Mathematical Foundations of Computer Science
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.
Network Dynamics and Simulation Science Laboratory
URL: http://ndssl.vbi.vt.edu/index.php
Contact: Madhav Marathe
The NDSSL is pursuing an advanced research and development program for interaction-based modeling, simulation, and associated analysis, experimental design, and decision support tools for understanding large biological, information, social, and technological systems. Extremely detailed, multi-scale computer simulations allow formal and experimental investigation of these systems. The need for such simulations is derived from questions posed by scientists, policy makers, and planners involved with very large complex systems. The simulation applications are underwritten by a theoretical program in discrete mathematics and theoretical computer science that is sustained by more than a decade of experience with the interplay of research and application. Laboratory members are currently pursuing active projects in Wireless Networks, Computational Epidemiology and Algorithms, Complex Networks and High Performance Computing.
Christopher L. Barrett Virginia Bioinformatics Institute
Professor
| Office: | Research Building XV |
|---|---|
| Email: | cbarrett@vbi.vt.edu |
| Phone: | (540) 231-1745 |
| Website: | http://ndssl.vbi.vt.edu/people/cbarrett.html |
| Office Hours: | By appointment |
|---|
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. |
|---|
Vicky Choi Northern Virginia Center
Assistant Professor
| Office: | 2222 KWII |
|---|---|
| Email: | vchoi@cs.vt.edu |
| Phone: | (540) 231-2919 |
| Website: | http://people.cs.vt.edu/~vchoi/ |
| Office Hours: |
|---|
Lenwood S Heath
Professor
| Office: | 2160J Torgersen Hall |
|---|---|
| Email: | heath@vt.edu |
| Phone: | (540) 231-4352 |
| Website: | http://people.cs.vt.edu/~heath/ |
| Office Hours: | TR: 1:00 - 3:00 pm |
|---|
Madhav Marathe Virginia Bioinformatics Institute
Professor
| Office: | 1800 Pratt Drive (RB XV) |
|---|---|
| Email: | marathe@vt.edu |
| Phone: | (540) 231-8832 |
| Website: | http://ndssl.vbi.vt.edu/people/mmarathe.php |
| Office Hours: | By appointment |
|---|
T. M. Murali
Associate Professor
| Office: | 2160B Torgersen |
|---|---|
| Email: | tmurali@vt.edu |
| Phone: | (540) 231-8534 |
| Website: | https://bioinformatics.cs.vt.edu/~murali/ |
| 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 |
|---|
Anil Vullikanti Virginia Bioinformatics Institute
Associate Professor
| Office: | RB XV, 1880 Pratt Dr., VBI |
|---|---|
| Email: | vsakumar@vt.edu |
| Phone: | (540) 231-3968 |
| Website: | http://ndssl.vbi.vt.edu/people/akumar.php |
| Office Hours: | McBryde 122-C: M: 1:30 - 2:30, T: 4:45 - 5:45, R: 8:30 - 10:00 am |
|---|
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.
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.
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.
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.
2008
Pati, A., Y. Jin, K. Klage, R. Helm, L. S. Heath, and N. Ramakrishnan,
"CMGSDB: Integrating Heterogeneous Caenorhabditis elegans Data Sources Using Compositional Data Mining",
Nucleic Acids Research, vol. 36, pp. D69-76, 2008.
Zhu, Q., Z. Adam, V. Choi, and D. Sankoff,
"Generalized gene adjacencies, graph bandwidth and clusters in yeast evolution",
RECOMB’08, 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.
Lee, M., R. Weidner, K. Bowman, A. Sandu, and K. Singh,
"Sensor-web Operations Explorer (SOX) for Integrated Air Quality Campaign",
IEEE ECMI 2008, 09/2008.
Alexe, M., and A. Sandu,
"ADJERKDENS, a Runge Kutta library for adjoint calculation",
submitted, 2008.
Alexe, M., and A. Sandu,
"On the discrete adjoints of variable step time integrators",
submitted, 2008.
Sandu, A. , and L. Zhang,
"Discrete Second Order Adjoints in Atmospheric Chemical Transport Modeling",
Jurnal of Computational Physics, vol. 227, no. 12, pp. 5949–5983, 2008.
Constantinescu, E. M., A. Sandu, and G. R. Carmichael,
"Modeling atmospheric chemistry and transport with dynamic adaptive resolution",
Computational Geosciences, 2008.
Liu, Z., and A. Sandu,
"Analysis of discrete adjoints of numerical methods for the advection equation",
International Journal for Numerical Methods for Fluids, vol. 56, no. 7, pp. 769–803, 2008.
Sandu, C., A. Sandu, B. Chan, and M. Ahmadian,
"A response spectral decomposition approach for the control of nonlinear mechanical systems",
International Journal of Heavy Vehicle Systems, vol. 15, no. 1, pp. 26, 2008.
Carmichael, G. R., T. Chai, A. Sandu, E. M. Constantinescu, and D. Daescu,
"Predicting air quality: improvements through advanced methods to integrate models and measurements",
Journal of Computational Physics, vol. 227, no. 7, pp. 3540–3571, 2008.
Perez, V. M., J. E. Renaud, and L. T. Watson,
"Homotopy curve tracking in approximate interior point optimization",
Optim. Engrg., 2008.
He, J., A. Verstak, L. T. Watson, and M. Sosonkina,
"Design and implementation of a massively parallel version of DIRECT",
Comput. Optim. Appl., 2008.
Ahuja, K., L. T. Watson, and S. C. Billups,
"Probability-one homotopy maps for mixed complementarity problems",
Comput. Optim. Appl., 2008.
Goel, T., R. T. Haftka, W. Shyy, and L. T. Watson,
"Pitfalls of using a single criterion for selecting experimental designs",
Internat. J. Numer. Methods Engrg., 2008.
Ji, S., L. T. Watson, and L. Carin,
"Semi-supervised learning of hidden Markov models via a homotopy method",
IEEE Trans. Pattern Anal. Machine Intell., 2008.
He, J., A. Verstak, L. T. Watson, and M. Sosonkina,
"Performance modeling and analysis of a massively parallel DIRECT—Part 1",
Internat. J. High Performance Comput. Appl., 2008.
He, J., A. Verstak, M. Sosonkina, and L. T. Watson,
"Performance modeling and analysis of a massively parallel DIRECT—Part 2",
Internat. J. High Performance Comput. Appl., 2008.
Kugele, S. C., M. W. Trosset, and L. T. Watson,
"Numerical integration in statistical decisiontheoretic methods for robust design optimization",
Structural Multidisciplinary Optim., 2008.
Giraud, L., A. Haidar, and L. T. Watson,
"Parallel scalability study of hybrid preconditioners in three dimensions",
Parallel Comput., 2008.
Phillips, R. D., L. T. Watson, R. H. Wynne, and C. E. Blinn,
"Feature reduction using a singular value decomposition for the iterative guided spectral class rejection hybrid classifier",
ISPRS J. Photogrammetry Remote Sensing, 2008.
He, J., L. T. Watson, and M. Sosonkina,
"Algorithm XXX: VTDIRECT95: serial and parallel codes for the global optimization algorithm DIRECT",
ACM Trans. Math. Software, 2008.
Zhang, L., and L. T. Watson,
"Analysis of the fitness effect of compensatory mutations",
J. Comput. Biol., 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.
Halloran, M. E., N. M. Ferguson, S. Eubank, L. I. M. Jr., D. A. T. Cummings, B. Lewis, S. Xu, C. Fraser, A. Vullikanti, T. C. Germann, et al.,
"Modeling targeted layered containment of an influenza pandemic in the United States.",
Proceedings of the National Academy of Sciences (PNAS), March, 2008.
Atkins, K., J. Chen, A. V. S. Kumar, M. Macauley, and A. Marathe,
"Locational Market Power in Network Constrained Markets",
Journal of Economic Behavior & Organization, 2008.
Khan, M., G. Pandurangan, and A. V. S. Kumar,
"Distributed Algorithms for Constructing Approximate Minimum Spanning Trees in a Wireless Sensor Networks",
IEEE Transactions on Parallel and Distributed Systems, 2008.
Choi, Y., M. Khan, A. V. S. Kumar, and G. Pandurangan,
"Work-Efficient Distributed Euclidean Minimum Spanning Tree,",
20th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA), Munich, Germany, June , 2008.
Chafekar, D., A. V. S. Kumar, M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Approximating the Capacity of Wireless Networks with SINR constraints",
27th IEEE International Conference on Computer Communications (INFOCOM), 2008.
Chafekar, D., D. Levin, S. Parthasarathy, A. V. S. Kumar, M. Marathe, and A. Srinivasan,
"On the capacity of asynchronous random-access wireless networks",
27th IEEE International Conference on Computer Communications (INFOCOM), 2008.
Atkins, K., C. Barrett, R. Beckman, K. Bisset, J. Chen, S. Eubank, A. Feng, X. Feng, S. Harris, B. Lewis, et al.,
An Interaction Based Composable Architecture for Building Scalable Models of Large Social, Biological, Information and Technical Systems,
, CT Watch, vol. 4, pp. 46-53, 2008.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Minimum Weighted Completion Time.",
Springer Encyclopedia of Algorithms, 2008.
Chafekar, D., A. V. S. Kumar, M. Marathe, and S. Parthasarathy,
"Power Efficient Throughput Maximization in Multi hop Wireless Networks",
Proc. IEEE Globecom 2008 Wireless Networking Symposium (GC'08 WN) , 2008.
Kumar, A. V. S., M. Marathe, S. Premaraju, and I. Pirwani,
"On the Complexity of Minimum Partition of Frequency-Agile Radio Networks",
Proc. IEEE DySPAN 2008, 2008.
Barrett, C., K. Bisset, G. Konjevod, M. Holzer, M. Marathe, and D. Wagner,
"Engineering Label-Constrained Shortest-Path Algorithms,",
Proc. 4th International Conference on Algorithmic Aspects in Information and Management (AAIM 2008 ), June, 2008.
Barrett, C., S. Eubank, and M. Marathe,
"An Interaction-Based Approach to Computational Epidemiology",
Proc. Computability in Europe 2008, Logic and Theory of Algorithms , 2008.
Chafekar, D., D. Levin, A. V. S. Kumar, M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Capacity of Asynchronous Random-Access Scheduling in Wireless Networks",
Proc. 27th IEEE International Conference on Computer Communications (INFOCOM) , 2008 , 2008.
Eubank, S., A. V. S. Kumar, and M. Marathe,
"Epidemiology and Wireless Communication: Tight Analogy or Loose Metaphor? ",
Bio-Inspired Computing and Communication Springer LNCS , 2008.
Kumar, V. S. A., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Minimum Weighted Completion Time",
Encyclopedia of Algorithms , M. Kao, Ed: Springer Verlag, 2008.
Barrett, C., S. Eubank, B. Lewis, and M. Marathe,
"Information Systems for Detection and Management of Pandemics",
Encyclopedia of Geographic Information Systems, S. Shekhar, X. Xiong, Eds. : Springer-Verlag, 2008.
2007
Choi, V., C. Zheng, Q. Zhu, and D. Sankoff,
"Algorithms enabling extraction of syteny blocks from comparative maps.",
The 7th Workshop on Algorithms in Bioinformatics, 2007.
Choi, V., Y. Huang, V. Lam, R. Laubenbacher, and K. Duca,
"Using Formal Concept Analysis for Microarray Data Comparison",
The Fifth Asia-Pacific Bioinformatics Conference, APBC2007, 2007.
Choi, V.,
"Faster Algorithms for Constructing Galois Lattice",
DIMACS book on Clustering Challenges in Biological Networks, 2007.
Choi, V., and N. Goyal,
"Alogirthmic Approaches to the Identification of Rigid Domains in Proteins",
Special issue of Algorithmica on algorithms for processing protein structures, 2007.
Cao, Y., D. Gillespie, and L. Petzold,
"The adaptive explicit-implicit tau-leaping method with automatic tau selection",
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 SCIenti c Computation And Di erential Equations), Santa Malo, France, July, 2007.
Heath, L. S., and A. A. Sioson,
"Multimodal Networks: Structure and Operations",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007.
Heath, L. S., and A. A. Sioson,
"Semantics of Multimodal Network Models,",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007.
Heath, L. S., and A. Pati,
"Predicting Markov Chain Order in Genomic Sequences",
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM): IEEE Computer Society Press, 2007.
Heath, L. S., and A. Pati,
"Genomic Signatures in de Bruijn Chains",
Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), vol. 4645, pp. pp. 216-227. , 2007.
Heath, L. S., and A. Pati,
"Genomic Signatures from DNA Word Graphs",
Proceedings of the Third International Symposium on Bioinformatics Research and Applications, ISBRA , vol. 4463, pp. pp. 317-328., 2007.
Pati, A., and L. S. Heath,
"Genomic signatures from DNA word graphs (poster)",
Grace Hopper Celebration of Women in Computing, , 10/2007.
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.
Agarwal, H., C. K. Mozumder, J. E. Renaud, and L. T. Watson,
"An inverse-measure-based unilevel architecture for reliability-based design optimization",
Structural Multidisciplinary Optim., vol. 33, pp. 217-227, 2007.
Zwolak, J. W., P. T. Boggs, and L. T. Watson,
"Algorithm 869: ODRPACK95: a weighted orthogonal distance regression code with bound constraints",
ACM Trans. Math. Software, vol. 33, 2007.
Adams, D. B., L. T. Watson, O. Seresta, and Z. Gurdal,
"Global/local iteration for blended composite laminate panel structure optimization subproblems",
Mech. Adv. Materials Structures, vol. 14, pp. 139-150, 2007.
Lee, J. N., F. A. Kamke, and L. T. Watson,
"Simulation of the hot-pressing of a multi-layered wood strand composite",
J. Composite Materials, vol. 41, pp. 879–904, 2007.
Phillips, R. D., L. T. Watson, and R. H. Wynne,
"Hybrid image classification and parameter selection using a shared memory parallel algorithm",
Comput. & Geosciences, vol. 33, pp. 875-897, 2007.
Zhang, L., and L. T. Watson,
"Note on the computation of critical effective population sizes",
J. Comput. Biol., vol. 14, pp. 950-960, 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.
Khan, M., G. Pandurangan, and A. V. S. Kumar,
"A Simple Randomized Scheme for Constructing Low-Weight k-Connected Spanning Subgraphs with Applications to Distributed Algorithms",
Theoretical Computer Science, vol. 385, no. 1-3, pp. 101-114, 2007.
Atkins, K., J. Chen, A. V. S. Kumar, and A. Marathe,
"Structural Properties of Electrical Networks.",
International Journal of Critical Infrastructure, 2007.
Barrett, C., K. Bisset, J. Chen, S. Eubank, B. Lewis, A. V. S. Kumar, M. Marathe, and H. Mortveit,
"Effect of Public Policies and Individual Behavior on the Co-evolution of Social Networks and Infectious Disease Dynamics",
DIMACS Workshop on Computational Methods for Dynamic Interaction Networks, Rutgers University, Septermber, 2007.
Eubank, S., A. V. S. Kumar, and M. Marathe,
Epidemiology and wireless communication tight analogy or loose metaphor,
: Bio-Inspired Computing and Communication, Springer Verlag. In press, 2007.
Barrett, C., B. Lewis, J. Chen, A. V. S. Kumar, S. Eubank, M. Marathe, and H. Mortveit,
"Interactions among human behavior, social networks, and societal infrastructures: A case study in computational epidemiology.",
Ravi S, Shukla S (eds.), Fundamental Problems in Computing: Essays in Honor of Professor Daniel J. Rosenkrantz. Springer Verlag, Vol. In press December, 2007.
Barrett, C., K. Bisset, S. Eubank, A. V. S. Kumar, M. Marathe, and H. Mortveit,
"Modeling and Simulation of Large Biological, Information and Socio-Technical Systems: An Interaction-Based Approach",
Proceedings of the Short Course on Modeling and Simulation of Biological Networks, AMS Lecture Notes, Series: PSAPM, revised and accepted, January 2007. In Press., 2007.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, A. Srinivasan, and S. Zust,
"Scheduling on Unrelated Machines under Tree-Like Precedence Constraints",
special issue of Algorithmica containing selected papers from RANDOM , 2007.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, R. E. Stearns, and M. Thakur,
"Predecessor Existence Problems for Finite Discrete Dynamical Systems",
Theoretical Computer Science, vol. 386, no. 1-2, pp. 3-37, 2007.
Barrett, C., K. Bisset, J. Chen, B. Lewis, S. Eubank, A. V. S. Kumar, M. Marathe, and H. Mortveit,
"Effect of Public Policies and Individual Behavior on the Co-evolution of Social Networks and Infectious Disease Dynamics ",
Proc. DIMACS/DyDAn Workshop on Computational Methods for Dynamic Interaction Networks, September, 2007.
Chafekar, D., A. V. S. Kumar, M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Cross-Layer Latency Minimization in Wireless Networks with SINR constraints",
Proc. 8th ACM International Symposium on Mobile Ad Hoc Networking and Computing (MobiHoc), September, 2007.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Provable algorithms for joint optimization of transport, routing and MAC layers in wireless ad hoc networks",
Proc. Discrete Algorithms and Methods for Mobile Computing and Communications (DIALM)-Principles of Mobile Computing (POMC) , 2007.
Thomas, R. W., L. A. DaSilva, M. Marathe, and K. N. Wood,
"Critical Design Decisions for Cognitive Networks",
Proc. ICC Wireless Adhoc and Sensor Networks Symposium, 2007.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, R. E. Stearns, and M. Thakur,
"Computational Aspects of Analyzing Social Network Dynamics",
Proc. International Joint Conference on Artificial Intelligence, (IJCAI 07), Hyderabad, India, pp. 2268-2273, January, 2007.
Barrett, C., J. Chen, S. Eubank, B. Lewis, V. S. A. Kumar, M. Marathe, and H. S. Mortveit,
"Interactions Among Individual Behavior, Social Networks, and Societal Infrastructures: A Case Study in Computational Epidemiology ",
Book Containing Chapters to celebrate Prof. Daniel Rosenkrantz's 60th Birthday: Springer, 2007.
Barrett, C., K. Bisset, S. Eubank, V. S. A. Kumar, M. Marathe, and H. S. Mortveit,
"Modeling and Simulation of Large Biological, Information and Socio-Technical Systems: An Interaction-Based Approach ",
Proceedings of the Symposia in Applied Mathematics, Short Course on Modeling and Simulation of Biological Networks, AMS Lecture Notes, Series, (PSAPM) 64, pp. 101-147, 2007.
2006
Li, P., A. Sioson, S. P. Mane, A. Ulanov, G. Grothaus, L. S. Heath, T. M. Murali, H. J. Bohnert, and R. Grene,
"Response diversity of Arabidopsis thaliana ecotypes in elevated CO/2 in the field.",
Plant Mol Biol, vol. 62, no. 4-5, pp. 593-609, 2006.
Abstract
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali,
"XcisClique: Analysis of regulatory bicliques.",
BMC Bioinformatics, vol. 7, no. 1, pp. 218, 2006.
Abstract
Choi, V., and N. Goyal,
"An Efficient Approximation Algorithm for Point Pattern Matching Under Noise",
The 7th International Symposium, Latin American Theoretical Informatics (LATIN 2006), 2006.
Choi, V.,
"On Updating Torsion Angles of Molecular Conformations",
Journal of Chemical Information and Modeling, vol. 46, no. 1, pp. pp438 – 444, 2006.
Petzold, L., S. T. Li, Y. Cao, and R. Serban,
"Sensitivity analysis of di erential-algebraic equations and partial di erential 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., L. Petzold, and D. Gillespie,
"Adaptive tau-leaping method for biochemical systems",
minisymposium talk in SIAM Annual Meeting 2006, Boston, Massachusetts, July, 2006.
Watkinson, J. I., L. Hendricks, A. A. Sioson, C. Vasquez-Robinet, L. S. Heath, M. Schuler, and H. J. Bohnert,
"Accessions of Solanum tuberosum ssp. andigena Show Differences in Photosynthetic Recovery After Drought Stress as Reflected in Gene Expression Profiles",
Plant Science , vol. 171, pp. pp. 745-758. , 2006.
Li, P. H., S. P. Mane, A. A. Sioson, C. V. Robinet, L. S. Heath, H. J. Bohnert, and R. Grene,
"Effects of Chronic Ozone Exposure on Gene Expression in Arabidopsis thaliana Ecotypes and in Thellungielia halophila",
Plant Cell and Environment , vol. 29, pp. pp. 854-868. , 2006.
Li, P. H., A. Sioson, S. P. Mane, A. Ulanov, G. Grothaus, L. S. Heath, T. M. Murali, H. J. Bohnert, and R. Grene,
"Response Diversity of Arabidopsis thaliana Ecotypes in Elevated [Co2] in the Field",
Plant Molecular Biology, vol. 62, pp. pp. 593-609, 2006.
Sioson, A. A., and L. S. Heath,
"Some Fundamental Operations on Multimodal Networks in Biology",
Philippine Computing Journal , vol. 1, pp. pp. 13-22. , 2006.
Sioson, A. A., S. P. Mane, P. Li, W. Sha, L. S. Heath, H. J. Bohnert, and R. Grene,
"The Statistics of Identifying Differentially Expressed Genes in Expresso and TM4: A Comparison",
BMC Bioinformatics , vol. 7, pp. 15 pages in main article; plus 5 pages in 2 additional files. , 2006.
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali,
"XcisClique: Analysis of Regulatory Bicliques",
BMC Bioinformatics, vol. 7, pp. 14 pages in main article; plus 16 pages in 7 additional files, 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.
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.
Setoodeh, S., D. B. Adams, Z. Gurdal, and L. T. Watson,
"Pipeline implementation of cellular automata for structural design on message-passing multiprocessors",
Math. Comput. Modeling, vol. 43, pp. 966-975, 2006.
Haftka, R. T., and L. T. Watson,
"Decomposition theory for multidisciplinary design optimization problems with mixed integer quasiseparable subsystems",
Optim. Engrg., vol. 7, pp. 135–149, 2006.
Setoodeh, S., Z. Gurdal, and L. T. Watson,
"Design of variable-stiffness composite layers using cellular automata",
Comput. Methods Appl. Mech. Engrg., vol. 195, pp. 836–851, 2006.
Su, H. - J., J. M. McCarthy, M. Sosonkina, and L. T. Watson,
"Algorithm 857: POLSYS GLP—a parallel general linear product homotopy code for solving polynomial systems of equations",
ACM Trans. Math. Software, vol. 32, pp. 561–579, 2006.
Kamke, F. A., L. T. Watson, J. N. Lee, and J. Shu,
"A Web-based problem solving environment for the wood-based composites industry",
Forest Products J., vol. 56, pp. 26-32, 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.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Provable Algorithms for Parallel Generalized Sweep Scheduling.",
Journal of Parallel and Distributed Computing, vol. 66, no. 6, pp. 807-821, 2006.
Duncan, C., S. Kobourov, and A. V. S. Kumar,
"Optimal Constrained Graph Exploration",
Transactions of Algorithms, vol. 2, no. 3, pp. 380-402, 2006.
Eidenbenz, S., A. V. S. Kumar, and S. Zust,
"Equilibria in Topology control games for ad hoc networks",
Mobile Networks and Applications, vol. 11, pp. 143-159, 2006.
Chen, J., A. V. S. Kumar, A. Marathe, and K. Atkins,
"Model Based Spatial Data Mining for Power Markets.",
SIAM-DM 2006 Workshop on Spatial Data Mining, April, 2006.
Atkins, K., J. Chen, A. V. S. Kumar, and A. Marathe,
"Structural Properties of Electrical Networks",
3rd International Conference on Critical Infrastructures, Septermber, 2006.
Atkins, K., J. Chen, A. V. S. Kumar, M. Macauley, and A. Marathe,
"Locational Market Power in Power Markets",
29th IAEE International Conference, June, 2006.
Barrett, C., G. Istrate, A. V. S. Kumar, M. Marathe, S. Thite, and S. Thulasidasan,
"Strong Edge Coloring for Channel Assignment in Wireless Radio Networks.",
IEEE International Workshop on ”Foundation and Algorithms for Wireless Networking (FAWN’2006), 2006.
Sundaram, R., A. V. S. Kumar, M. Marathe, M. Thakur, and S. Thulasidasan,
"Scaling Laws for the Internet over Urban Regions.",
ISMA 2006 WIT:Workshop on the Internet Topology, May, 2006.
Eubank, S., A. V. S. Kumar, M. Marathe, A. Srinivasan, and N. Wang,
"Structure of Social Contact Networks, and their impact on Epidemics.",
AMS-DIMACS Special Issue on Epidemiology, 2006.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, and R. E. Stearns,
"Dichotomy Results for Reachability Problems in Sequential Dynamical Systems",
J. Computer and System Science , vol. 72, no. 8, pp. 1317-1345, 2006.
Bailey-Kellogg, C., N. Ramakrishnan, and M. Marathe,
"Spatial data mining to support pandemic preparedness. ",
SIGKDD Explorations, vol. 8, no. 1, pp. 80-82, 2006.
III, H. H. B., M. Marathe, and R. E. Stearns,
"The Complexities of Unquantified, Quantified and Stochastic Constrained Satisfaction Problems ",
special issue of Discrete Applied Mathematics , 2006.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, R. E. Stearns, and M. Thakur,
"Computational Complexity of Analyzing the Dynamic Reliability of Interdependent Infrastructures ",
Proc. 3rd International Conference on Critical Infrastructures (CRIS06) , August, 2006.
Kumar, A. V. S., M. Marathe, M. T. R. Sundaram, and S. Thulasidasan,
"Scaling Laws for the Internet over Urban Regions, ",
CAIDA (Cooperative Association for Internet Data Analysis), ISMA 2006 WIT: Workshop on the Internet Topology , 2006.
Chen, J., M. Marathe, R. Rajaraman, and R. Sundaram,
"The Confluent Capacity of the Internet: Congestion vs. Dilation",
Proceedings of IEEE International Conference on Distributed Computing Systems (ICDCS ), 2006.
Istrate, G., A. Hansson, M. Marathe, S. Thulasidasan, and C. Barrett,
"Semantic compression of TCP traces, ",
Proceedings of the IFIP NETWORKING Conference, F. Boavida et al. (editors), pp. 123-135, 2006.
Barrett, C., G. Istrate, A. V. S. Kumar, M. Marathe, S. Thite, and S. Thulasidasan,
"Strong Edge Coloring for Channel Assignment in Wireless Radio Networks",
Proceedings of the First IEEE International Workshop on Foundations and Algorithms for Wireless Networking (FAWN'06) , pp. 106-110, 2006.
Barrett, C., S. Eubank, and M. Marathe,
"Modeling and Simulation of Large Biological, information and Socio-Technical Systems: An Interaction Based Approach ",
Interactive Computing: A new Paradigm, Ed. D. Goldin, S. Smolka and P. Wegner: Springer Verlag, pp. 353-394, 2006.
Eubank, S., V.S. Anil Kumar, M. Marathe, A. Srinivasan, and N. Wang,
"Structure of Social Contact Networks and Their Impact on Epidemics",
AMS-DIMACS Special Issue on Epidemiology, pp. 181-213, 2006.
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.
Choi, V.,
"YUCCA: An Efficient Small Molecule Docking Algorithm",
Chemistry and Biodiversity, vol. 11, pp. 1517 – 1524, 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., 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.
Brueni, D. J., and L. S. Heath,
"The PMU Placement Problem",
SIAM Journal on Discrete Mathematics, vol. 19, pp. pp. 744-761. , 2005.
John C. Gordon, J. B. Myers, T. Folta, V. Shoja, L. S. Heath, and A. Onufriev,
"H++: A Server for Estimating pK(a)s and Adding Missing Hydrogens to Macromolecules",
Nucleic Acids Research , vol. 33, no. 2, pp. pp. W368-W371, 2005.
Mane, S., C. Vasquez-Robinet, A. A. Sioson, L. S. Heath, and R. Grene,
"Effects of Drought Stress on Phospholipid Signaling in Arabidopsis (Poster)",
InterDrought-II, The Second International Conference on Integrated Approaches to Sustain and Improve Plant Production Under Drought Stress, Rome, Italy, 09/2005.
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali,
"XcisClique: Analyzing Regulatory Bicliques in Arabidopsis thaliana (Poster)",
8th Annual Conference on Computational Genomics , Cambridge, MA,, 11/2005.
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.
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.
Papila, M., R. T. Haftka, and L. T. Watson,
"Pointwise bias error bounds and min-max design for response surface approximations",
AIAA J., vol. 43, pp. 1797–1807, 2005.
Zwolak, J. W., J. J. Tyson, and L. T. Watson,
"Globally optimized parameters for a model of mitotic control in frog egg extracts",
IEE Systems Biol., vol. 152, pp. 81-92, 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.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Scheduling on Unrelated Machines Under Tree-Like Precedence Constraints",
Algorithmica, Special issue, 2005.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Approximation Algorithms for Scheduling on Multiple Machines.",
Proc. of the 46th Annual IEEE Symposium on Foundations of Computer Science (FOCS), 2005.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Scheduling on Unrelated Machines Under Tree-Like Precedence Constraints.",
Proc. op APPROX-RANDOM 2005, Springer Verlag LNCS, vol. 3624, pp. 146-157, 2005.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Algorithmic Aspects of Capacity in Wireless Networks",
ACM SIGMETRICS, 2005.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, A. Srinivasan, and S. Zust,
"Provable Algorithms for Parallel Sweep Scheduling on Unstructured Meshes.",
International Parallel and Distributed Processing Symposium (IPDPS), 2005.
Barrett, C., M. Drozda, D. Engelhart, A. V. S. Kumar, M. Marathe, M. Morin, S. S. Ravi, and J. P. Smith,
"Understanding Protocol Performance and Robustness of Ad hoc Networks Through Structural Analysis",
Proc. International Conference onWireless and Mobile Computing, Networking and Communications (WiMob 2005), 2005.
Liu, R., E. Lloyd, M. Marathe, R. Ramanathan, and S. Ravi,
"Algorithmic Aspects of Topology Control Problems For Ad-hoc Networks",
ACM/Baltzer J. Mobile Networks and Applications (MONET), vol. 10, pp. 19-34, 2005.
Barrett, C., S. Eidenbenz, L. Kroc, M. Marathe, and J. Smith,
"Parametric Probabilistic Routing in Sensor Networks",
ACM/Baltzer J. Mobile Networks and Applications (MONET), vol. 10, no. 4, pp. 529-544, 2005.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Approximation Algorithms for Scheduling on Multiple Machines ",
Proc. 46th Annual IEEE Symposium on Foundations of Computer Science (FOCS'05), pp. 254-263 , 2005.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Scheduling on Unrelated Machines Under Tree-Like Precedence Constraints",
APPROX-RANDOM, 2005.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"Algorithmic aspects of capacity in wireless networks",
ACM SIGMETRICS, 2005.
Barrett, C., S. Eidenbenz, L. Kroc, M. Marathe, and J. Smith,
"Probabilistic multi-path vs. deterministic single-path protocols for dynamic ad-hoc network scenarios",
ACM Symposium on Applied Computing (SAC), pp. 1166-1173, 2005.
Barrett, C., M. Morin, C. Engelhart, M. Marathe, J. Smith, M. Drozda, and A. V. Kumar,
"Understanding Protocol Performance and Robustness of Ad-Hoc Networks Through Structural Analysis ",
Proc. IEEE International Conference on Wireless and Mobile Computing, Networking and Communications (WiMob) , 2005.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, A. Srinivasan, and S. Zust,
"Provable Algorithms for Parallel Sweep Scheduling on Unstructured Meshes",
Proc. International Parallel and Distributed Processing Symposium (IPDPS) , 2005.
Eubank, S., A. V. Kumar, M. Marathe, A. Srinivasan, and N. Wang,
"Structural and Algorithmic Aspects of Massive Social Networks",
Proc. ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 718-727, 2005.
III, H. H. B., M. Marathe, R. E. Stearns, and D. J. Rosenkrantz,
"A Survey of Periodically Specified Problems",
Computational Complexity and Statistical Physics , Oxford University Press, Santa Fe Institute Lectures in the Sciences of Complexity , G. Istrate, C. Moore, A. Percus Eds, pp. 285-318, 2005.
2004
Choi, V., P. K. Agarwal, H. Edelsbrunner, and J. Rudolph,
"Local Search Heuristic for Rigid Protein Docking",
The 4th Workshop on Algorithms in Bioinformatics (WABI 2004), vol. 3240, pp. pp. 218–229, 2004.
Choi, V., and N. Goyal,
"A Combinatorial Shape Matching Algorithm for Rigid Protein Docking",
The Fifteenth Annual Symposium on Combinatorial Pattern Matching (CPM 2004), vol. 3109, pp. pp 285-296, 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 di erential equations by the adjoint method",
SIAM J. Scienti c 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.
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.
Heath, L. S., and N. A. Loehr,
"Efficient Algorithms for Finding Conway Polynomials,",
Journal of Symbolic Computation , vol. 38, pp. pp. 1003-1024. , 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.
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.
Perez, V. M., J. E. Renaud, and L. T. Watson,
"An interior point sequential approximate optimization methodology",
Structural Multidisciplinary Optim., vol. 27, pp. 360–370, 2004.
Su, H. - J., J. M. McCarthy, and L. T. Watson,
"Generalized linear product homotopy algorithms and the computation of reachable surfaces",
ASME J. Comput. Information Sci. Engrg., vol. 4, pp. 226–234, 2004.
Zombori, B. G., F. A. Kamke, and L. T. Watson,
"Sensitivity analysis of internal mat environment during hot-pressing",
Wood Fiber Sci., vol. 36, pp. 195–209, 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.
Eubank, S., H. Guclu, A. V. S. Kumar, M. Marathe, A. Srinivasan, Z. Toroczkai, and N. Wang,
"Modeling disease outbreaks in realistic urban social networks",
Nature, vol. 429, pp. 180-184, 2004.
Balakrishnan, H., C. Barrett, A. V. S. Kumar, M. Marathe, and S. Thite,
"The distance-2 matching problem and its relationship to the MAC-layer capacity of ad hoc networks",
IEEE Journal on Selected Areas in Communication, vol. 22, no. 6, pp. 1069-1079, 2004.
Kumar, A. V. S., M. Marathe, S. Parthasarathy, and A. Srinivasan,
"End-to-end packet scheduling in ad hoc networks",
ACM Symposium on Discrete Algorithms (SODA), 2004.
Eubank, S., A. V. S. Kumar, M. Marathe, A. Srinivasan, and N. Wang,
"Structural and Algorithmic aspects of massive social networks",
ACM Symposium on Discrete Algorithms (SODA), 2004.
Barrett, C., S. Eubank, A. V. S. Kumar, and M. Marathe,
"Understanding Large-Scale Social and Infrastructure Networks: a Simulation Based Approach",
SIAM News, vol. 37, 2004.
Eubank, S., H. Guclu, A. V. Kumar, M. Marathe, A. Srinivasan, Z. Toroczkai, and N. Wang,
"Modelling Disease Outbreaks in Realistic Urban Social Networks",
Nature, vol. 429, pp. 180-184, 2004.
Balakrishnan, H., C. Barrett, A. Kumar, M. Marathe, and S. Thite,
"The Distance 2-Matching Problem and Its Relationship to the MAC Layer Capacity of Ad-hoc Wireless Networks ",
IEEE J. Selected Areas in Communications, vol. 22, no. 6, pp. 1069-1079 , 2004.
Konjevod, G., S. Krumke, and M. Marathe,
"Budget Constrained Minimum Cost Connected Medians",
Journal of Discrete Algorithms, vol. 2, no. 4, pp. 453-469, 2004.
Marathe, M., L. D. Risenger, and A. Panconesi,
"Experimental Analysis of a Simple Distributed Edge Coloring Algorithm ",
Journal of Experimental Algorithmics, vol. 9, pp. 1-23, 2004.
Barrett, C., M. Marathe, S. S. Ravi, and J. Smith,
"A Mobility and Traffic Generation Framework for Modeling and Simulating Ad~hoc Communication Networks ",
Scientific Programming, vol. 12, no. 1, pp. 1-23, 2004.
Barrett, C., C. Englehart, M. Marathe, and A. Sivasubramanium,
"Approximate Connectivity Graph Generation in Mobile Ad Hoc Radio Networks ",
Elsevier Journal of Systems and Software, vol. 73, pp. 63-74, 2004.
Kumar, A. V. S., M. Marathe, S. Parthasarthy, and A. Srinivasan,
"End-to-End Packet Scheduling in Ad-hoc Radio Networks",
ACM-SIAM Symposium on Discrete Algorithms (SODA), 2004.
Engelhart, C., A. Sivasubramaniam, C. Barrett, M. Marathe, J. Smith, and M. Morin,
"A Spatial Analysis of Mobility Models: Application to Wireless Ad Hoc Network Simulation",
Annual Simulation Symposium, 2004.
2003
Bespamaytnikh, S., V. Choi, H. Edelsbrunner, and J. Rudolph,
"Accurate Rigid Protein Docking by Shape Complementarity Alone",
Technical Report, Department of Computer Science, Duke University, 2003.
Choi, V., and M. Farach-Colton,
"BARNACLE: An Assembly Algorithm for Clone-based Sequences of Whole Genomes",
Gene, vol. 320, pp. 165-176, 2003.
Rathinam, M., L. Petzold, Y. Cao, and D. Gillespie,
"Sti ness 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 di erential-algebraic equations and partial di erential equations",
Proceedings,Workshop on Modeling and Simulation in Chemical Engineering, Coimbra, Portugal, 2003.
Watkinson, J. I., A. A. Sioson, C. Vasquez-Robinet, M. Shukla, D. Kumar, M. Ellis, L. S. Heath, N. Ramakrishnan, B. I. Chevone, L. T. Watson, et al.,
"Photosynthetic Acclimation is Reflected in Specific Patterns of Gene Expression in Drought-Stressed Loblolly Pine",
Plant Physiology , vol. 133, no. 4, pp. pp. 1702-1716, 2003.
Heath, L. S., and J. P. C. Vergara,
"Sorting by Short Swaps",
Journal of Computational Biology, vol. 10, no. 5, pp. pp. 775-789. , 2003.
Slotta, D. J., L. S. Heath, N. Ramakrishnan, R. Helm, and M. Potts,
"Clustering Mass Spectrometry Data using Order Statistics",
Proteomics, vol. 3, no. 9, pp. pp. 1687-1691. , 2003.
Sioson, A. A., J. I. Watkinson, C. Vasquez-Robinet, M. Ellis, M. Shukla, D. Kumar, N. Ramakrishnan, L. S. Heath, R. Grene, B. I. Chevone, et al.,
"Expresso and Chips: Creating a Next Generation Microarray Experiment Management Systems",
Proceedings of the Next Generation Software Workshop, 17th International Parallel and Distributed Processing Symposium (IPDPS'03),, Nice, France, IEEE Computer Society, 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.
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.
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.
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.
Kumar, A. V. S., and R. Hariharan,
"Covering Rectilinear Polygons with Axis-Parallel Rectangles",
SIAM Journal of Computing, vol. 32, no. 6, pp. 1509-1541, 2003.
Chandru, V., A. DuttaSharma, and A. V. S. Kumar,
"The Algorithmics of Folding Proteins on Lattices",
Discrete Applied Mathematics, vol. 127, no. 1, pp. 145-161, 2003.
Eidenbenz, S., A. V. S. Kumar, and S. Zust,
"Equilibria in Topology control games for ad hoc networks",
proceedings of the Workshop on Discrete Algorithms and Methods for Mobile Computing and Communications and Principles of Mobile Computing (DIALPOMC), Septermber, 2003.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, and R. E. Stearns,
"On Some Special Classes of Sequential Dynamical Systems",
Annals of Combinatorics, pp. 381-408, 2003.
Barrett, C., D. Cook, V. Faber, G. Hicks, A. Marathe, M. Marathe, A. Srinivasan, Y. Sussmann, and H. Thornquist,
"Statistical Analysis of Algorithms: A Case Study of Market-Clearing Mechanisms in the Power Industry ",
Journal of Graph Algorithms and Applications (JGAA) , vol. 7, no. 1, pp. 3-31, 2003.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, and R. E. Stearns,
"Reachability Problems for Sequential Dynamical Systems with Threshold Functions,",
Theoretical Computer Science, pp. 41-64, March, 2003.
Krumke, S., R. Liu, E. Lloyd, M. Marathe, R. Ramanathan, and S. Ravi,
"Topology Control Problems Under Symmetric and Asymmetric Thresholds",
Proc. International Conference on Ad hoc and Wireless Networks (ADHOC-NOW'03) , Montreal, Canada, pp. 187--198, October , 2003.
Barrett, C., S. Eidenbenz, L. Kroc, M. Marathe, and J. Smith,
"Parametric Probabilistic Sensor Network Routing",
Proc. 2nd ACM International Workshop on Wireless Sensor Networks (WSNA'03) , San Deigo, pp. 122-131, 2003.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, and R. E. Stearns,
"Predecessor and Permutation Existence Problems for Sequential Dynamical Systems ",
Proc. Discrete Models for Complex Systems, Lyon, France, pp. 69-80, June , 2003.
Barrett, C., C. Englehart, M. Marathe, and A. Sivasubramanium,
"Approximate Connectivity Graph Generation in Mobile Ad Hoc Radio Networks ",
36th IEEE Annual Simulation Symposium, Orlando, Florida, March-April, 2003.
Barrett, C., K. Bisset, R. Jacob, G. Konjevod, and M. Marathe,
"Analyzing Interaction Between Network Protocols, Topology and Traffic in Wireless Radio Networks ",
Proc. European Symposium on Algorithms (ESA), Rome, September, 2003.
Burch, C., R. Carr, S. Krumke, M. Marathe, C. Phillips, and E. Sundberg,
"A decomposition-based pseudoapproximation algorithm for network flow inhibition ",
Network Interdiction and Stochastic Integer Programming , D.L. Woodruff (ed): Kluwer Academic Press, pp. 51-68, 2003.
2002
Choi, V., J. Bailey, G. Schuler, Z. Gu, P. Li, M. Farach-Colton, and E. Eichler,
"The Sequence and Assembly of Highly Duplicated Regions in the Human Genome",
Genome Sequencing & Biology meeting , Cold Spring Harbor Laboratory, 2002.
Cao, Y., S. Li, L. Petzold, and R. Serban,
"Adjoint sensitivity analysis for di erential-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 di erential-algebraic equations: algorithms and software",
J. Comp. Appl. Math., 2002.
Heath, L. S., N. Ramakrishnan, R. R. Sederoff, R. W. Whetten, B. I. Chevone, C. A. Struble, V. Y. Jouenn, D. Chen, L. M. van Zyl, and R. Grene,
"Studying the Functional Genomics of Stress Responses in Loblolly Pine using the Expresso Microarray Management System",
Comparative and Functional Genomics , vol. 3, pp. pp. 226-243. , 2002.
Grene, R., Neval Erturk, and L. S. Heath,
"Role of Superoxide Dismutase (SODs) in Controlling Oxidative Stress in Plants",
Journal of Experimental Botany, vol. 53, pp. pp. 1331-1341. , 2002.
Heath, L. S.,
"Networks in Bioinformatics",
Proceedings of the 2002 International Symposium on Parallel Architectures, Algorithms, and Networks (I-SPAN 2002), pp. pp. 141-150. , 2002.
Slotta, D. J., L. S. Heath, N. Ramakrishnan, R. Helm, and M. Potts,
"Computational Approaches to Combining Predictive Biological Models",
Advanced Simulation Technologies Conference (HPC 2002), 2002, , pp. pp. 75-80. , 2002.
Slotta, D. J., L. S. Heath, and N. Ramakrishnan,
"Clustering Mass Spectrometry Data using Order Statistics (Abstract)",
First Annual Proteomics Data Mining Conference, Duke University, Durham, NC, 09/2002.
Watkinson, J. I., A. A. Sioson, M. Shukla, L. S. Heath, N. Ramakrishnan, B. I. Chevone, L. T. Watson, J. W. Weller, R. R. Sederoff, L. M. van Zyl, et al.,
"Identifying Changes in Gene Expression During Drought Stress Using Expresso (Poster)",
ASPB (American Society of Plant Biologists) Plant Biology 2002, Denver, CO, 08/2002.
Heath, L. S., and N. Ramakrishnan,
"The Emerging Landscape of Bioinformatics Software Systems",
IEEE Computer , vol. 35, pp. pp. 41-45. , 07/2002.
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.
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.
Kumar, A. V. S., and M. Marathe,
"Improved Results for Stackelberg Scheduling Strategies.",
The 29th International Colloquium on Automata, Languages and Programming, 2002 (ICALP), Lecture Notes in Computer Science, 2380, Springer, 2002.
III, H. H. B., M. Marathe, R. V. S. S. Ravi, D. J. Rosenkrantz, and R. E. Stearns,
"Parallel Approximation Schemes for a Class of Planar and Near Planar Combinatorial Problems ",
Information and Computation, vol. 173, no. 1, pp. 40-63, 2002.
Doddi, S., M. Marathe, and B. Moret,
"Point Set Labeling with Specified Positions",
International Journal of Computational Geometry, vol. 12, no. 1-2, pp. 29-66, 2002.
Barrett, C., M. Marathe, S. S. Ravi, and J. Smith,
"A Mobility and Traffic Generation Framework for Modeling and Simulating Ad~hoc Communication Networks ",
Proc. 6th ACM Symposium on Applied Computing (SAC), Madrid, Spain, pp. 122-126, March, 2002.
Barrett, C., C. Engelhart, M. Marathe, and A. Sivasubramanium,
"Analyzing the Short-Term Fairness of IEEE 802.11 in Wireless Multi-hop Radio Networks ",
Proc. 10th IEEE/ACM International Symposium on Modeling, Analysis and Simulation of Computer and Telecommunication Systems, (MASCOTS'02) , October , 2002.
Marathe, M.,
"Towards a Predictive Complexity Theory",
Proc. 29th International Colloquium on Automata Languages and Programming , , Malaga, Spain, pp. 22-31, 2002.
Marathe, M.,
"Routing in Very large Multi-Modal Time Dependent Networks: Theory and Practice",
Proc. Algorithmic MeThods and Models for Optimization of RailwayS (ATMOS 2002) , Malaga, Spain, 2002.
Anil, V. S., and M. Marathe,
"Improved Results for Stackelberg Scheduling Strategies",
29th International Colloquium on Automata Languages and Programming, Malaga, Spain, pp. 776-787, 2002.
Krumke, S., M. Marathe, D. Poensgen, S. Ravi, and H. Wirth,
"Budgeted Maximum Graph Coverage, ",
Proc. 28th International Workshop on Graph Theoretic Concepts in Computer Science, (WG), Cesky, Czech Republic, August , 2002.
Barrett, C., M. Drozda, A. Marathe, and M. Marathe,
"Characterizing the Interaction Between Routing and MAC Protocols in Ad-hoc Networks, ",
3rd ACM international Symposium on Mobile Ad Hoc Networking and Computing, Lausanne, Switzerland, pp. 92-103, June , 2002.
Liu, R., E. Lloyd, M. Marathe, R. Ramanathan, and S. Ravi,
"Algorithmic Aspects of Topology Control Problems For Ad-hoc Networks",
3rd ACM international Symposium on Mobile Ad Hoc Networking and Computing, Lausanne, Switzerland, June , 2002.
Barrett, C., M. Drozda, and M. Marathe,
"A Comparative Experimental Study of Media Access Protocols for Wireless Radio Networks ",
Proc. IEEE Wireless Communications and Networking Conference (WCNC): Florida , pp. 405-411, 2002.
Barrett, C., S. Eubank, M. Marathe, H. Mortveit, and C. Reidys,
"Science and Engineering of Large Scale Socio-Technical Simulations",
Proc. 1st International Conference on Grand Challenges in Simulations, San Antonio Texas, 2002.
2001
Choi, V., and M. Farach-Colton,
"A Simple Sequence Assembly Algorithm for the Human Genome",
RECOMB Satellite Meeting on DNA Sequence Assembly , 2001.
Choi, V., and M. Golin,
"Lopsided Trees, II: Algorithms and Applications",
Technical Report, HKUST, 2001.
Choi, V., and M. Golin,
"Lopsided Trees, I: Analyses",
Algorithmica, vol. 31, pp. 240-290, 2001.
Petzold, L., R. Serban, S. Li, S. Raha, and Y. Cao,
"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.
Green, E. L., L. S. Heath, and C. A. Struble,
"Constructing Homomorphism Spaces and Endomorphism Rings,",
Journal of Symbolic Computation , vol. 32, pp. pp. 101-117. , 2001.
Ganley, J. L., and L. S. Heath,
"The Pagenumber of $k$-Trees is $O(k)$",
Discrete Applied Mathematics , vol. 109, pp. pp. 215-221. , 2001.
Alscher, R. G., B. I. Chevone, L. S. Heath, and N. Ramakrishnan,
"Expresso -- A Problem Solving Environment for Bioinformatics: Finding Answers With Microarray Technology",
Advanced Simulation Technologies Conference (HPC 2001), 2001, , pp. pp. 64-69., 2001.
Green, E. L., L. S. Heath, and C. A. Struble,
"Constructing Endomorphism Rings Via Duals",
International Symposium on Symbolic and Algebraic Computation (ISSAC 2000), 2001.
Rosenberg, A. L., and L. S. Heath,
Graph Separators, with Applications,
, Norwell, Massachusetts, Kluwer Academic Publishers, pp. 264 pp, 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.
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.
Kumar, A. V. S., and R. Hariharan,
"Markovian Coupling v/s Conductance for the Jerrum-Sinclair Chain.",
Random Structures and Algorithms, vol. 18, no. 1, pp. 1-17, 2001.
Duncan, C., S. Kobourov, and A. V. S. Kumar,
"Optimal Constrained Graph Exploration",
Proceedings of the 12th ACM Symposium on Discrete Algorithms (SODA), pp. 807-814, 2001.
Krysta, P., and A. V. S. Kumar,
"Approximation algorithms for minimum size 2-connectivity problems.",
Proceedings of the 18th International Symposium on Theoretical Aspects of Computer Science (STACS), Lecture Notes in Computer Science, n. 2010, Springer, pp. 431- 442, 2001.
Krumke, S. O., M. Marathe, and S. S. Ravi,
"Models and Approximation Algorithms for Channel Assignment in Radio Networks ",
Wireless Journal, vol. 7, no. 6, pp. 575-584, 2001.
Arikati, S. R., A. Dessmark, A. Lingas, and M. Marathe,
"Approximation Algorithms for Maximum Two-Dimensional Pattern Matching",
Theoretical Computer Science, vol. 255, no. 51-62, 2001.
Barrett, C., R. Jacob, and M. Marathe,
"Formal Language Constrained Path Problems",
SIAM J. Computing, vol. 30, no. 3, pp. 809-837, June, 2001.
Krumke, S. O., M. Marathe, H. Noltemeier, S. S. Ravi, and H. C. Wirth,
"Upgrading Bottleneck Constrained Forests",
Discrete Applied Mathematics, vol. 108, no. 1-2, pp. 129-142, 2001.
Barrett, C., D. Cook, V. Faber, G. Hicks, A. Marathe, M. Marathe, A. Srinivasan, Y. Sussmann, and H. Thornquist,
"Experimental Analysis of Algorithms for Bilateral-Contract Clearing Mechanisms Arising in Deregulated Power Industry ",
Proc. 5th Workshop on Algorithmic Engineering (WAE), Aarhus, Denmark, pp. 171-184, August , 2001.
III, H. H. B., R. E. Stearns, and M. Marathe,
"Complexity and Approximability of Quantified and Stochastic Satisfiability Problems",
Proc. Workshop on Theory and Applications of Satisfiability testing, 2001.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, and R. E. Stearns,
"Analysis Problems for Sequential Dynamical Systems and Communicating State Machines",
Proc. 26th Mathematical Foundations of Computer Science (MFCS 01) , August, 2001.
III, H. H., R. Stearns, and M. Marathe,
"Strongly Local Reductions and the Complexity/Efficient Approximability of Algebra and Optimization on Abstract Algebraic Structures ",
International Conference on Symbolic and Algebraic Computations (ISSAC) , July, 2001.
Barrett, C., H. H. B. III, M. Marathe, S. S. Ravi, D. J. Rosenkrantz, R. E. Stearns, and P. Tosic,
"Garden of Eden and Fixed Point Configurations in Sequential Dynamical Systems ",
Proc. International Conference on Discrete Models in Combinatorics, Computation and Geometry (DM-CCG) , pp. 95-110, June, 2001.
Istrate, G., M. Marathe, and S. S. Ravi,
"Adversarial Models in Evolutionary Game Dynamics, 2001",
Proc. 12th ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 719-720, January , 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.
Heath, L. S., and J. P. C. Vergara,
"Sorting by Short Block-Moves",
Algorithmica , vol. 28, pp. pp. 323-352. , 2000.
Heath, L. S., N. Ramakrishnan, R. R. Sederoff, L. M. van Zyl, D. Chen, Y. - H. Sun, B. I. Chevone, S. - H. Li, K. Ye, R. Whetten, et al.,
"Effects of Drought Stress on Gene Expression Patterns in the Needles of Loblolly Pine Trees: Towards a PSE for the Analysis of Microarray Data (Poster)",
Gordon Conference on Biological Regulatory Mechanisms, Holderness, NH, 07/2000.
D. Daescu, G. R. Carmichael, and A. Sandu,
"Adjoint implementation of Rosenbrock methods applied to variational data assimilation",
American Meteorological Society, pp. 346–354, May 15–19, 2000.
S. He, G. R. Carmichael, A. Sandu, and B. Hotchkiss,
"Application of ADIFOR for air pollution model sensitivity studies",
Environmental Modeling and Software, vol. 15, pp. 549–557, 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.
Kumar, A. V. S., S. Arya, and R. Hariharan,
"Hardness of Set Covering with Intersection 1",
Proceedings of the 27th International Colloquium on Automata, Languages and Programming (ICALP), Lecture Notes in Computer Science, vol 1853, pp 624-635, 2000, 2000.
Doddi, S., M. Marathe, R. S. S. D. Taylor, and P. Widmayer,
"Approximation algorithms for clustering to minimize the sum of diameters ",
Nordic Journal of Computing, vol. 7, no. 3, pp. 185-203, August, 2000.
Doddi, S., M. Marathe, and B. Moret,
"Point Set Labeling with Specified Positions",
Proc. ACM Symposium on Computational Geometry (SoCG) , Hong Kong, pp. 182-190, June, 2000.
Dowell, L. J., M. Drozda, B. Henderson, V. Loose, M. Marathe, and D. Roberts,
"Scalability of ELISIMS: Comprehensive Detailed Simulation of Electric Power Industry ",
Proc. IEEE International Conference on Systems, Man and Cybernetics, (SMC) , Nashville, October , 2000.
Doddi, S., M. Marathe, R. S. S. D. Taylor, and P. Widmayer,
"Approximation algorithms for clustering to minimize the sum of diameters ",
Proc. 7th Scandinavian Workshop on Algorithm Theory, (SWAT) July, Bergen, Norway, July, 2000.
Marathe, M., S. Krumke, and M. Marathe,
"Budget Constrained Minimum Cost Connected Medians",
Proc. 26th International Workshop on Graph Theoretic Concepts in Computer Science, (WG) Proc. 26th International Workshop on Graph Theoretic Concepts in Computer Science, (WG) , Konsantz, Germany, June, 2000.
Marathe, M., L. D. Risenger, and A. Panconesi,
"Experimental Analysis of a Simple Distributed Edge Coloring Algorithm ",
Proc. 12th ACM Symposium on Parallel Algorithms and Architectures, (SPAA), Maine, pp. 166-175, July , 2000.
Carr, R., S. Doddi, G. Konjevod, and M. Marathe,
"On the Red-Blue Set Cover Problem",
Proc. 11th ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 345-353, January , 2000.
Czabarka, E., G. Konjevod, M. Marathe, A. G. Percus, and D. C. Torney,
"Algorithms for Optimizing Production DNA Sequencing",
Proc. 11th ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 399-408, January , 2000.
Cook, D., V. Faber, G. Hicks, M. Marathe, A. Srinivasan, and Y. Sussmann,
"Combinatorial Problems Arising in Deregulated Electrical Power Industry: Survey and Future Directions ",
Proc. Approximation and Complexity in Numerical Optimization: Continuous and Discrete Problems , P. M. Pardalos, Editor: Kluwer Academic Publishers, pp. 138-162, 2000.
III, H. H. B., R. E. Stearns, and M. Marathe,
"On the Efficient Approximability of "HARD" Problems: A Survey",
Proc. Approximation and Complexity in Numerical Optimization: Continuous and Discrete Problems , P. M. Pardalos, Editor: Kluwer Academic Publishers, pp. 308-322, 2000.
1999
Cao, Y., and Q. Li,
"Predictor-corrector formula for solving index-2 di erential-algebraic equations",
Mathematica Numerica Sinica,, 1999.
Heath, L. S., S. V. Pemmaraju, and A. Trenk,
"Stack and Queue Layouts of Directed Acyclic Graphs: Part I,",
SIAM Journal on Computing , vol. 28, pp. pp. 1510-1539. , 1999.
Heath, L. S., and S. V. Pemmaraju,
"Stack and Queue Layouts of Directed Acyclic Graphs: Part II",
SIAM Journal on Computing , vol. 28, pp. pp. 1588-1626, 1999.
Brunick, G. P., E. L. Green, L. S. Heath, and C. A. Struble,
"Efficient Construction of Drinfel'd Doubles,",
International Symposium on Symbolic and Algebraic Computation (ISSAC'99),, 1999.
Heath, L. S., and N. A. Loehr,
"New Algorithms for Generating Conway Polynomials over Finite Fields",
Tenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), 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.
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.
Kumar, A. V. S., and R. Hariharan,
"Markovian Coupling v/s Conductance for the Jerrum-Sinclair Chain",
Proceedings of the 40th Annual IEEE Symposium on Foundations of Computer Science (FOCS), pp. 241-252, 1999.
Kumar, A. V. S., and R. Hariharan,
"Covering Rectilinear Polygons with Axis-Parallel Rectangles",
Proceedings of the 31st Annual ACM Symposium on Theory of Computing (STOC), pp. 445-454, 1999.
Jacob, R., M. Marathe, and K. Nagel,
"A Computational Study of Routing Algorithms for Realistic Transportation Networks ",
ACM J. Experimental Algorithmics , vol. 4, no. 6, 1999.
1998
Cao, Y., and Q. Li,
"A-stable explicit nonlinear Runge-Kutta methods",
Tsinghua Science & Technoloty, 1998.
Cao, Y., and Q. Li,
"Nonlinear Runge-Kutta methods for solving di erential-algebraic equations",
Chinese J. Numer. Math., April, 1998.
Heath, L. S., and J. P. C. Vergara,
"Sorting by Bounded Block-Moves",
Discrete Applied Mathematics , vol. 88, no. 2, pp. pp. 181-206. , 1998.
Heath, L. S., and J. P. C. Vergara,
"Edge-Packing in Planar Graphs",
Theory of Computing Systems , vol. 31, pp. pp. 629-662. , 1998.
Ganley, J. L., and L. S. Heath,
"An Experimental Evaluation of Local Search Heuristics for Graph Partitioning,",
Computing , vol. 60, pp. pp. 121-132. , 1998.
Heath, L. S., and J. P. C. Vergara,
"Edge-Packing Planar Graphs by Cyclic Graphs",
Discrete Applied Mathematics , vol. 81, pp. pp. 169-180. , 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.
1997
Heath, L. S., and S. V. Pemmaraju,
"Stack and Queue Layouts of Posets,",
SIAM Journal on Discrete Mathematics , vol. 10, pp. pp. 599-625. , 1997.
Heath, L. S.,
"Graph Embeddings and Simplicial Maps",
Theory of Computing Systems , vol. 30, pp. pp 51-65., 1997.
Heath, L. S., D. Hix, L. T. Nowell, W. C. Wake, G. A. Averboch, E. Labow, S. A. Guyer, D. J. Brueni, R. K. France, K. Dalal, et al.,
"Envision: A User-Centered Database of Computer Science Literature",
Communications of the ACM , vol. 38, pp. pp. 52-53, 1997.
Ganley, J. L., and L. S. Heath,
"Optimal and Random Partitions of Random Graphs",
The Computer Journal , vol. 37, pp. pp. 641-643. , 1997.
Green, E. A., L. S. Heath, and B. J. Keller,
"Opal: A System for Computing Noncommutative Gröbner Bases (System Description)",
Eighth International Conference on Rewriting Techniques and Applications (RTA-97), 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.
1996
Choi, V., and M. Golin,
Lopsided Trees: Analyses, Algorithms, and Applications,
, pp. pages 538-549, 1996.
Nowell, L. T., R. K. France, D. Hix, L. S. Heath, and E. A. Fox,
"Visualizing Search Results: Some Alternatives to Query-Document Similarity",
19th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, , pp. pp. 67-75. , 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.
Kumar, A. V. S.,
"Recognition of Counting and Balancing Networks is Hard",
National Seminar on Theoretical Computer Science, India, July, 1996.
1995
Heath, L. S., and S. V. Pemmaraju,
"Recognizing Leveled-Planar Dags in Linear Time",
Proceedings of Graph Drawing '95, vol. 1027: Springer, pp. pp. 300-311. , 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
Heath, L. S., and S. V. Pemmaraju,
"New Results for the Minimum Weight Triangulation Problem",
Algorithmica , vol. 12, pp. pp. 533-552. , 1994.
Ganley, J. L., and L. S. Heath,
"Heuristics for Laying Out Information Graphs",
Computing , vol. 52, pp. pp. 389-405. , 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
Heath, L. S., P. K. Paripati, and J. W. Roach,
"Representing Polyhedra: Faces are Better than Vertices",
Computational Geometry: Theory and Applications, vol. 3, pp. pp. 327-351. , 1993.
Fox, E. A., D. Hix, L. T. Nowell, D. J. Brueni, W. C. Wake, L. S. Heath, and D. Rao,
"Users, User Interfaces, and Objects: Envision, a Digital Library",
Journal of the American Society for Information Science , vol. 44, pp. pp. 480-491. , 1993.
Heath, L. S.,
Lower Bounds for Graph Embeddings Via Algebraic Topology (Extended Abstract),
, pp. pp. 311-317. , 1993.
Fox, E. A., L. S. Heath, and D. Hix,
"A User-Centered Database from the Computer Science Literature",
AAAS Workshop on Advances in Data Management for the Scientist and Engineer, Boston, Massachusetts, 02/1993.
Brueni, D. J., B. Cross, E. A. Fox, L. S. Heath, D. Hix, L. T. Nowell, and W. C. Wake,
What If There Were Desktop Access to the Computer Science Literature?,
, pp. pp. 15-22. , 1993.
Heath, L. S., S. V. Pemmaraju, and A. Trenk,
"Stack and Queue Layouts of Directed Acyclic Graphs",
Planar Graphs , Providence, Rhode Island, American Mathematical Society, pp. pp. 5-1, 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.
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
Heath, L. S., and A. L. Rosenberg,
"Laying Out Graphs Using Queues",
SIAM Journal on Computing , vol. 21, pp. pp. 927-958. , 1992.
Heath, L. S., and S. Istrail,
"The Pagenumber of Genus $g$ Graphs is $O(g),$",
Journal of the Association for Computing Machinery , vol. 39, pp. pp. 479-501. , 1992.
Heath, L. S., F. T. Leighton, and A. L. Rosenberg,
"Comparing Queues and Stacks as Mechanisms for Laying Out Graphs",
SIAM Journal on Discrete Mathematics, vol. 5, pp. pp. 398-412. , 1992.
Fox, E. A., L. S. Heath, Q. F. Chen, and A. M. Daoud,
"Practical Minimal Perfect Hash Functions for Large Databases",
Communications of the ACM , vol. 35, pp. pp. 105-121. , 1992.
Fox, E. A., Q. F. Chen, and L. S. Heath,
"A Faster Algorithm for Constructing Minimal Perfect Hash Functions",
15th Annual International Conference on Research and Development in Information Retrieval, 1992, , pp. pp. 266-273. , 1992.
Wartik, S., E. A. Fox, L. S. Heath, and Q. F. Chen,
"Hashing",
Information Retrieval: Data Structures and Algorithms, Engelwood Cliffs, NJ, Prentice-Hall, pp. pp. 293-362. , 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.
1991
Fox, E. A., Q. F. Chen, A. M. Daoud, and L. S. Heath,
"Order-Preserving Minimal Perfect Hash Functions and Information Retrieval,",
ACM Transactions on Information Systems , vol. 9, pp. pp. 281-308. , 1991.
Heath, L. S.,
Edge Coloring Planar Graphs with Two Outerplanar Subgraphs,
, pp. pp. 195-202. , 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.
1990
Heath, L. S.,
"Covering a Set with Arithmetic Progressions is NP-Complete",
Information Processing Letters , vol. 34, pp. 293-298. , 1990.
Heath, L. S., F. T. Leighton, and A. L. Rosenberg,
Graph Layout Using Queues (Extended Abstract),
, pp. pp. 305-314. , 1990.
Heath, L. S., P. K. Paripati, and J. W. Roach,
Polyhedra: Faces are Better than Vertices (Extended Abstract),
, pp. pp. 191-199. , 1990.
1989
Fox, E. A., Q. F. Chen, L. S. Heath, and S. Datta,
"A More Cost Effective Algorithm for Finding Minimal Perfect Hash Functions",
Seventeenth Annual ACM Computer Science Conference, 1989,, pp. pp. 114-122. , 1989.
1988
Heath, L. S., A. L. Rosenberg, and B. T. Smith,
"The Physical Mapping Problem for Parallel Architectures",
Journal of the Association for Computing Machinery, vol. 35, pp. pp. 603-634. , 1988.
1987
Heath, L. S.,
"Embedding Outerplanar Graphs in Small Books",
SIAM Journal on Algebraic and Discrete Methods, vol. 8, pp. pp. 198-218. , 1987.
Heath, L. S., and S. Istrail,
The Pagenumber of Genus $g$ Graphs is $O(g),$,
, pp. pp. 388-397. , 1987.
Belkin, N., C. Borgman, H. Brooks, T. Bylander, W. Croft, P. Daniels, S. Deerwester, E. A. Fox, P. Ingwersen, R. Rada, et al.,
"Distributed Expert-Based Information Systems: An Interdisciplinary Approach",
IP&M, vol. 23, no. 5, pp. 395-409, 1987.
1984
Heath, L. S.,
Embedding Planar Graphs in Seven Pages,
, pp. pp. 74-83. , 1984.
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
CAREER: Computational Methods For The New Generation Of Air Quality Models
Granting Institution: National Science Foundation
Amount: $221,965
Formulating A Theoretical Framework For Assessing Network Loads For Effective Deployment In Net-Centric Operations And Warfare
Granting Institution: Air Force Office of Scientific Research
Amount: $275,000
Mathematical Software for Optimization And Nonlinear Systems Of Equations On Terascale Computers
Granting Institution: Department of Energy
Amount: $346,255
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
Short Cycle Surrogate Based Design Optimization
Granting Institution: National Science Foundation
Amount: $111,952
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