Publications and presentations citing W&M HPC resources, 2005-2009
A. J. Bever, C. K. Harris, C. R. Sherwood and R. P. Signell. Deposition and flux of sediment from the Po River, Italy: an idealized and wintertime numerical modeling study.Marine Geology, 260(1-4), doi:10.1016/j.margeo.2009.01.007, May 2009, pp. 69-80.
M. A. Huertas and G. D. Smith. A population density model of the driven LGN/PGN. In Stochastic Methods in Neuroscience, C. Laing and G. J. Lord, eds., Oxford University Press, Sept. 2009.
W. Purwanto, S. Zhang and H. Krakauer. Excited state calculations using phaseless auxiliary-field quantum Monte Carlo: potential energy curves of low-lying C2 singlet states.Journal of Chemical Physics, 130(9), doi:10.1063/1.3077920, Mar. 2009.
J. Shen and B. Hong. A modeling tracer age study of vertical mixing and cross-channel transport in the Chesapeake Bay.11th International Conference on Estuarine and Coastal Modeling (ECM11), Seattle, WA, Nov. 2009.
C. Chang and S. Zhang. Spatially inhomogeneous phase in the two-dimensional repulsive Hubbard model.Physical Review B, 78(16), doi:10.1103/PhysRevB.78.165101, Oct. 2008.
A. Chernikov and N. Chrisochoides. Algorithm 872: parallel 2D constrained Delaunay mesh generation.ACM Transactions on Mathematical Software, 34(1), doi:10.1145/1322436.1322442, Jan. 2008, pp. 6:1-6:20.
H. DeRemigio, J. R. Groff and G. D. Smith. Calcium release site ultrastructure and the dynamics of puffs and sparks.Mathematical Medicine and Biology, 25(1), doi:10.1093/imammb/dqn004, Mar. 2008, pp. 65-85.
H. DeRemigio, M. D. LaMar, P. Kemper and G. D. Smith. Markov chain models of coupled calcium channels: Kronecker representations and iterative solution methods.Physical Biology, 5(3):036003, doi:10.1088/1478-3975/5/3/036003, Sept. 2008.
J. R. Groff and G. D. Smith. Ryanodine receptor allosteric coupling and the dynamics of calcium sparks.Biophysical Journal, 95(1), doi:10.1529/biophysj.107.119982, July 2008, pp. 135-154.
J. R. Groff and G. D. Smith. Calcium-dependent inactivation and the dynamics of calcium puffs and sparks.Journal of Theoretical Biology, 253(7), doi:10.1016/j.jtbi.2008.03.026, Aug. 208, pp. 483-499.
W. Purwanto, W. A. Al-Saidi, H. Krakauer and S. Zhang. Eliminating spin contamination in auxiliary-field quantum Monte Carlo: realistic potential energy curve of F2.Journal of Chemical Physics, 128(11), doi:10.1063/1.2838983, Mar. 2008.
V. Saba, M. Friedrichs and M. Carr. Estimating oceanic primary productivity: an evaluation of ocean color algorithms and general circulation models.Poster presentation, 2008 Ocean Sciences Meeting, Orlando, FL, Mar. 2008.
V. Saba, M. Friedrichs and M. Carr. Estimating oceanic primary productivity: an evaluation of ocean color algorithms and general circulation models.Presentation, NASA Carbon Cycle & Ecosystems Joint Science Workshop, Adelphi, MD, Apr. 2008.
V. Saba, M. Friedrichs and M. Carr. Assessing the skill of oceanic primary productivity model estimates within various ecosystems worldwide. Presentation, Advances in Marine Ecosystem Modeling Research (AMEMR 2008), Plymouth, UK, Jun. 2008.
V. Saba, M. Friedrichs and M. Carr. An increase in primary productivity at BATS and HOT: do ocean color models agree? Presentation, Ocean Carbon & Biogeochemistry Workshop, Woods Hole, MA, 2008.
G. S. B. Williams, E. J. Molinelli and G. D. Smith. Modeling local and global intracellular calcium responses mediated by diffusely distributed inositol 1,4,5-trisphosphate receptors.Journal of Theoretical Biology, 253(1), doi:10.1016/j.jtbi.2008.02.040, July 2008, pp. 170-188.
G. S. B. Williams, M. A. Huertas, E. A. Sobie, M. S. Jafri and G. D. Smith. Moment closure for local control models of calcium-induced calcium release in cardiac myocytes.Biophysical Journal, 95(4), doi:10.1529/biophysj.107.125948, Aug. 2008, pp. 1689-1703.
N. Archip, O. Clatz, S. Whalen, D. Kacher, A. Fedorov, A. Kot, N. Chrisochoides, F. Jolesz, A. Golby, P. Black and S. Warfield. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery.NeuroImage, 35(2), doi:10.1016/j.neuroimage.2006.11.060, Apr. 2007, pp. 609-624.
A. Chernikov. Parallel generalized Delaunay mesh refinement. Ph.D. dissertation, College of William and Mary, hdl:10288/6655, 2007.
N. Chrisochoides, A. Fedorov, A. Kot, N. Archip, D. Goldberg-Zimring, D. Kacher, S. Whalen, R. Kikinis, F. Jolesz, O. Clatz, S. Warfield, P. Black and A. Golby. Grid-enable software environment for enhanced dynamic data-driven visualization and navigation during image-guided neurosurgery.Proceedings of the 2007 International Conference on Computational Science, Part I (ICCS 2007), Lecture Notes in Computer Science 4487, doi:10.1007/978-3-540-72584-8_129, Beijing, May 2007, pp. 980-987.
M. Chung, G. Ciardo and R. Siminiceanu. Caching, hashing, and garbage collection for distributed state space construction.Participants Proceedings of the Sixth International Workshop on Parallel and Distributed Methods in Verification (PDMC 2007), CTIT Workshop Proceedings 07-04, Berlin, July 2007, pp. 121-136.
M. Chung, G. Ciardo and R. Siminiceanu. Distributed saturation. Technical Report 2007-05, National Institute of Aerospace, 2007.
H. DeRemigio, P. Kemper, M. D. LaMar and G. D. Smith. Markov chain models of coupled intracellular calcium channels: Kronecker structured representations and benchmark stationary distribution calculations. Technical Report WM-CS-2007-06, Department of Computer Science, College of William and Mary, June 2007.
M. A. Huertas and G. D. Smith. The dynamics of luminal depletion and the stochastic gating of Ca2+-activated Ca2+ channels and release sites.Journal of Theoretical Biology, 246(2), Elsevier, doi:10.1016/j.jtbi.2007.01.003, May 21, 2007, pp. 332-354.
D. Malyarenko, E. Tracy, M. Sasinowski, J. Semmes and C. Bunai. NCI CPTI R01-Y1 progress report and research accomplishments. Clinical Proteomic Technologies Initiative, National Cancer Institute, June 2007.
D. Malyarenko, W. Cooke, M. Tracy, L. Cazares, W. Fuller, R. Drake, J. Semmes, K. Miller, J. Miller, M. Sasinowski, K. Kuschner, E. Tracy, D. Manos and C. Bunai. Enhancement of MS signal processing toward improved cancer biomarker discovery: progress and plans. Invited talk and poster presentation, Clinical Proteomic Technologies Initiative for Cancer Annual Meeting (CPTI '07), Rockville, MD, Oct. 2007.
J. R. McCombs. Toward a Robust and Efficient Iterative Eigensolver. Ph.D. dissertation, Department of Computer Science, College of William and Mary, April 2007.
G. S. B. Williams, M. A. Huertas, E. A. Sobie, M. S. Jafri, and G. D. Smith. A probability density approach to modeling local control of calcium-induced calcium release in cardiac myocytes.Biophysical Journal, 92(7), doi:10.1529/biophysj.106.099861, Apr. 2007, pp. 2311-2328.
W. Al-Saidi, H. Krakauer, and S. Zhang. Auxiliary-field quantum Monte Carlo study of TiO and MnO molecules.Physical Review B, Vol. 73, No. 7, Article 075103, American Physical Society, February 2006.
W. Al-Saidi, S. Zhang, and H. Krakauer. Auxiliary field quantum Monte Carlo study of atoms and molecules using localized basis sets. 2006 Workshop on Fundamental Physics of Ferroelectrics, Williamsburg, VA, February 2006.
N. Archip, A. Fedorov, B. Lloyd, N. Chrisochoides, A. Golby, P. Black, and S. Warfield. Integration of patient specific modeling and advanced image processing techniques for image-guided neurosurgery.SPIE Medical Imaging 2006: Visualization, Image-Guided Procedures, and Display, K. Cleary and R. Galloway, eds., Proceedings Vol. 6141, San Diego, Mar. 2006.
A. Bever. Physical processes behind delta propagation and flood layer dynamics, Po River, Italy. Masters thesis, Virginia Institute of Marine Science, College of William and Mary, hdl:10288/7566, 2006.
A. N. Chernikov and N. P. Chrisochoides. Parallel guaranteed quality Delaunay uniform mesh refinement.SIAM Journal on Scientific Computing, Vol. 28, No. 5, Nov. 2006, pp. 1907-1926.
N. Chrisochoides. Parallel mesh generation. In Numerical Solution of Partial Differential Equations on Parallel Computers, A. M. Bruaset, P. Bjorstad, A. Tveito, eds., Lecture Notes in Computational Science and Engineering, Vol. 51, Springer-Verlag, 2006, pp. 237-265.
N. Chrisochoides, A. Fedorov, A. Kot, N. Archip, P. Black, O. Clatz, A. Golby, R. Kikinis, and S. K. Warfield. Toward real-time image guided neurosurgery using distributed and grid computing.Supercomputing 2006: Proceedings of the ACM/IEEE SC 2006 Conference, Tampa, FL, Nov. 2006.
A. Gupta, M. Zangrilli, A. Sundararaj, P. A. Dinda, and B. B. Lowekamp. Free network measurement for adaptive virtualized distributed computing.Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), April 25-29, 2006, Rhodes Island, Greece, CD-ROM, 10 pp.
M. A. Huertas and G. D. Smith. A two-dimensional population density approach to modeling the dLGN/PGN network.Neurocomputing, Vol. 69, No. 10-12, Elsevier, doi:10.1016/j.neucom.2005.12.093, June 2006, pp. 1286-1290.
M. A. Huertas and G. D. Smith. A multivariate population density model of the dLGN/PGN relay.Journal of Computational Neuroscience, 21(2), Springer Netherlands, doi:10.1007/s10827-006-7753-2, Oct. 2006, pp. 171-189.
L. Linardakis and N. Chrisochoides. Delaunay decoupling method for parallel guaranteed quality planar mesh refinement.SIAM Journal on Scientific Computing, Vol. 27, No. 4, pp.1394-1423.
J. R. McCombs and A. Stathopoulos. Iterative validation of eigensolvers: a scheme for improving the reliability of hermitian eigenvalue solvers.SIAM Journal on Scientific Computing, Vol. 28, No. 6, Dec. 2006, pp. 2337-2358.
S. Means, A. J. Smith, J. Shepherd, J. Shadid, J. Fowler, R. Wojcikiewicz, T. Mazel, and G. D. Smith. Reaction diffusion modeling of calcium dynamics with realistic ER geometry.Biophysical Journal, 91(2), doi:10.1529/biophysj.105.075036, July 2006, pp. 537-557.
M. Rivara, C. Calderon, A. Fedorov, and N. Chrisochoides. Parallel decoupled terminal-edge bisection method for 3D mesh generation. In Engineering with Computers, Springer London, Vol. 22, No. 2, Sept. 2006, pp. 111-119.
C. Yue, R. Mills, A. Stathopoulos, and D. S. Nikolopoulos. Runtime support for memory adaptation in scientific workloads via local disk and remote memory.Proceedings of the 15th IEEE International Symposium on High Performance Distributed Computing (HPDC-15), Paris, France, June 19-23, 2006.
M. Zangrilli and B. B. Lowekamp. Transparent optimization of grid server selection with real-time passive network measurements.GridNets 2006, San Jose, CA, Oct. 1-2, 2006.
M. Zangrilli Bryan. Passive available bandwidth: applying self-induced congestion analysis to application-generated traffic. Ph.D. dissertation, Department of Computer Science, College of William and Mary, Dec. 2006.
X. Zhao, R. A. Outlaw, J. J. Wang, M. Y. Zhu, G. D. Smith, and B. C. Holloway. Thermal desorption of hydrogen from carbon nanosheets.Journal of Chemical Physics 124, 194704, May 21, 2006, 6 pp.
W. Al-Saidi, H. Krakauer, and S. Zhang. An auxiliary quantum Monte Carlo approach for electronic structure.2005 Workshop on Fundamental Physics of Ferroelectrics, Williamsburg, VA, February 2005.
C. D. Antonopoulos, X. Ding, A. Chernikov, F. Blagojevic, D. S. Nikolopoulos, and N. Chrisochoides. Multigrain parallel Delaunay mesh generation: challenges and opportunities for multithreaded architectures.Proceedings of the 19th ACM International Conference on Supercomputing (ICS'2005), Cambridge, MA, June 2005, ACM Press, pp. 367-376.
K. Barker and N. Chrisochoides. Practical performance model for optimizing dynamic load balancing of adaptive applications.19th IEEE International Parallel and Distributed Processing Symposium (IPDPS '05), Denver, April 4-8, 2005.
H. DeRemigio and G. D. Smith. The dynamics of stochastic attrition viewed as an absorption time on a terminating Markov chain.Cell Calcium, Vol. 38, No. 2, Aug. 2005, pp. 73-86.
A. Gupta, M. Zangrilli, A. Sundaraj, P. A. Dinda, and B. B. Lowekamp. Free network measurement for adaptive virtual machine distributed computing. Technical Report WM-CS-2005-05, Department of Computer Science, College of William and Mary, June 2005.
M. A. Huertas, J. R. Groff, and G. D. Smith. Feedback inhibition and throughput properties of an integrate-and-fire-or-burst network model of retinogeniculate transmission.Journal of Computational Neuroscience, Vol. 19, No. 2, October 2005, pp. 147-180.
M. A. Huertas, J. R. Groff, and G. D. Smith. The effect of feedback inhibition on throughput properties of the dorsal lateral geniculate nucleus.Neurocomputing, Vol. 65-66, doi:10.1016/j.neucom.2004.11.007, June 2005, pp. 499-505.
A. Kot, A. Chernikov, and N. Chrisochoides. Out-of-core parallel Delaunay mesh generation.17th IMACS World Congress: Scientific Computation, Applied Mathematics and Simulation, Paris, July 11-15, 2005.
A. Kot, A. Chernikov, and N. Chrisochoides. Parallel out-of-core Delaunay refinement.3rd IEEE Workshop on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications, Sofia, Bulgaria, September 5-7, 2005, pp. 183-190.
D. I. Malyarenko, W. E. Cooke, B.-L. Adam, G. Malik, H. Chen, E. R. Tracy, M. W. Trosset, M. Sasinowski, O. J. Semmes, and D. M. Manos. Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometic records for serum peptides using time series analysis techniques.Clinical Chemistry, Vol. 51, 2005, pp. 65-74.
B. Mazzag, C. Tignanelli, and G. D. Smith. The effect of residual Ca2+ on the stochastic gating of Ca2+-regulated Ca2+ channel models.Journal of Theoretical Biology, Vol. 235, Issue 1, July 2005, pp. 121-150.
V. Nguyen, R. Mathias, and G. D. Smith. A stochastic automata network descriptor for Markov chain models of instantaneously-coupled intracellular Ca2+ channels.Bulletin of Mathematical Biology, Vol. 67, Issue 3, May 2005, pp. 393-432.
W. Purwanto. Quantum Monte Carlo method for boson ground states: application to trapped bosons with attractive and repulsive interactions. Ph.D. dissertation, Department of Physics, College of William and Mary, Williamsburg, VA, January 10, 2005.
G. D. Smith. Modeling intracellular calcium: diffusion, dynamics, and domains. In Modeling in the Neurosciences: From Biological Systems to Neuromimetic Robotics, 2nd edition, G. N. Reeke, R. R. Poznanski, K. A. Lindsay, J. R. Rosenberg, and O. Sporns, eds. CRC Press, 2005, pp. 339-374.
M. Zangrilli and B. B. Lowekamp. Applying principles of active available bandwidth algorithms to passive TCP traces.Passive and Active Measurement, C. Dovrolis, ed., 6th. Intl. Workshop on Passive and Active Measurement (PAM 2005), Springer, Lecture Notes in Computer Science, Vol. 3431, March 2005, pp. 333-336.
S. Zhang, H. Krakauer, W. Al-Saidi, and M. Suewattana. Quantum simulations of realistic systems by auxiliary fields.Computer Physics Communications (Proceedings of the Europhysics Conference on Computational Physics 2004), M. Ferrario, S. Melchionna, and C. Piereoni, eds., Elsevier, Vol. 169, Issues 1-3, July 2005, pp. 394-399.