Appendix User Bibliography




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Computer and Computation


CCR060004

  1. E. Givelberg and K. Yelick, “Immersed Boundary Method Simulations in Titanium.” Available from http://www.cs.berkeley.edu/~givelber

CCR070001

  1. Barrett, S. Eubuank and M. Marathe, Modeling and Simulation of Large Biological, Information and Socio-Technical Systems: An Interaction Based Approach, to appear in Interactive Computation: The New Paradigm, D. Goldin, S. Smolka and P. Wegner Eds. Springer Verlag, (2005).

  2. S. Eubank, V.S. Anil Kumar, M. Marathe, A. Srinivasan and N. Wang. Structure o Social Contact Networks and their Impact on Epidemics. to appear in AMS-DIMACS Special Volume on Epidemiology, (2005).

Advanced Scientific Computing


ASC040031

  1. Charles Lively, Performance Analysis and Modeling of GYRO, Master's thesis, Department of Computer Science, Texas A&M University, June 2006.

  2. Sameh Sharkawi, Performance Analysis of CAM, Master's thesis, Department of Computer Science, Texas A&M University, June 2006.

  3. Xingfu Wu, Valerie Taylor, Shane Garrick, Dazhi Yu, and Jacques Richard, Performance Analysis, Modeling and Prediction of a Parallel Multiblock Lattice Boltzmann Application Using Prophesy System, IEEE International Conference on Cluster Computing (poster paper), September 25-28, 2006, Barcelona, Spain.

  4. Xingfu Wu, Valerie Taylor, and Joseph Paris, A Web-based Prophesy Automated Performance Modeling System, the IASTED International Conference on Web Technologies, Applications and Services (WTAS2006), July 17-19, 2006, Calgary, Canada

CTS010003

  1. S. Biswas, A. Esmaeeli, and G. Tryggvason, “Comparison of results from DNS of bubbly flows with a two-fluid model for two-dimensional laminar flows,” Int. J. Multiphase Flows 31 (2005), 1036-1048.

  2. Esmaeeli and G. Tryggvason, “A DNS study of the buoyant rise of bubbles at O (100) Reynolds number,.” Physics of Fluids 17, 093303 2005 (19 pages)

  3. J. Lu, A. Fernandez, and G. Tryggvason, “The effect of bubbles on the wall shear in a turbulent channel flow,” Physics of Fluids 17, 095102 (2005) (12 pages)

  4. J. Lu, S. Biswas, and G. Tryggvason, “a DNS study of laminar bubbly flow in a vertical channel,” To be submitted to the International Journal of Multiphase Flow.

ASC040025

  1. Rajkumar Murthy, Parallel alternating explicit implicit domain decomposition algorithm, Master’s thesis, May 2006, Department of Computer Science, Texas Tech University, Lubbock, Texas.

  2. Y. Zhuang, "An alternating explicit implicit domain decomposition method for the parallel solution of parabolic equations", accepted by Journal of Computational and Applied Mathematics.

  3. Y. Zhuang and X. Sun, "A highly parallel algorithm for the numerical simulation of unsteady diffusion processes", Proc. 19th IEEE International Parallel & Distributed Processing Symposium (IPDPS 2005), Denver, 2005.

  4. Y. Zhuang and X. Sun, "Domain decomposition algorithms for the numerical simulation of diffusion processes on massively parallel computers", submitted.

ASC060005

  1. Esmaeeli. Phase Distribution of Bubbly Flows under Terrestrial and Microgravity Conditions. Fluid-Dynamics and Materials Processing, 1, 63, (2005).

  2. Esmaeeli and G. Tryggvason. A Direct Numerical Simulation Study of the Buoyant Rise of Bubbles at Reynolds number. Phys. Fluids, 17, 093303, 1, (2005).

  3. Esmaeeli, A. and Tryggvason, G. (2005): A DNS studyof the buoyant rise of bubbles at O (100) Reynolds number, Phys. Fluids (accepted).

  4. Esmaeeli and G. Tryggvason. Using Front-Tracking to Study the Dynamics of Heterogeneous Continuum Systems (Invited Talk). Workshop on Multiphase Flow and Reacting Flow Simulations. Purdue University, West Lafayette, July 05.

ASC060007

  1. Porter, D. H., and P. R. Woodward, 2005. “Using PPM to Model Turbulent Stellar Convection,” a chapter to appear in a book, Implicit Large Eddy Simulation, edited by F. Grinstein.

  2. Porter, D. H., and P. R. Woodward, 2005. “Simulating Compressible Turbulent Flow with the PPM Gas Dynamics Scheme,” to appear in a book, Implicit Large Eddy Simulation, edited by F. Grinstein.

  3. Porter, D. H., P. R. Woodward, and A. Iyer, “Initial experiences with grid-based volume visualization of fluid flow simulations on PC clusters,” accepted for publ. in Proc. Visualization and Data Analysis 2005 (VDA2005), San Jose, CA, Jan., 2005; available at www.lcse.umn.edu/VDA2005.

  4. Woodward, P. R., D. H. Porter, S. E. Anderson, B. K. Edgar, A. Puthenveetil, and T. Fuchs, “Parallel Computation of Turbulent Flows with the Piecewise-Parabolic Method,” Proc. ParCFD 2005 conference, Univ. of Maryland, June, 2005, available at www.lcse.umn.edu/parcfd.

  5. Woodward, P. R., 2005. “A Complete Description of the PPM Compressible Gas Dynamics Scheme,” internal document available on the LCSE Web site at www.lcse.umn.edu. A shorter version of this document will appear in a book Implicit Large Eddy Simulation, edited by F. Grinstein.

MCA06N043

  1. Uzun, A. and Hussaini, M. Y., High Frequency Noise Generation in the Near-Nozzle Region of a Jet, AIAA Paper 2006-2499.

  2. Uzun, A., Hussaini, M. Y. and Streett, C. L., Large-Eddy Simulation of a Wing Tip Vortex on Overset Grids, AIAA Journal, 2006, 44(6), 1229-1242.

MCA06N056

  1. Nystrom, N., D. Weisser, J. Lim, Y. Wang, Brown, S. T., Reddy, R., Stone, N. T., Woodward, P. R., Porter, D. H., Di Matteo, T., Kale, L. V., and Zheng, G., “Enabling Computational Science on the Cray XT3,” Proc. CUG (Cray User Group) Conference, Zurich, May, 2006.

  2. Porter, D. H., and P. R. Woodward, 2006. “Using PPM to Model Turbulent Stellar Convection,” in Implicit Large Eddy Simulation: Computing Turbulent Fluid Dynamics, edited by F. Grinstein, L. Margolin, W. Rider, Cambridge Univ. Press; also available at www.lcse.umn.edu/ILES.

  3. Porter, D. H., and P. R. Woodward, 2006. “Simulating Compressible Turbulent Flow with the PPM Gas Dynamics Scheme,” in Implicit Large Eddy Simulation: Computing Turbulent Fluid Dynamics, edited by F. Grinstein, L. Margolin, W. Rider, Cambridge Univ. Press; also available at www.lcse.umn.edu/ILES.

  4. Porter, D. H., P. R. Woodward, and A. Iyer, “Initial experiences with grid-based volume visualization of fluid flow simulations on PC clusters,” accepted for publ. in Proc. Visualization and Data Analysis 2005 (VDA2005), San Jose, CA, Jan., 2005; available at www.lcse.umn.edu/VDA2005.

  5. Woodward, P. R., D. H. Porter, S. E. Anderson, B. K. Edgar, A. Puthenveetil, and T. Fuchs, “Parallel Computation of Turbulent Flows with the Piecewise-Parabolic Method,” Proc. ParCFD 2005 conference, Univ. of Maryland, June, 2005, available at www.lcse.umn.edu/parcfd.

  6. Woodward, P. R., D. H. Porter, S. E. Anderson, and T. Fuchs, “Towards an Improved Numerical Treatment of Compressible Turbulence in Astrophysical Flows,” submitted to Proc. CalSpace-IGPP International Conference on Numerical Modeling of Space Plasma Flows, Astronum-2006, March 27-30, Palm Springs, CA, editor Nikolai Pogorelov; available at www.lcse.umn.edu/IGPP.

  7. Woodward, P. R., D. H. Porter, S. E. Anderson, T. Fuchs, and F. Herwig, “Large-Scale Simulations of Turbulent Stellar Convection Flows and the Outlook for Petascale Computation,” Proc. SciDAC- 2006, June 25-29, 2006, Denver, CO; available at www.lcse.umn.edu/SciDAC2006.

  8. Woodward, P. R., 2005. “A Complete Description of the PPM Compressible Gas Dynamics Scheme,” internal document available on the LCSE Web site at www.lcse.umn.edu. A shorter version of this document will appear in a book Implicit Large Eddy Simulation, edited by F. Grinstein.

Distributed and Parallel Processing, Vectorization


ASC060008

  1. M. Parashar, H. Klie, U. Catalyurek, T. Kurc, W. Bangerth, V. Matossian, J. Saltz, and M. F. Wheeler. Application of grid-enabled technologies for solving optimization problems in data-driven reservoir studies. Future Generation of Computer Systems, (21):19–26, 2005.

Cross-Disciplinary Activities


MCA01S027

  1. A. Case, T.E. Cheatham, III, T.A. Darden, H. Gohlke, R. Luo, K. M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang, and R. Woods. “The AMBER biomolecular simulation programs” J. Comp. Chem. 26, 1668-1688 (2005)

  2. T.E. Cheatham, III “Molecular modeling and atomistic simulation of nucleic acids” in Ann. Reports Comp. Chem., Ed: Spellmeyer, D. Vol. 1, pp. 75-89 (Elsevier) (2005)

  3. T.E. Cheatham, III and D.A. Case, “Applying AMBER biomolecular simulation methods to DNA and RNA: Insight into the dynamics, interactions and energetics of varied nucleic acid structures” in Computational Studies of DNA and RNA (Wiley, Editor: Sponer) [in press] (2006)

  4. S.B. Dixit, D.L. Beveridge, D.A. Case, T.E. Cheatham III, E. Giudice, F. Lankas, R. Lavery, J. Maddocks, R. Osman, H. Sklenar, K.M. Thayer, and P. Varnai “Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II. Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.” Biophys. J. 89, 3721-3740 (2005)

  5. T. N. Truong, M. Nayak, H. Huynh, T. Cook, P. Marajan, L.T. Tran, J. Bharath, S. Jain, H.B. Pham, N. Nguyen, Y. Kim, S. Choe, T.E. Cheatham, III, and J. Facelli, “Computational Science and Engineering Online (CSE-Online): A cyberinfrastructure for scientific computing”, J. Chem. Info. Mod. [pending minor revision] (2006)
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