating Scientific Discovery",
International Conference on Computational Science (ICCS 2009): Springer, Heidelberg, pp. 237-247, 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.
Randhawa, R., C. A. Shaffer, and J. J. Tyson,
"Model aggregation: a building-block approach to creating large macromolecular regulatory networks",
Bioinformatics, vol. 25, no. 24, pp. 3289-3295, 2009.
Wainer, G. A., C. A. Shaffer, R. M. McGraw, and M. J. Chinni,
"Proceedings of the 2009 Spring Simulation Multiconference, SpringSim 2009",
2009 Spring Simulation Multiconference, SpringSim 2009, San Diego, California, USA, SCS/ACM, 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.
Akhtar, I., J. Borggaard, T. Iliescu, and C. J. Ribbens,
"Modeling high frequency modes for accurate low-dimensional galerkin models",
39th AIAA Fluid Dynamics Conference, San Antonio, TX, 2009.
2008
Panning, T. D., L. T. Watson, N. A. Allen, K. C. Chen, C. A. Shaffer, and J. J. Tyson,
"Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle",
Journal of Global Optimization, vol. 40, no. 4, Hingham, MA, USA, Kluwer Academic Publishers, pp. 719–738, 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.
Shu, J., L. T. Watson, N. Ramakrishnan, F. A. Kamke, and C. North,
"Unification of problem solving environment implementation layers with XML-based specifications",
Advances in Engineering Software, vol. 39, no. 3, pp. 189-201, March, 2008.
Anandakrishnan, R., and A. Onufriev,
"Analysis of basic clustering algorithms for nu- merical estimation of statistical averages in biomolecules",
J. Comp. Biol., vol. 15, pp. 165–18, 2008.
Onufriev, A.,
"Implicit Solvent Models inMolecular Dynamics Simulations",
Annual Review of Computational Chemistry, 2008.
Giraud, L., A. Haidar, and L. T. Watson,
"Mixed-precision preconditioners in parallel domain decomposition solvers",
Lecture Notes in Computational Science and Engineering: Domain Decomposition Methods in Science and Engineering XVII: U. Langer, M. Discacciati, D. Keyes, O. Widlund, and W. Zulehner (eds.), Springer, Berlin, 2008.
Akhtar, I., A. H. Nayfeh, and C. J. Ribbens,
"A galerkin model of the pressure field in incompressible flows",
46th AIAA Aerospace Sciences Meeting and Exhibit, Reno, NV, January, 2008.
Abstract
2007
Mishra, D., C. A. Shaffer, N. Ramakrishnan, L. T. Watson, K. K. Bae, J. He, A. A. Verstak, and W. H. Tranter,
"S4W: a problem-solving environment for wireless system design",
Software: Practice & Experience, vol. 37, no. 14, New York, NY, USA, John Wiley & Sons, Inc., pp. 1539–1558, 2007.
Panning, T. D., L. T. Watson, C. A. Shaffer, and J. J. Tyson,
"A Mathematical Programming Formulation for the Budding Yeast Cell Cycle",
Simulation, vol. 83, no. 7, San Diego, CA, USA, Society for Computer Simulation International, pp. 497–514, 2007.
Thomas, L., C. A. Shaffer, L. Mili, and E. Thomas,
"Automated Detection of Severe Surface Defects on Barked Hardwood Logs",
Forest Product Journal, vol. 57, no. 4, pp. 50–56, April, 2007.
Thomas, E., L. Thomas, and C. A. Shaffer,
"Defect detection on hardwood logs using high resolution laser scan data",
Proceedings of the 15th International Symposium on Non-Distructive Testing of Wood, August, 2007.
Randhawa, R., C. A. Shaffer, and J. J. Tyson,
"Fusing and Composing Macromolecular Regulatory Network Models",
Proceedings of the 2007 High Performance Computing Symposium (HPC 2007), pp. 337–344, March, 2007.
Sandu, A. , and E. M. Constantinescu,
"Multirate Adams-Bashforth integration of hyperbolic systems",
Journal on Scientific Computing, vol. submitted, 2007.
Sandu, A. ,
On consistency properties of discrete adjoint linear multistep methods,
, no. CS-TR-07-4: Computer Science Department, Virginia Tech, 2007.
Hakami, A., D. K. Henze, J. H. Seinfeld, K. Singh, A. Sandu, S. Kim, D. Byun, and Q. Li,
"The adjoint of CMAQ",
Environmental Science and Technology, vol. 41, no. 22, pp. 7807–7817, 2007.
Constantinescu, E. M., A. Sandu, T. Chai, and G. R. Carmichael,
"Autoregressive models of background errors for chemical data assimilation",
Journal of Geophysical Research, vol. 112, no. D12309, 2007.
Constantinescu, E. M., and A. Sandu,
"Multirate timestepping methods for hyperbolic conservation laws",
Journal on Scientific Computing, vol. 33, no. 3, pp. 239–278, 2007.
Constantinescu, E. M., A. Sandu, T. Chai, and G. R. Carmichael,
"Ensemble-based chemical data assimilation. I: General approach",
Quarterly Journal of the Royal Meteorological Society, vol. 133, no. 626, pp. 1229–1243, July, 2007.
Constantinescu, E. M., A. Sandu, T. Chai, and G. R. Carmichael,
"Ensemble-based chemical data assimilation. II: Covariance localization",
Quarterly Journal of the Royal Meteorological Society, vol. 133, no. 626, pp. 1245–1256, July, 2007.
Chai, T., G. R. Carmichael, Y. Tang, A. Sandu, M. Hardesty, P. Pilewskie, S. Whitlow, E. V. Browell, M. A. Avery, V. Thouret, et al.,
"Four dimensional data assimilation experiments with ICARTT (International Consortium for Atmospheric Transport and Transformation) ozone measurements",
Journal of Geophysical Research, vol. 112, no. D12S15, 2007.
Constantinescu, E. M., A. Sandu, T. Chai, and G. R. Carmichael,
"Assessment of ensemble-based chemical data assimilation in an idealized setting",
Atmospheric Environment, vol. 41, no. 1, pp. 18-36, 2007.
Mongan, J., A. Svrcek-Seiler, and A. Onufriev,
"Analysis of integral expressions for effective Born radii",
J. Chem. Phys., vol. 127, 2007.
Mongan, J., C. Simmerling, J. A. McCammon, D. A. Case, and A. Onufriev,
"Generalized Born Model with a Simple, Robust Molecular Volume Correction",
J. Chem. Theory and Comput, vol. 3, pp. 156-169, 2007.
Saha, N., L. T. Watson, K. Kafadar, N. Ramakrishnan, A. Onufriev, S. P. Mane, and C. Vasquez-Robinet,
"Validation and estimation of parameters for a general probabilistic model of the PCR process",
J. Comp. Biol., vol. 14, pp. 102–117, 2007.
Fenley, A. T., J. C. Gordon, and A. Onufriev,
"An Analytical Approach to Computing Biomolecular Electrostatic Potential",
J. Chem. Phys, 2007.
Iyer, M. A., L. T. Watson, and J. B. Birch,
"pRIPPLE: a parallel version of a polynomial-time piecewise linear estimation algorithm",
Proc. 2007 Spring Simulation Multiconf., Business and Industry Symp., Vol. II, M. J. Ades, M. J. Chinni, J. A. Hamilton, Jr., J. M. D. Hill, H. Rajaei, and C.-H. Wu (eds.), Soc. for Modeling and Simulation Internat., vol. 2, San Diego, CA, pp. 99–103, 2007.
Phillips, R. D., L. T. Watson, and R. H. Wynne,
"A shared memory parallel algorithm for hybrid image classificatio",
Proc. 2007 Spring Simulation Multiconf., High Performance Computing Symp., M. J. Ades, M. J. Chinni, J. Nutaro, T. ¨Oren, H. Rajaei, and L. Watson (eds), Soc. for Modeling and Simulation Internat., vol. 1, pp. 405–411, 2007.
Iyer, M. A., and L. T. Watson,
"RIPPLE: residual initiated polynomial-time piecewise linear estimation",
Proc. IEEE SoutheastCon 2007, Richmond, VA, pp. 444-449, 2007.
Kugele, S. C., L. T. Watson, and M. W. Trosset,
"Interplay of numerical intergation with gradient based optimization algorithms for robust design optimization",
Proc. IEEE SoutheastCon 2007, Richmond, VA, pp. 472–477, 2007.
Kugele, S. C., L. T. Watson, and M. W. Trosset,
"Multidimensional numerical integration for robust design optimization",
Proc. 45th ACM Southeast Conf., Winston-Salem, NC, pp. 472–477, 2007.
Iyer, M. A., and L. T. Watson,
"A performance comparison of RIPPLE and LMS for high dimensional piecewise linear functions",
Proc. 45th ACM Southeast Conf., Winston-Salem, NC, 2007.
Phillips, R. D., L. T. Watson, R. H. Wynne, and C. E. Blinn,
"Data reduction using the singular value decomposition for a hybrid classifier",
Proc. 2007 Internat. Conf. on Scientific Computing: H. R. Arabnia, J. Y. Yang, and M. Q. Yang (eds.), CSREA Press, USA, pp. 183–188, 2007.
Zhang, J., and L. T. Watson,
"A modified uniformization method for the chemical master equation",
Proc. 7th IEEE Internat. Conf. on Bioinformatics and Bioengineering, Boston, MA, pp. 1429–1433, 2007.
Sudarsan, R., and C. J. Ribbens,
"“ReSHAPE: A framework for dynamic resizing and scheduling of homogeneous applications in a parallel environment",
Proceedings of the International Conference on Parallel Processing (ICPP-2007), Washington, DC, IEEE Computer Society, pp. 44, 2007.
Sudarsan, R., and C. J. Ribbens,
"Efficient multidimensional data redistribution for resizable parallel computations",
Proceedings, Fifth International Symposium on Parallel and Distributed Processing and Applications (ISPA-07), Berlin, Springer-Verlag, pp. 182–194, 2007.
Belgin, M., C. J. Ribbens, and G. Back,
"An operation stacking framework for large ensemble computations",
Proceedings of the 21st ACM International Conference on Supercomputing (ICS07), New York, B. Smith (ed.), 2007, ACM, pp. 83–92, 2007.
2006
Thomas, L., L. Mili, E. Thomas, and C. A. Shaffer,
"Defect Detection on Hardwood Logs Using Laser Scanning",
Wood and Fiber Science, vol. 38, no. 4, pp. 682–695, October, 2006.
Allen, N. A., K. C. Chen, C. A. Shaffer, J. J. Tyson, and L. T. Watson,
"Computer Evaluation of Network Dynamics Models with Application to Cell Cycle Control in Budding Yeast",
IEE Proceedings – Systems Biology, vol. 153, no. 1, pp. 13–21, January, 2006.
Shaffer, C. A., R. Randhawa, and J. J. Tyson,
"The role of composition and aggregation in modeling macromolecular regulatory networks",
WSC '06: Proceedings of the 38th conference on Winter simulation: Winter Simulation Conference, pp. 1628–1636, 2006.
Sauro, H. M., D. Harel, M. Kwiatkowska, C. A. Shaffer, A. M. Uhrmacher, M. Hucka, P. Mendes, L. Strömback, and J. J. Tyson,
"Challenges for modeling and simulation methods in systems biology",
WSC '06: Proceedings of the 38th conference on Winter simulation: Winter Simulation Conference, pp. 1720–1730, 2006.
Thomas, E., L. Thomas, C. A. Shaffer, and L. Mili,
"Using External High-Resolution Log Scanning to Determine Internal Defect Characteristics",
Proceedings of the 15th Central Hardwood Forestry Conference, pp. 497–505, February, 2006.
Panning, T. D., L. T. Watson, N. A. Allen, C. A. Shaffer, and J. J. Tyson,
"Deterministic Global Parameter Estimation for a Budding Yeast Model",
Proceedings of the 2006 High Performance Computing Symposium (HPC'06), pp. 195–201, 2006.
Vass, M., C. A. Shaffer, N. Ramakrishnan, L. T. Watson, and J. J. Tyson,
"The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. Vol. 3, no. 2, pp. 155–164, April-June, 2006.
Miehe, P., and A. Sandu,
"Forward, Tangent Linear, and Adjoint Runge Kutta Methods in KPP–2.2 for Efficient Chemical Kinetic Simulations",
Applied Numerical Mathematics, 2006.
Sandu, A. ,
"On the Properties of Runge-Kutta Discrete Adjoints",
Lecture Notes in Computer Science, vol. LNCS 3994,: "International Conference on Computational Science", pp. 550–557, 2006.
Hakami, A., J. H. Seinfeld, T. Chai, Y. Tang, G. R. Carmichael, and A. Sandu,
"Adjoint sensitivity analysis of ozone non-attainment over the continental United States",
Environmental Science and Technology, 2006.
Sandu, C., A. Sandu, and L. and Li,
"Modeling of stochastic terrain profiles and soil parameters",
SAE 2005 Transactions – Journal of Commercial Vehicles, vol. 114, no. 2, pp. 211–220, 2006.
Chai, T., G. R. Carmichael, A. Sandu, Y. Tang, and D. N. Daescu,
"Chemical data assimilation with TRACE-P aircraft measurements",
Journal of Geophysical Research, vol. 111, no. D02301, 2006.
Sandu, A. , and R. Sander,
"Modeling chemical kinetic systems in Fortran90 and Matlab with KPP-2.1",
Atmospheric Chemistry and Physics, vol. 6, pp. 187–195, 2006.
Sandu, A. ,
"Piecewise polynomial solutions of aerosol dynamics",
Aerosol Science and Technology, vol. 40, pp. 1–13, 2006.
Sandu, A. , C. Sandu, and M. Ahmadian,
"Modeling multibody dynamic systems with uncertainties. Part I: theoretical and computational aspects",
Multibody System Dynamics, vol. 15, no. 4, pp. 369–391, 2006.
Sandu, A. , C. Sandu, and M. Ahmadian,
"Modeling multibody dynamic systems with uncertainties. Part II: numerical applications",
Multibody System Dynamics, vol. 15, no. 3, pp. 245–266, 2006.
Ruscio, J. Z., and A. Onufriev,
"A computational study of nucleosomal DNA flexibility",
Bio- phys J , vol. 91, pp. 4121-4132, 2006.
Saha, N., L. T. Watson, K. Kafadar, A. Onufriev, N. Ramakrishnan, C. Vasquez-Robinet, and J. Watkinson,
"A general probabilistic model of the PCR process",
Appl. Math. Comput, vol. 182 , pp. 232–243, 2006.
Sigalov, G., A. Fenley, and A. Onufriev,
"Analytical Linearized Poisson–Boltzmann Ap- proach: Beyond the Generalized Born Approximation",
J. Chem. Phys., vol. 124, 2006.
Myers, J., G. Grothaus, and A. Onufriev,
"A simple, robust approach to calculat- ing partition function of protonation microstates in biomolecules.",
Proteins: Structure, Function, and Bioinformatics, vol. 63, pp. 928 - 938 , 2006.
Shu, J., L. T. Watson, B. G. Zombori, and F. A. Kamke,
"WBCSim: an environment for modeling wood-based composites manufacture",
Engrg. Computers, vol. 21, pp. 259–271, 2006.
Hosder, S., B. Grossman, R. T. Haftka, W. H. Mason, and L. T. Watson,
"Quantitative relative comparison of CFD simulation uncertainties for a transonic diffuser problem",
Comput. & Fluids, vol. 35, pp. 1444–1458, 2006.
Goel, T., R. T. Haftka, W. Shyy, and L. T. Watson,
"Pointwise RMS bias error estimates for design of experiments",
Proc. 44th AIAA Aerospace Sciences Meeting & Exhibit, AIAA Paper 2006-0724, Reno, NV, pp. 22 pages, 2006.
Iyer, M. A., L. T. Watson, and M. W. Berry,
"SHEPPACK: a Fortran 95 package for interpolation using the modified Shepard algorithm",
Proc. 44th ACM Southeast Conf., Melbourne, FL, pp. 476–481, 2006.
Iyer, M. A., and L. T. Watson,
"An interpolation method for high dimensional scattered data",
Proc. 2006 Spring Simulation Multiconf., Business and Industry Symp., J. A. Hamilton, Jr., R. MacDonald, and M. J. Chinni (eds.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 217–222, 2006.
He, J., A. Verstak, L. T. Watson, and M. Sosonkina,
"Performance studies of a parallel global search algorithm on System X",
Proc. 2006 Spring Simulation Multiconf., High Performance Computing Symp., J. A. Hamilton, Jr., R. MacDonald, and M. J. Chinni (eds.), Soc. for Modeling and Simulation Internat, San Diego, CA, 209–214, 2006.
Watson, L. T., M. W. Trosset, and S. C. Kugele,
"Statistical decision-theoretic methods for robust design optimization",
Proc. 2006 NSF Design, Service, and Manufacturing Grantees and Research Conf., CD-ROM, St. Louis, MO, pp. 13 pages, 2006.
Goel, T., R. T. Haftka, W. Shyy, and L. T. Watson,
"Combining bias and variance based criteria for selecting experimental designs",
Proc. 2006 NSF Design, Service, and Manufacturing Grantees and Research Conf., CD-ROM, St. Louis, MO, pp. 16 pages, 2006.
Polys, N., D. Bowman, C. North, R. Laubenbacher, and K. Duca,
"PathSim Visualizer: An Information-Rich Virtual Environment for Systems Biology",
Web3D Symposium, Monterey, CA, ACM Press, 2006.
Abstract
2005
Allen, N. A., C. A. Shaffer, and L. T. Watson,
"Building modeling tools that support verification, validation, and testing for the domain expert",
WSC '05: Proceedings of the 37th conference on Winter simulation: Winter Simulation Conference, pp. 419–426, 2005.
Sandu, A. , E. M. Constantinescu, W. Liao, G. R. Carmichael, T. Chai, J. H. Seinfeld, and D. Daescu,
"Ensemble Filter Data Assimilation for Atmospheric Chemical and Transport Models",
International Conference on Computational Science (ICCS05): International Conference on Computational Science, pp. 648–656, 2005.
Constantinescu, E. M., W. Liao, and A. Sandu,
"Mesh Refinement Strategies in Air Quality Modeling",
High Performance Computing Symposium (HPC 2005): High Performance Computing Symposium, pp. 158–163, 2005.
Constantinescu, E. M., and A. Sandu,
"On Adaptive Mesh Refinement for Atmospheric Pollution Models",
Lecture Notes in Computer Science, vol. 3515: "International Conference on Computational Science", pp. 798–806, 2005.
Hakami, A., D. K. Henze, J. H. Seinfeld, T. Chai, Y. Tang, G. R. Carmichael, and A. Sandu,
"Adjoint inverse modeling of black carbon during ACE-Asia",
Journal of Geophysical Research, vol. 110, no. D14, 2005.
Sandu, A. , W. Liao, G. R. Carmichael, D. K. Henze, and J. H. Seinfeld,
"Inverse modeling of aerosol dynamics using adjoints – theoretical and numerical considerations",
Aerosol Science and Technology, vol. 39, pp. 1–18, 2005.
Sandu, A. , D. Daescu, G. R. Carmichael, and T. Chai,
"Adjoint sensitivity analysis of regional air quality models",
Journal of Computational Physics, vol. 204, pp. 222–252, 2005.
Case, D. A., T. Darden, T. Cheatham, H. Gohlke, K. Merz, A. Onufriev, R. Luo, and R. Woods,
"The Amber Bio-molecular Simulation Programs",
Journal of Computational Chemistry , vol. 26, pp. 1668-1688, 2005.
Sigalov, G., P. Scheffel, and A. Onufriev,
"Incorporating various dielectric environments into the generalized Born model",
J. Chem. Phys., vol. 122, 2005.
Onufriev, A., and G. M. Ullmann,
"Decomposing Complex Ligand Binding into Simple Com- ponents: Connections between Microscopic and Macroscopic models.",
J. Phys. Chem. , vol. 108, pp. 11157–11169, 2005.
Haftka, R. T., and L. T. Watson,
"Multidisciplinary design optimization with quasiseparable subsystems",
Optim. Engrg., vol. 6, pp. 9–20, 2005.
Zwolak, J. W., J. J. Tyson, and L. T. Watson,
"“Parameter estimation for a mathematical model of the cell cycle in frog eggs",
J. Comput. Biology, vol. 12, pp. 48–63, 2005.
Gantovnik, V. B., Z. Gurdal, L. T. Watson, and C. M. Anderson-Cook,
"A genetic algorithm for mixed integer nonlinear programming problems using separate constraint approximations",
AIAA J., vol. 43, pp. 1844–1849, 2005.
Hosder, S., B. Grossman, R. T. Haftka, W. H. Mason, and L. T. Watson,
"Observations on CFD simulation uncertainties",
Proc. 9th AIAA/ISSMO Symp. on Multidisciplinary Analysis and Optimization, CD-ROM, Atlanta, GA, pp. 18 pages, 2005.
Adams, D. B., L. T. Watson, O. Seresta, and Z. Gurdal,
"Global/local iteration for blended composite laminate panel structure optimization subproblems",
Proc. High Performance Computing Symposium 2005, M. Parashar and L. Watson (eds.) Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 151-157, 2005.
He, J., M. Sosonkina, L. T. Watson, A. Verstak, and J. W. Zwolak,
"Data-distributed parallelism with dynamic task allocation for a global search algorithm",
Proc. High Performance Computing Symposium 2005, M. Parashar and L. Watson (eds.), Soc. for Modeling and Simulation Internat.: San Diego, CA, pp. 164–172, 2005.
Barkhi, R., T. James, and L. T. Watson,
"Problem characteristics determining the appropriateness of genetic algorithm approaches",
Proc. Business and Industry Symposium 2005, M. J. Ades and T. Hang (eds.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 135–139, 2005.
Phillips, R. D., L. T. Watson, and R. H. Wynne,
"Hybrid image classification using a shared memory parallel algorithm",
Proc. 16th William T. Pecora Memorial Symp., CD-ROM, Sioux Falls, SD, pp. 12 pages, 2005.
Belgin, M., and C. J. Ribbens,
"Improving the performance of HPC applications by using operation stacking",
Proceedings of ICCSE2005, The International Conference on Computational Science and Engineering, H. Dag and Y. Deng (eds.), Istanbul Technical University, pp. 183–190, 2005.
Ribbens, C. J., S. Varadarajan, M. Chinnusamy, and G. Swaminathan,
"Balancing computational science and computer science research on a terascale computing facility",
Proceedings of ICCS 2005, the 5th International Conference on Computational Science, Berlin, V. Sunderam, G. van Albada, P. Sloot, J. Dongarra (eds.), Springer-Verlag, pp. 60–67, 2005.
2004
He, J., A. Verstak, L. T. Watson, C. A. Stinson, N. Ramakrishnan, C. A. Shaffer, T. S. Rappaport, C. R. Anderson, K. Bae, J. Jiang, et al.,
"Globally Optimal Transmitter Placement for Indoor Wireless Communication Systems",
IEEE Transactions on Wireless Communications, vol. 3, no. 6, pp. 1906–1911, November, 2004.
Vass, M., N. Allen, C. A. Shaffer, N. Ramakrishnan, L. T. Watson, and J. J. Tyson,
"The JigCell Model Builder and Run Manager",
Bioinformatics, vol. 20, no. 18, Oxford, UK, Oxford University Press, pp. 3680–3681, 2004.
Skidmore, R. R., A. Verstak, N. Ramakrishnan, T. S. Rappaport, L. T. Watson, J. He, S. Varadarajan, C. A. Shaffer, J. Chen, K. K. Bae, et al.,
"Towards integrated PSEs for wireless communications: experiences with the S4W and SitePlanner\textregistered projects",
SIGMOBILE Mob. Comput. Commun. Rev., vol. 8, no. 2, New York, NY, USA, ACM, pp. 20–34, 2004.
Thomas, L., L. Mili, C. A. Shaffer, and E. Thomas,
"Defect Detection on Hardwood Logs Using High Resolution Three-dimensional Laser Scan Data",
IEEE International Conference on Image Processing, ICIP, pp. 243–246, October, 2004.
He, J., M. Sosonkina, C. A. Shaffer, J. J. Tyson, L. T. Watson, J. W. Zwolak, and J. Meyer,
"A Hierarchical Parallel Scheme for a Global Search Algorithm",
Proceedings of the 2004 High Performance Computing Symposium (HPC'04): Society for Modeling and Simulation International, pp. 43–50, 2004.
Heath, L. S., C. J. Ribbens, and S. V. Pemmaraju,
"Processor-Efficient Sparse Matrix-Vector Multiplication",
Computers and Mathematics with Applications , vol. 48, pp. pp. 589-608. , 2004.
Sandu, A. , D. Daescu, G. R. Carmichael, and T. Chai,
"Parallel Chemical Data Assimilation in Atmospheric Models",
SIAM Conference on Parallel Processing PP04, vol. Session CP, pp. San Francisco, 2004.
Sandu, A. , C. Belwal, and E. M. Constantinescu,
Parallel Adaptive Simulations of Regional Air Quality,
: SIAM Conference on Parallel Processing for Scientific Computing, 2004.
Sandu, A. , C. Sandu, B. Chan, and M. Ahmadian,
"Control of mechanical systems using a parameterized spectral decomposition approach",
Sixth annual symposium on advanced vehicle technology, no. IMECHE-200, pp. 9, November 14-19, 2004.
Sandu, C., A. Sandu, B. Chan, and M. Ahmadian,
"Treating uncertainties in multi-body dynamic systems using a polynomial chaos spectral decomposition",
Sixth annual symposium on advanced vehicle technology, no. IMECHE-200, pp. 9, November 14-19, 2004.
Chai, T., G. R. Carmichael, D. Daescu, and A. Sandu,
"Analysis of Trace-P observations using a 4D-Var data assimilation technique",
{Proceedings of the 84-th American Meteorological Society annual meeting}, vol. Session 8:, no. 8.4, pp. 6, January 11-15, 2004.
Carmichael, G. R., A. Sandu, D. Daescu, T. Chai, J. H. Seinfeld, P. Hess, and T. Anderson,
"Chemical data assimilation in support of air quality forecasting",
Proceedings of the 84-th American Meteorological Society annual meeting, vol. Session 2:, no. 2.1, pp. 6, January 11-15, 2004.
Sandu, A. , W. Liao, G. R. Carmichael, D. Henze, J. H. Seinfeld, T. Chai, and D. Daescu,
"Computational aspects of data assimilation for aerosol dynamics",
Lecture Notes in Computer Science, vol. 3038: Springer-Verlag GmbH, pp. 709–716, June, 2004.
Belwal, C., A. Sandu, and E. M. Constantinescu,
"Adaptive resolution modeling of air pollution",
ACM Symposium on Applied Computing (SAC-2004), pp. 235–239, March, 2004.
Tang, Y., G. R. Carmichael, L. W. Horowitz, I. Uno, J. H. Woo, D. G. Streets, D. Dabdub, G. Kurata, A. Sandu, J. Allan, et al.,
"Multi-scale simulations of tropospheric chemistry in the Eastern Pacific and U.S. West coast during spring 2002",
Journal of Geophysical Research - Atmospheres, vol. 109, no. D23, 2004.
Tang, Y., G. R. Carmichael, J. H. Seinfeld, D. Dabdub, R. J. Weber, B. Huebert, A. D. Clarke, S. A. Guazzotti, D. A. Sodeman, K. A. Prather, et al.,
"Three-dimensional studies of aerosol ions and their size distribution in East Asia during spring 2001",
Journal of Geophysical Research, vol. 109, no. D19, 2004.
Henze, D. K., J. H. Seinfeld, W. Liao, A. Sandu, and G. R. Carmichael,
"Inverse modeling of aerosol dynamics: condensational growth",
Journal of Geophysical Research, vol. 109, no. D14, 2004.
Onufriev, A., D. Bashford, and D. A. Case,
"Exploring protein native states and large-scale conformational changes with a modified Generalized Born model",
Proteins, vol. 55, pp. 383-394, 2004.
Feig, M., A. Onufriev, M. S. Lee, W. Im, D. A. Case, and C. L. Brooks.,
"Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures",
Journal of Computational Chemistry , vol. 468, pp. 96–111, 2004.
Goncalves, M. A., E. A. Fox, L. T. Watson, and N. A. Kipp,
"Streams, structures, spaces, scenarios, societies (5S): a formal model for digital libraries",
ACM Trans. Infor. Systems, vol. 22, pp. 270–312, 2004.
Goncalves, M. A., E. A. Fox, L. T. Watson, and N. A. Kipp,
"Streams, structures, spaces, scenarios, societies (5S): a formal model for digital libraries",
ACM Trans. Infor. Systems, vol. 22, pp. 270–312, 2004.
Zwolak, J. W., J. J. Tyson, and L. T. Watson,
"Finding all steady state solutions of chemical kinetic models",
Nonlinear Anal.: Real World Appl., vol. 5, pp. 801-814, 2004.
Liu, B., R. T. Haftka, and L. T. Watson,
"Global-local structural optimization using response surfaces of local optimization margins",
Structural Multidisciplinary Optim., vol. 27, pp. 352–359, 2004.
Schutte, J., R. T. Haftka, and L. T. Watson,
"Decomposition and two-level optimization of structures with discrete sizing variables",
AIAA Paper 2004–1541, in Proc. AIAA/ASME/- ASCE/AHS/ASC 45th Structures, Structural Dynamics, and Materials Conf., CD-ROM, Palm Springs, CA, pp. 5 pages, 2004.
Agarwal, H., J. C. Lee, L. T. Watson, and J. E. Renaud,
"A unilevel method for reliability based design optimization",
Proc. AIAA/ASME/ASCE/AHS/ASC 45th Structures, Structural Dynamics, and Materials Conf., CD-ROM, Palm Springs, CA, pp. 19 pages, 2004.
Setoodeh, S., Z. Gurdal, M. Abdalla, and L. T. Watson,
"Design of variable stiffness composite laminates for maximum bending stiffness",
AIAA Paper 2004–4528, in Proc. 10th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conf., CD-ROM, Albany, NY, pp. 8 pages, 2004.
Adams, D. B., S. Setoodeh, L. T. Watson, and Z. Gurdal,
"Pipeline implementation of cellular automata for structural design on message-passing multiprocessors",
AIAA Paper 2004–4444, in Proc. 10th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conf., CD-ROM, Albany, NY, pp. 9 pages, 2004.
Gantovnik, V., Z. Gurdal, and L. T. Watson,
"Linear Shepard interpolation for high dimensional piecewise smooth functions",
AIAA Paper 2004–4486, in Proc. 10th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conf., CD-ROM, Albany, NY, 2004.
Seresta, O., Z. Gurdal, and L. T. Watson,
"Optimal design of composite wing structure with blended laminates",
AIAA Paper 2004–4349, in Proc. 10th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conf., CD-ROM, Albany, NY, pp. 13 pages, 2004.
Agarwal, H., J. E. Renaud, V. M. Perez, and L. T. Watson,
"Homotopy methods for constraint relaxation in unilevel reliability based design optimization",
AIAA Paper 2004–4402, in Proc. 10th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conf., CD-ROM, Albany, NY, pp. 12 pages, 2004.
Tadepalli, S., C. J. Ribbens, and S. Varadarajan,
"GEMS: A job management system for fault tolerant grid computing",
Proceedings High Performance Computing Symposium 2004, San Diego, CA, J. Meyer (ed.), Soc. for Modeling and Simulation Internat., pp. 59-66, 2004.
2003
Allen, N. A., C. A. Shaffer, M. T. Vass, N. Ramakrishnan, and L. T. Watson,
"Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling support environment",
Simulation, vol. 79, no. 12, pp. 674–688, December, 2003.
Rubin, E. J., C. A. Shaffer, N. Ramakrishnan, L. T. Watson, R. Dymond, D. Kibler, R. Dietz, J. Chanat, V. Lohani, D. Bosch, et al.,
"From Landscapes to Waterscapes: A PSE for Landuse Change Analysis",
Engineering with Computers, vol. 19, no. 1, pp. 9–25, July, 2003.
Verstak, A., N. Ramakrishnan, L. T. Watson, J. He, C. A. Shaffer, K. K. Bae, J. Jiang, W. H. Tranter, and T. S. Rappaport,
"BSML: A binding schema markup language for data interchange in problem solving environments",
Sci. Program., vol. 11, no. 3, Amsterdam, The Netherlands, The Netherlands, IOS Press, pp. 199–224, 2003.
Allen, N. A., C. A. Shaffer, M. T. Vass, N. Ramakrishnan, and L. T. Watson,
"Improving the development process for eukaryotic cell cycle models with a modeling support environment",
WSC '03: Proceedings of the 35th conference on Winter simulation: Winter Simulation Conference, pp. 782–790, 2003.
Su, Y., T. M. Murali, V. Pavlovic, M. Schaffer, and S. Kasif,
"RankGene: identification of diagnostic genes based on expression data.",
Bioinformatics, vol. 19, no. 12, pp. 1578–9, 2003.
Allen, N., L. Calzone, K. C. Chen, A. Ciliberto, N. Ramakrishnan, C. A. Shaffer, J. C. Sible, J. J. Tyson, M. Vass, L. T. Watson, et al.,
"Modeling Regulatory Networks at Virginia Tech",
Omics Journal of Integrative Biology, vol. Vol. 7, no. 3, pp. pages 285–300, Fall, 2003.
Sandu, A. , D. Negrut, C. Sandu, E. J. Haug, and F. A. Potra,
"Rosenbrock Nystrom integrator for SSODE of mechanical systems",
Proceedings of ASME International (DETC-2003), no. VIB-48329, pp. 8, September 6-10, 2003.
Carmichael, G. R., D. Daescu, A. Sandu, and T. Chai,
"Computational aspects of chemical data assimilation into atmospheric models",
Springer Lecture Notes in Computer Science, no. 2660, pp. 269–278, June, 2003.
Sandu, A. , and C. T. Borden,
"Discretization of aerosol dynamics with B-splines",
ACM Symposium on Applied Computing (SAC-2003), pp. 189–193, March 13-18, 2003.
Sandu, A. ,
"Computational Sciences track editorial",
{ACM Symposium on Applied Computing (SAC-2003)}, pp. 141–142, March 13-18, 2003.
Sandu, A. , D. N. Daescu, T. Chai, G. R. Carmichael, J. H. Seinfeld, P. G. Hess, T. L. Anderson, and F. Darema,
"Computational aspects of 4D-Var chemical data assimilation in atmospheric models",
Dynamic Data Driven Applications Systems: Kluwer Academic Publishers, 2003.
Sandu, A. , and C. T. Borden,
"A framework for the numerical treatment of aerosol dynamics",
Applied Numerical Mathematics, vol. 45, pp. 475–497, 2003.
Sandu, A. , D. Negrut, E. J. Haug, F. A. Potra, and C. Sandu,
"A Rosenbrock-Nystrom state space implicit method for the dynamic analysis of mechanical systems: I – Theoretical development",
Journal of Multibody Dynamics, vol. 217, no. K4, pp. 263–272, 2003.
Negrut, D., A. Sandu, E. J. Haug, F. A. Potra, and C. Sandu,
"A Rosenbrock-Nystrom state space implicit method for the dynamic analysis of mechanical systems: II – The Method and numerical results",
Journal of Multibody Dynamics, vol. 217, no. K4, pp. 273–282, 2003.
Daescu, D., A. Sandu, and G. R. Carmichael,
"Direct and adjoint sensitivity analysis of chemical kinetic systems with KPP: II – Numerical validation and applications",
Atmospheric Environment, vol. 37, pp. 5097–5114, 2003.
Sandu, A. , D. Daescu, and G. R. Carmichael,
"Direct and adjoint sensitivity analysis of chemical kinetic systems with KPP: I – Theory and software tools",
Atmospheric Environment, vol. 37, pp. 5083–5096, 2003.
Allawi, H. T., M. W. Kaiser, A. Onufriev, W. - P. Ma, A. E. Brogaard, D. A. Case, B. P. Neri, and V. I. Lyamichev,
"Modeling of Flap Endonuclease Interactions with DNA Substrate.",
Journal of Molecular Biology, vol. 328, pp. 537–554, 2003.
Onufriev, A., D. A. Case, and D. Bashford,
"Structural details, pathways, and energetics of unfolding apomyoglobin",
Journal of Molecular Biology, vol. 325, pp. 555–567, 2003.
Onufriev, A., A. Smondyrev, and D. Bashford,
"Proton Affinity Changes Driving Uni- directional Proton Transport in the Bacteriorhodopsin Photocycle",
Journal of Molecular Biology , vol. 232, pp. 1183–1193, 2003.
Mateescu, G., C. J. Ribbens, and L. T. Watson,
"A domain decomposition preconditioner for Hermite collocation problems",
Numer. Methods Partial Differential Equations, vol. 19, pp. 135–151, 2003.
Dymond, R., V. Lohani, D. Kibler, D. Bosch, E. J. Rubin, R. Dietz, J. Chanat, C. Speir, C. A. Shaffer, N. Ramakrishnan, et al.,
"From landscapes to waterscapes: a PSE for landuse change analysis",
Engineering with Computers, vol. 19, pp. 9–25, 2003.
Adams, D. B., L. T. Watson, and Z. Gurdal,
"Optimization and blending of composite laminates using genetic algorithms with migration",
Mech. Adv. Materials Structure, vol. 10, pp. 183-203, 2003.
Zombori, B. G., F. A. Kamke, and L. T. Watson,
"Simulation of internal conditions during the hot-pressing process",
Wood Fiber Sci., vol. 35, pp. 2-23, 2003.
Adams, D. B., L. T. Watson, Z. Gurdal, and C. M. Anderson-Cook,
"A genetic algorithm with optimization and blending of composite laminates by locally reducing laminate thickness",
Adv. Engrg. Software, vol. 35, pp. 35-43, 2003.
Perez, V. M., J. E. Renaud, and L. T. Watson,
"Homotopy curve tracking in approximate interior point optimization",
AIAA Paper 2003–1670, in Proc. AIAA/ASME/ASCE/AHS 44th Structures, Structural Dynamics, and Materials Conf., CD-ROM, Norfolk, VA, pp. 11 pages, 2003.
Gantovnik, V. B., Z. Gurdal, L. T. Watson, and C. Anderson-Cook,
"A genetic algorithm for mixed nonlinear programming problems using separate constraint approximations",
AIAA Paper 2003–1700, in Proc. AIAA/ASME/ASCE/AHS 44th Structures, Structural Dynamics, and Materials Conf., CD-ROM, Norfolk, VA, pp. 7 pages, 2003.
Zwolak, J. W., J. J. Tyson, and L. T. Watson,
"Finding all steady state solutions of chemical kinetic models",
Proc. High Performance Computing Symposium 2003, I. Banicescu (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 47-53, 2003.
Ribbens, C. J.,
"High performance computing",
Virginia Tech Scholarly Review, pp. 11-15, 2003.
Mateescu, G., C. J. Ribbens, and L. T. Watson,
"A domain decomposition preconditioner for hermite collocation problems",
Num. Meth. PDEs, vol. 19, pp. 135-151, 2003.
Bora, P., C. J. Ribbens, S. Prabhakar, G. Swaminathan, M. Chinnusamy, A. Jeyakumar, and B. Diaz-Acosta,
"Issues in runtime algorithm selection for grid environments",
Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments, Los Alamitos, CA, I. Banicescu (ed.), IEEE Press, pp. 80–87, 2003.
Ribbens, C. J., P. Bora, D. M. Ventra, J. Hauck, S. Prabhakar, and C. Taylor,
"From cluster to Grid: a case study in scaling-up a molecular electronics simulation code",
Proceedings of the High Performance Computing Symposium 2003, San Diego, I. Banicescu (ed.), Society for Modeling and Simulation International, pp. 54-62, 2003.
2002
He, J., L. T. Watson, N. Ramakrishnan, C. A. Shaffer, A. Verstak, J. Jiang, K. Bae, and W. H. Tranter,
"Dynamic Data Structures for a Direct Search Algorithm",
Comput. Optim. Appl., vol. 23, no. 1, Norwell, MA, USA, Kluwer Academic Publishers, pp. 5–25, 2002.
Watson, L. T., V. K. Lohani, D. F. Kibler, R. L. Dymond, N. Ramakrishnan, and C. A. Shaffer,
"Integrated Computing Environments for Watershed Management",
ASCE Journal of Computing in Civil Engineering, vol. 16, no. 4, pp. 259–268, October, 2002.
Ramakrishnan, N., L. T. Watson, D. G. Kafura, C. J. Ribbens, and C. A. Shaffer,
"Programming Environments for Multidisciplinary Grid Communities",
Concurrency and Computation: Practice and Experience, vol. 13–15, pp. 1241–1273, Nov–December, 2002.
Vass, M., J. M. Carroll, and C. A. Shaffer,
"Supporting creativity in problem solving environments",
C&C '02: Proceedings of the 4th conference on Creativity & cognition, New York, NY, USA, ACM, pp. 31–37, 2002.
Sandu, A. , D. Daescu, and G. R. Carmichael,
"Adjoint data assimilation for aerosol dynamics",
Proceedings of the second International Conference on Air Polution Modeling and Simulation (APMS-2001), pp. 319–331, 2002.
Damian, V., A. Sandu, M. Damian, F. Potra, and G. R. Carmichael,
"The Kinetic PreProcessor KPP – a software environment for solving chemical kinetics",
(Computers and Chemical Engineering), vol. 26, pp. 1567–1579, 2002.
Miehe, P., A. Sandu, G. R. Carmichael, Y. Tang, and D. Daescu,
"A Communication Library for the Parallelization of Air Quality Models on Structured Grids",
Atmospheric Environment, vol. 36, pp. 3917–3930, 2002.
Onufriev, A., D. Bashford, and D. A. Case,
"The Generalized Born Approximation: The Importance of Being Perfect",
Journal of Computational Chemistry , vol. 23, 2002.
Ragon, S. A., Z. Gurda, and L. T. Watson,
"A comparison of three algorithms for tracing nonlinear equilibrium paths of structural systems",
Internat. J. Solids Structures, vol. 39, pp. 689–698, 2002.
Watson, L. T.,
"Probability-one homotopies in computational science",
J. Comput. Appl. Math., vol. 140, pp. 785–807, 2002.
Billups, S. C., and L. T. Watson,
"A probability-one homotopy algorithm for nonsmooth equations and mixed complementarity problems",
SIAM J. Optim., vol. 12 , pp. 606–626, 2002.
Kim, H., R. T. Haftka, W. H. Mason, L. T. Watson, and B. Grossman,
"Probabilistic modelling of errors from structural optimization based on multiple starting points",
Optim. Engrg., vol. 3, pp. 415–430, 2002.
Slotta, D. J., B. Tatting, L. T. Watson, Z. Gurdal, and S. Missoum,
"Convergence analysis for cellular automata applied to truss design",
Engrg. Comput., vol. 19, pp. 953–969, 2002.
Missoum, S., Z. Gurdal, and L. T. Watson,
"A displacement based optimization method for geometrically nonlinear frame structures",
Structural Multidisciplinary Optim., vol. 24, pp. 195–204, 2002.
Gantovnik, V. B., Z. Gurdal, and L. T. Watson,
"A genetic algorithm with memory for optimal design of laminated sandwich composite panels",
Composite Structures, vol. 58, pp. 513-520, 2002.
Perez, V. M., J. E. Renaud, and L. T. Watson,
"Adaptive experimental design for construction of response surface approximations",
AIAA J., vol. 40, pp. 2495–2503, 2002.
Kim, H., W. H. Mason, L. T. Watson, B. Grossman, M. Papila, and R. T. Haftka,
"Protection against modeling and uncertainties in design optimization",
Modeling and Simulation-Based Life Cycle Engineering, Spon Press, London, 2002, pp. 231–246, 2002.
Zwolak, J. W., J. J. Tyson, and L. T. Watson,
"Parameter estimation in a cell cycle model for frog egg extracts",
Proc. High Performance Computing Symposium 2002, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 67-74, 2002.
Adams, D. B., L. T. Watson, and Z. Gurdal,
"Blending of composite panel designs using genetic algorithms",
Proc. 16th Internat. Parallel & Distributed Processing Symp., CD-ROM, IEEE Computer Soc., Los Alamitos, CA, pp. 6 pages, 2002.
Gantovnik, V. B., Z. Gurdal, and L. T. Watson,
"Genetic algorithm with memory for optimal design of laminated sandwich composite panels",
AIAA Paper 2002–1221, in Proc. AIAA/- ASME/ASCE/AHS/ASC 43rd Structures, Structural Dynamics, and Materials Conf., CD-ROM, Denver, CO, pp. 8 pages, 2002.
Gantovnik, V. B., Z. Gurdal, and L. T. Watson,
"Genetic algorithm with memory for optimal design of laminated sandwich composite panels",
AIAA Paper 2002–1221, in Proc. AIAA/- ASME/ASCE/AHS/ASC 43rd Structures, Structural Dynamics, and Materials Conf., CD-ROM, Denver, CO, pp. 8 pages, 2002.
Kim, H., M. Papila, R. T. Haftka, W. H. Mason, L. T. Watson, and B. Grossman,
"Estimating optimization error statistics via optimization runs from multiple starting points",
AIAA Paper 2002–5576, in Proc. 9th AIAA/ISSMO Symp. on Multidisciplinary Analysis and Optimization, CD-ROM, Atlanta, GA, pp. 14 pages, 2002.
Perez, V. M., J. E. Renaud, and L. T. Watson,
"An interior point sequential approximate optimization methodology",
AIAA Paper 2002–5505, in Proc. 9th AIAA/ISSMO Symp. on Multidisciplinary Analysis and Optimization, CD-ROM, Atlanta, GA, pp. 12 pages, 2002.
Cox, S. E., W. E. Hart, R. T. Haftka, and L. T. Watson,
"DIRECT algorithm with box penetration for improved local convergence",
AIAA Paper 2002–5581, in Proc. 9th AIAA/ISSMO Symp. on Multidisciplinary Analysis and Optimization, CD-ROM, Atlanta, GA, pp. 15 pages, 2002.
Kamke, F. A., L. T. Watson, B. Zombori, and J. Shu,
"A web-based problem solving environment for wood-based composite applications",
Proc. Internat. Academy of Wood Science Annual Meeting, Bejing, China, pp. 96–106, 2002.
Prabhakar, S., C. J. Ribbens, and P. Bora,
"Multifaceted web services: an approach to secure and scalable grid scheduling",
The Web and the GRID: from e-science to e-business, Proceedings of Euroweb 2002, Swindon, UK, B. Matthews, B. Hopgood, M. Wilson (eds.) British Computer Society, pp. 116–125, 2002.
2001
Duff, J. F., P. Merkey, and A. Sandu,
"Parallel molecular dynamics using MPI on a Scyld-style Beowulf cluster",
Proceedings of the 10th SIAM Conference on Parallel Processing for Scientific Computing, pp. 272–279, 2001.
Sandu, A. ,
A spectral method for solving aerosol dynamics,
, no. CSTR-01-04, 1400 Townsend Drive, Houghton, MI 49931, Department of Computer Science, Michigan Technological University, 2001.
Onufriev, A., D. A. Case, and G. M. Ullmann,
"A Novel View of pH Titration in Biomolecules.",
Biochemistry , vol. 40, 2001.
Goel, A., C. A. Baker, C. A. Shaffer, B. Grossman, W. H. Mason, L. T. Watson, and R. T. Haftka,
"VizCraft: a problem solving environment for configuration design of a high speed civil transport",
Computer Science and Engineering, vol. 3, no. 1, pp. 56–66, 2001.
Baker, C. A., L. T. Watson, B. Grossman, W. H. Mason, and R. T. Haftka,
"Parallel global aircraft configuration design space exploration",
Internat. J. Comput. Res., vol. 10, pp. 501–515, 2001.
Zombori, B. G., F. A. Kamke, and L. T. Watson,
"Simulation of the mat formation process",
Wood Fiber Sci., vol. 33, pp. 564–580, 2001.
Watson, L. T., and C. A. Baker,
"A fully-distributed parallel global search algorithm",
Engrg. Comput., vol. 18 , pp. 155–169, 2001.
Cox, S. E., R. T. Haftka, C. A. Baker, B. Grossman, W. H. Mason, and L. T. Watson,
"Global multidisciplinary optimization of a high speed civil transport",
J. Global Optim., vol. 21, pp. 415–433, 2001.
Kim, H., M. Papila, W. H. Mason, R. T. Haftka, L. T. Watson, and B. Grossman,
"“Detection and repair of poorly converged optimization runs",
AIAA J., vol. 39, pp. 2242–2249, 2001.
Hosder, S., L. T. Watson, B. Grossman, W. H. Mason, H. Kim, R. T. Haftka, and S. Cox,
"Polynomial response surface approximations for the multidisciplinary design optimization of a high speed civil transport",
Optim. Engrg., vol. 2, pp. 431–452, 2001.
Watson, L. T.,
"Globally convergent homotopy methods",
Encyclopedia of Optimization, Kluwer, Norwell, MA, A. Floudas and P. M. Pardalos (eds.), 2001.
Watson, L. T.,
"Multidisciplinary design optimization",
Encyclopedia of Optimization, Kluwer, Norwell, MA, C. A. Floudas and P. M. Pardalos (eds.), 2001.
Billups, S. C., A. L. Speight, and L. T. Watson,
"Nonmonotone path following methods for nonsmooth equations and complementarity problems",
Applications and Algorithms of Complementarity, M. C. Ferris, O. L. Mangasarian, and J.-S. Pang (eds.), Kluwer, Norwell, MA, 2001.
Adams, D. B., L. T. Watson, and Z. Gurdal,
"Global/local optimization and blending using genetic algorithms with migration",
Proc. 10th SIAM Conf. on Parallel Processing for Scientific Computing, CD-ROM, SIAM, Philadelphia, PA, pp. 8 pages, 2001.
Watson, L. T., and C. A. Baker,
"A fully distributed parallel global search algorithm",
Proc. 10th SIAM Conf. on Parallel Processing for Scientific Computing, CD-ROM, SIAM, Philadelphia, PA, pp. 10 pages, 2001.
Zwolak, J. W., J. J. Tyson, and L. T. Watson,
"Estimating rate constants in cell cycle models",
Proc. High Performance Computing Symposium 2001, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 53–57, 2001.
Gurdal, Z., and L. T. Watson,
"Structural design using cellular automata",
Proc. Third Internat. Conf. on Intelligent Processing and Manufacturing of Materials, J. A. Meech, S. M. Veiga, M. M. Veiga, S. R. LeClair, and J. F. Maguire (eds.), CD-ROM, Vancouver, Canada, pp. 4 pages, 2001.
Farkas, D., M. Duranduru, W. A. Curtin, and C. J. Ribbens,
"Multiple-dislocation emission from the crack tip in the ductile fracture of Al",
Philosophical Magazine A, vol. 81, pp. 1241–1255, 2001.
Kohn, S., G. Kumfert, J. Painter, and C. J. Ribbens,
"Divorcing language dependencies from a scientific software library",
Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing, Philadelphia, PA, C. Koelbel and J. Meza (eds.), SIAM, 2001.
2000
Shaffer, C. A., L. T. Watson, D. G. Kafura, N. Ramakrishnan, and A. Tentner,
"Features of Problem Solving Environments for Computational Science",
Proceedings of the 2000 High Performance Computing Symposium (HPC'00), San Diego, CA, Society for Computer Simulation International, pp. 242–247, April 2000.
Onufriev, A., D. A. Case, and D. Bashford,
"A Modification of the Generalized Born Model Suitable for Macromolecules",
Journal of Physical Chemistry B , vol. 104, 2000.
McMahon, M. T., and L. T. Watson,
"A distributed genetic algorithm with migration for the design of composite laminate structures",
Parallel Algorithms Appl., vol. 14, pp. 329–362, 2000.
Wise, S. M., A. J. Sommese, and L. T. Watson,
"Algorithm 801: POLSYS PLP: A partitioned linear product homotopy code for solving polynomial systems of equations",
ACM Trans. Math. Software, vol. 26, pp. 176–200, 2000.
Watson, L. T.,
"Theory of globally convergent probability-one homotopies for nonlinear programming",
SIAM J. Optim., vol. 11, pp. 761–780, 2000.
Sosonkina, M., J. T. Melson, Y. Saad, and L. T. Watson,
"Preconditioning strategies for linear systems arising in tire design",
Numer. Linear Algebra Appl., vol. 7, pp. 743–757, 2000.
Baker, C. A., L. T. Watson, S. E. Cox, B. Grossman, R. T. Haftka, and W. H. Mason,
"Study of a global design space exploration method for aerospace vehicles",
Proc. 5th NASA High Performance Computing and Communications Computational Aerosciences Workshop, CD-ROM, Mountain View, CA, pp. 10 pages, 2000.
Ragon, S., Z. Gurdal, and L. T. Watson,
"A comparison of three algorithms for tracing nonlinear equilibrium paths of structural systems",
Proc. AIAA/ASME/ASCE/AHS/ASC 41st Structures, Structural Dynamics, and Materials Conf., CD-ROM, Atlanta, GA, pp. 11 pages, 2000.
Kim, H., M. Papila, W. H. Mason, R. T. Haftka, L. T. Watson, and B. Grossman,
"Detection and correction of poorly converged optimizations by iteratively reweighted least squares",
AIAA Paper 2000-1525, in Proc. AIAA/ASME/ASCE/AHS/ASC 41st Structures, Structural Dynamics, and Materials Conf., CD-ROM, Atlanta, GA, 2000.
Baker, C. A., L. T. Watson, B. Grossman, R. T. Haftka, and W. H. Mason,
"Parallel global aircraft configuration design space exploration",
Proc. High Performance Computing Symposium 2000, A. Tentner (ed.), Soc. for Computer Simulation Internat., San Diego, CA, pp. 101–106, 2000.
Cox, S. E., R. T. Haftka, C. Baker, B. Grossman, W. H. Mason, and L. T. Watson,
"Global optimization for noise and multiple local optima",
Proc. Internat. Workshop on Multidisciplinary Design Optim., Pretoria, South Africa, pp. 50–59, 2000.
Kim, H., R. T. Haftka, W. H. Mason, L. T. Watson, and B. Grossman,
"A study of the statistical description of errors from structural optimization",
AIAA Paper 2000–4840–CP, in Proc. 8th AIAA/USAF/NASA/ISSMO Symp. on Multidisciplinary Analysis and Optimization, CD-ROM, Long Beach, CA, 2000.
Baker, C. A., L. T. Watson, B. Grossman, R. T. Haftka, and W. H. Mason,
"Parallel global aircraft configuration design space exploration",
AIAA Paper 2000–4763–CP, in Proc. 8th AIAA/USAF/NASA/ISSMO Symp. on Multidisciplinary Analysis and Optimization, CD-ROM, Long Beach, CA, 2000.
Ramakrishnan, N., and C. J. Ribbens,
"Mining and visualizing recommendation spaces for elliptic PDEs with continuous attributes",
ACM Trans. Math. Softw., vol. 26, pp. 254–273, 2000.
Goel, A., C. Phanouriou, F. A. Kamke, C. J. Ribbens, C. A. Shaffer, and L. T. Watson,
"WBCSim: A prototype PSE for wood-based composites simulations",
Enabling Technologies for Computational Science: Frameworks, Middleware and Environments, pp. 187-196, 2000.
1999
Goel, A., C. Phanouriou, F. A. Kamke, C. J. Ribbens, C. A. Shaffer, and L. T. Watson,
"WBCSim: A Prototype Problem Solving Environment for Wood-Based Composites Simulations",
Engineering with Computers, vol. 15, no. 2, pp. 198–210, 1999.
Goel, A., C. Baker, C. A. Shaffer, B. Grossman, R. Haftka, W. Mason, and L. T. Watson,
"VizCraft: A Multidimensional Visualization Tool for Aircraft Configuration Design",
VISUALIZATION '99: Proceedings of the 10th IEEE Visualization 1999 Conference (VIS '99), Washington, DC, USA, IEEE Computer Society, 1999.
Shaffer, C. A., L. T. Watson, and D. G. Kafura,
"Component Frameworks for Problem Solving Environments in Computational Science",
Proceedings of the 1st Symposium on Reusable Architectures and Components for Developing Distributed Information Systems (RACDIS'99), pp. 653–656, August, 1999.
Carmichael, G. R., A. Sandu, C. H. Song, S. He, M. Phadnis, D. Daescu, V. Damian-Iordache, F. A. Potra, and Z. Zlatev,
"Computational challenges of modeling interactions between aerosol and gas phase processes",
NATO Advanced Study Institute on Computational Challenges in Air Pollution Modeling, pp. 99–136, 1999.
Onufriev, A., and J. B. Marston,
"Enlarged Symmetry and Coherence in Arrays of Quan- tum Dots.",
Phys. Rev. B, vol. 59, 1999.
Mateescu, G., C. J. Ribbens, L. T. Watson, and C. - Y. Wang,
"Effect of a sawtooth boundary on Couette flow",
Computers & Fluids, vol. 28, pp. 801–813, 1999.
Mateescu, G., and C. J. Ribbens,
"An Iterative Substructuring Preconditioner for Collocation with Hermite Bicubics",
Proceedings of the Eleventh International Conference on Domain Decomposition Methods, Bergen,, C-H Lai, P. E. Bjorstad, M. Cross, and O. Widlund, (eds.), DDM.org, pp. 73–81, 1999.
1998
Shaffer, C. A., D. L. Knill, and L. T. Watson,
"Visualization for multiparameter aircraft designs",
VIS '98: Proceedings of the conference on Visualization '98, Los Alamitos, CA, USA, IEEE Computer Society Press, pp. 491–494, 1998.
Goel, A., C. Phanouriou, F. A. Kamke, C. J. Ribbens, C. A. Shaffer, and L. T. Watson,
WBCSim: A Prototype Problem Solving Environment for Wood-Based Composites Simulations,
, Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1998.
Shan, H., G. R. Carmichael, A. Sandu, and B. Hotchkis,
"Exploring the effects of aerosols and photochemistry and radiative processes in the troposphere using automatic differentiation",
Proceedings of the First International Conference on Air Pollution Modeling and Simulation (APMS-1998), pp. 12, 1998.
Pilkey, D. F., C. J. Ribbens, and D. J. Inman,
"High performance computing issues for model reduction/expansion",
Advances in Engineering Software, vol. 29, pp. 389–393, 1998.
Mateescu, G., and C. J. Ribbens,
"Parallel algorithm for the solution of high order discretization of elliptic PDEs",
Proceedings of the ASME Fluids Engineering Division—1998: ASME, New York, pp. 105–112, 1998.
1997
Jay, L. O., A. Sandu, F. A. Potra, and G. R. Carmichael,
"Improved QSSA methods for atmospheric chemistry integration",
SIAM Journal on Scientific Computing, vol. 18, no. 1, pp. 182–202, 1997.
Embree, M., and C. J. Ribbens,
"On the scalability of parallel Krylov subspace methods",
Proceedings of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, Philadelphia, SIAM, 1997.
1996
Jay, L. O., A. Sandu, F. A. Potra, G. R. Carmichael, E. Kreuzer, and O. Mahrenholtz,
"Efficient Numerical Integration for Atmospheric Chemistry",
Special issue of ZAMM: Applied sciences, no. 4, pp. 450–453, 1996.
Carmichael, G. R., A. Sandu, F. A. Potra, V. Damian-Iordache, and M. Damian-Iordache,
"The current state and the future directions in air quality modeling",
Systems Analysis Modelling Simulation, vol. 25, pp. 75–105, 1996.
Carmichael, G. R., A. Sandu, F. A. Potra, and V. Damian-Iordache,
"An overview of sensitivity analysis for atmospheric chemistry models via automatic differentiation",
Air Pollution IV - Monitoring, Simulation and Control, vol. B. Caussad, pp. Computational Mechanics Publications, Southampton, Boston, 1996.
Onufriev, A., and J. B. Marston,
"Memory Loss and Auger Processes in a Many-Body Theory of Charge Transfer",
Phys. Rev. B., vol. 53, 1996.
1995
Sandu, A. , G. R. Carmichael, and F. A. Potra,
"Using automatic differentiation for sensitivity analysis of atmospheric chemistry models",
Office for Official Publications of the European Communities, no. L–2985, pp. 49–51, 1995.
1994
Bright, J. S., C. A. Shaffer, P. S. Nagarkatti, and M. Nagarkatti,
"Computer Simulation of the Immune System",
Proceedings of the Fourteenth Annual Seminar of Cancer Researchers in Virginia, pp. {17}., March, 1994.
McQuain, W. D., C. J. Ribbens, L. T. Watson, and R. C. Melville,
"Preconditioned iterative methods for sparse linear algebra problems arising in circuit simulation",
Computers Math. Applic., vol. 27, pp. 25-45, 1994.
McQuain, W. D., C. J. Ribbens, C. - Y. Wang, and L. T. Watson,
"Steady viscous flow in a trapezoidal cavity",
Comput. & Fluids, vol. 23, pp. 613–626, 1994.
1993
L.W. Carstensen, J., C. A. Shaffer, R. W. Morrill, and E. A. Fox,
"GeoSim: A GIS-Based Simulation Laboratory for Introductory Geography",
Journal of Geography, vol. 92, no. 5, pp. 217–222, September/Octobe, 1993.
Onufriev, A., and D. S. Chernavskii,
"ATP Synthesis By Free and Membrane-Bound H+-ATPase of the Chloroplasts in Conditions of a pH shift",
Biophysics, vol. 38, no. 1005, 1993.
Ribbens, C. J., G. G. Pitts, and L. T. Watson,
"Parallel ELLPACK for shared memory multiprocessors",
Comput. Systems Engrg., vol. 4, pp. 531-540, 1993.
Chakraborty, A., D. C. S. Allison, C. J. Ribbens, and L. T. Watson,
"The parallel complexity of embedding algorithms for the solution of systems of nonlinear equations",
IEEE Trans. Parallel Distrib. Sys., vol. 4, pp. 458–465, 1993.
Shankar, J., C. J. Ribbens, R. T. Haftka, and L. T. Watson,
"Computational study of a nonhierarchical decomposition algorithm",
Comput. Optim. Appl., vol. 2, pp. 273–293, 1993.
Ribbens, C. J., L. T. Watson, and C. deSa,
"Toward parallel mathematical software for elliptic partial differential equations",
ACM Trans. Math. Softw., vol. 13, pp. 30-46, 1993.
1992
deSa, C., K. M. Irani, C. J. Ribbens, L. T. Watson, and H. F. Walker,
"Preconditioned iterative methods for homotopy curve tracking",
SIAM J. Sci. Stat. Comput., vol. 13, pp. 30–46, 1992.
Ribbens, C. J.,
"A moving mesh scheme for adaptive domain decomposition",
Unstructured Scientific Computation on Scalable Multiprocessors, Cambridge, MA, P. Mehrotra, J. Saltz, and R. Voigt (eds.), MIT Press, 1992.
Ribbens, C. J.,
"On adaptive domain decomposition with moving subdomains",
Fifth International Symposium on Domain Decomposition Methods for Partial Differential Equations, Philadelphia, D. Keyes, et al. (eds.), SIAM, 1992.
Beattie, C., and C. J. Ribbens,
"Parallel solution of a generalized symmetric eigenvalue problem",
Parallel Processing for Scientific Computing, Philadelphia, J. Dongarra, et al. (eds.), SIAM, 1992.
Ribbens, C. J., and G. G. Pitts,
"Strategies for parallelizing PDE software",
Advances in Computer Methods for Partial Differential Equations VII, R. Vichnevetsky, New Brunswick, N.J., D. Knight, and G. Richter (eds.), IMACS, 1992.
1991
Shaffer, C. A.,
"Real-time robot arm collision detection for telerobotics",
Comput. Electr. Eng., vol. 17, no. 3, Tarrytown, NY, USA, Pergamon Press, Inc., pp. 205–215, 1991.
,
"Getting Around on a Sphere",
Graphics Gems II, San Diego, CA, USA, Academic Press Professional, Inc., 1991.
Irani, K. M., M. P. Kamat, C. J. Ribbens, H. F. Walker, and L. T. Watson,
"Experiments with conjugate gradient algorithms for homotopy curve tracking",
SIAM J. Optim., vol. 1, pp. 222–251, 1991.
Chakraborty, A., D. C. S. Allison, C. J. Ribbens, and L. T. Watson,
"Note on unit tangent vector computation for homotopy curve tracking on a hypercube",
Parallel Comput., vol. 17, pp. 1385–1395, 1991.
Allison, D. C. S., K. M. Irani, C. J. Ribbens, and L. T. Watson,
"High dimensional homotopy curve tracking on a shared memory multiprocessor",
J. Supercomputing, vol. 5, pp. 347–366, 1991.
1989
Ribbens, C. J.,
"A fast adaptive grid scheme for elliptic partial differential equations",
ACM Trans. Math. Softw., vol. 15, pp. 179–197, 1989.
Ribbens, C. J.,
"Parallelization of adaptive grid domain mappings",
Parallel Processing for Scientific Computing, Philadelphia, G. Rodrigue (ed.), SIAM, 1989.
1988
Dyksen, W. R., C. J. Ribbens, and J. R. Rice,
"The performance of numerical methods for elliptic problems with mixed boundary conditions",
Num. Meth. PDEs, vol. 4, pp. 347–361, 1988.
1987
Dyksen, W. R., and C. J. Ribbens,
"Interactive ELLPACK: an interactive problem-solving environment for elliptic partial differential equations",
ACM Trans. Math. Softw., vol. 13, pp. 113–132, 1987.
Ribbens, C. J.,
"A priori grid adaption strategies for elliptic PDEs",
Advances in Computer Methods for Partial Differential Equations VI, R., New Brunswick, N.J., Vichnevetsky and R.S. Stepleman (eds.), IMACS,, 1987.
1986
Shaffer, C. A.,
"An Empirical Comparison of Vectors, Rasters, and Quadtrees for Representing Geographic Data",
Proceedings of the International Colloquium on the Construction and Display of Geoscientific Maps Derived from Databases, Geologisches Jahrbuch A 104, pp. 99–115, December, 1986.
1984
Rice, J. R., C. J. Ribbens, and W. A. Ward,
"A simple macro processor",
ACM Trans. Math. Softw., vol. 10, pp. 410–416, 1984.
HokieSpeed
Contact: Wu Feng
HokieSpeed is a 209 node cpu/gpu cluster housed in Virginia Tech's Advanced Research Computing (ARC) facility. The team that designed and deployed HokieSpeed was led by Dr. Wu Feng of the Department of Computer Science. Each system node contains two 2.40-gigahertz Intel Xeon E5645 6-core CPUs, and two NVIDIA 2050 448-core GPUs, for a total of more than 2,500 CPU cores and more than 185,000 GPU cores. The system has an aggregate 4992 GB of memory and is interconnected with quad data rate (QDR) InfiniBand. It made its debut in November 2011 as the 11th ranked system on the Green500 list.
A Chemical Data Assimilation Test Bed For The Interpretation And Analysis Of The 2004 NEAQS/ITCT Observation
Granting Institution: National Oceanic and Atmospheric Administration (subcontract from University of Iowa)
Amount: $114,338
A Computational Framework for the Integrating of Air Quality Models and Measurements Using Adjoints
Granting Institution: National Science Foundation (subcontract from University of Iowa)
Amount: $429,194
A Framework For Adversarial Social Networks
Granting Institution: Defense Threat Reducation Agency
Amount: $450,000
CAREER: Computational Methods For The New Generation Of Air Quality Models
Granting Institution: National Science Foundation
Amount: $221,965
Effective Computer Modeling For Next Generation Breast Cancer Research
Granting Institution: Department of Defense
Amount: $119,925
Multirate Time Integration Algorithms For Adaptive Simulations Of PDE's
Granting Institution: National Science Foundation
Amount: $180,000
Multiscale Modeling Simulation And Sensitivity Analysis of Biochemical Systems Motivated By Pulsatile Insulin Secretion
Granting Institution: National Science Foundation
Amount: $131,568
Novel tools to understand the role of ions in nucleic acid structure and function
Granting Institution: National Institutes of Health
Amount: $433, 580
On The Effects Of Culture And Society On Adversarial Attitudes And Behaviors
Granting Institution: Air Force Office of Scientific Research
Amount: $690,000
Refinement and Analysis of Log Surface Defect Detection Methods using High-Resolution Laser Scanner
Granting Institution: USDA Forest Service
Amount: $50,000
Sensor-Web Operation Scenario Exploration System For Integrated Aerosol And Trace-Gas Observation
Granting Institution: California Institute of Technology
Amount: $100,000
Short Cycle Surrogate Based Design Optimization
Granting Institution: National Science Foundation
Amount: $111,952
Social Network Analysis Classification
Granting Institution: Air Force Office of Scientific Research
Amount: $354,994
Solution Of Inverse Problems With Adaptive Models
Granting Institution: National Science Foundation
Amount: $186,143
Statistical Decision - Theoretic Methods for Robust Design Optimization
Granting Institution: National Science Foundation
Amount: $200,000
Stochastic Models Of Cell Cycle Regulation In Eukaryotes
Granting Institution: National Institute of General Medical Sciences
Amount: $3,424,192
Sustainable Engineered Materials From Renewable Resouces: Design And Manufacture A High-Performance Composites
Granting Institution: USDA-CREES
Amount: $48,921
TCNP Driving Biological Problem: Year 4 Renwal: Using Composition to Integerate a Cell Cycle Model with Morphological Checkpoints
Granting Institution: University of Connecticut
Amount: $20,925
TCNP Driving Biological Problems: Using Composition to Integrate a Cell Cycle Model with Morphological Checkpoints
Granting Institution: University of Connecticut
Amount: $17,738
The Eukaryotic Cell Cycle as a Test Case for Modeling Cellular Regulation in a Collaborative PSE
Granting Institution: DARPA
Amount: $2,442,399
The Virginia Institute For Performance Engineering And Research
Granting Institution: Institute for Advanced Learning and Research
Amount: $111,437