# Publications and presentations citing W&M HPC resources, 2005-2009

##### 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 C**_{2}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.

##### 2008

- 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 F**_{2}.*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.

##### 2007

- 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 Ca**^{2+}-activated Ca^{2+}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.

##### 2006

- 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.

##### 2005

- 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 Ca**^{2+}on the stochastic gating of Ca^{2+}-regulated Ca^{2+}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 Ca**^{2+}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.