TCAMC References

1

Dexuan Xie and L. Ridgway Scott, The Parallel U-Cycle Multigrid Method Special issue of ETNA for Copper Mountain Multigrid 97 Conference, to appear, 1997.

2

Andrew V. Ilin, Babak Bagheri, Ralph W. Metcalfe, and Ridgway Scott, Error Control and Mesh Optimization for High Order Finite Element Approximation of Incompressible Viscous Flow Research Report UH/MD 231, Department of Mathematics, the University of Houston, 1997.

3

L. R. Scott and Dexuan Xie, Parallel Linear Stationary Iterative Methods, 1997.

4

Stanislaw T. Wlodek, Jan Antosiewicz, and James M. Briggs, On the Mechanism of Acetylcholinesterase Action: The Electrostatically Induced Acceleration of the Catalytic Acylation Step J. Amer. Chem. Soc., 119(35), pg. 8159-8165, 1997.

5

Stanislaw T. Wlodek, Terry W. Clark, L. R. Scott, and J. McCammon, Molecular Dynamics of Acetylcholinesterase Dimer Complexed with Tacrine J. Amer. Chem. Soc., 119(40), pg. 9513-9522, 1997.

6

Z. H. Zhou, W. Chiu, K. Haskell, H. Spears, Jr., J. Jakana, F. J. Rixon and L. R. Scott, Refinement of Herpesvirus B-Capsid Structure on Parallel Supercomputers Biophysical Journal, In press, 1997.

7

K. H. Haskell, Z. H. Zhou, H. Spears, Jr., W. Chiu, and L. R. Scott, Improved 3D Reconstruction of Virus Structure through Parallel Processing Eighth SIAM Conference on Parallel Processing for Scientific Computing, SIAM, Minneapolis, MN, March, 1997.

8

T.W. Clark, Attributes of Molecular Dynamics Calculations: Accounting for CPU Cycles, Proceedings of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, March, 1997, to appear.

9

T.W.Clark, R.von Hanxleden, and K.Kennedy, Experiences in Data-Parallel Programming , Scientific Programming, 6, pp. 153-158, 1997.

10

A. Ilin and L.R.Scott. Loop splittings for high-performance computers. J. of Supercomp. Appl. and High Perf. Computing, to appear in 1997.

11

Terry W.Clark, and L. Ridgway Scott, Parallelism and Hazards in Molecular Dynamics Algorithm, 1997.

12

A. M. Micu, B. Bagheri, A. V. Ilin, L. R. Scott, and B. M. Pettitt, Numerical Considerations in the Computation of the Electrostatic Free Energy of Interaction within the Poisson-Boltzmann Theory Journal of Computational Physics, 136, pp. 263-271, 1997.

13

L.R.Scott, A. Ilin, R. Metcalfe and B. Bagheri. Fast algorithms for solving high-order finite element equations for incompressible flow. In Proceedings of the International Conference on Spectral and High Order Methods, Houston, TX, 1995, Houston Journal of Mathematics, University of Houston, 1996.

14

Terry W. Clark, Parallel Programming Approach For Scientific Application, Ph.D. Dissertation, December 1996, Dept of Computer Science, University of Houston. postscript (6176 kB)

15

A. Ilin, B. Bagheri, L.R.Scott, J.M.Briggs, and J.A.Mc Cammon. Parallelization of Poisson-Boltzmann and Brownian Dynamics calculation. In Parallel Computing in Computational Chemistry, pages 170-185, Washington D.C., 1995. ACS Books.

16

A. Ilin, B. Bagheri, L.R.Scott, J.A.Mc Cammon and V.P.Il'in. Parallelization of preconditioned conjugate gradients for Poisson-Boltzmann calculation. In Proceedings of the International Congress on Industrial and Applied Mathematics, page 308, Hamburg, 1995. Akademie-Verlag.

17

J.D.Madura, J.M.Briggs, R.C.Wade, M.E.Davis, B.A.Luty, A. Ilin, J.Antosciewicz, M.K.Gilson, B.Bagheri, L.R.Scott and J.A.McCammon. Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program Comp. Phys. Commun., 91, pages 57-95, 1995.

18

A. Ilin, and L. R. Scott. High Performance Programming for the KSR1. Research Report UH/MD 196, Department of Mathematics, the University of Houston, 1995.

19

A. Ilin, and L. R. Scott. Loop Splitting for Superscalar Architectures. Research Report UH/MD 195, Department of Mathematics, the University of Houston, 1995.

20

Cannon, W.R., J.M. Briggs, J. Shen, J.A. McCammon, and F.A. Quiocho. Conservative and Nonconservative Mutations in Proteins: Anomalous Mutations in a Transport Receptor Analyzed by Free Energy and Quantum Chemical Calculations. Protein Science, 4, 387-393, 1995.

21

Ilin, A., B. Bagheri, L.R. Scott, J.M. Briggs, and J.A. McCammon. Parallelization of Poisson-Boltzmann and Brownian Dynamics Calculations. Amer. Chem. Soc. Sympos. Series, No. 592, pp. 170-185 , 1995.

22

Gilson, M.K., J.A. McCammon, and J.D. Madura. Molecular Dynamics Simulation with a Continuum Electrostatic Model of the Solvent. J. Comp. Chem. 16, 1081-1095, 1995.

23

Antosiewicz, J., J.A. McCammon, S. Wlodek, and M.K. Gilson. Simulation of Charge-Mutant Acetylcholinesterases. Biochemistry, 34, 4211-4219 , 1995.

24

Pomes, R., J.A. McCammon, and R. Willson. Free Energy Simulations of the HyHEL-10/HEL Antibody - Antigen Complex. Prot. Eng., 8, 663-675 , 1995.

25

Madura, J.D., J.M. Briggs, R.C. Wade, M.E. Davis, B.A. Luty, A. Ilin, J. Antosiewicz, M.K. Gilson, B. Bagheri, L.R. Scott, and J.A. McCammon. Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program. Comp. Phys. Comm. 91, 57-95, 1995.

26

Wlodek, S.T., J. Antosiewicz, M.K. Gilson, J.A. McCammon, T.W. Clark, and L.R. Scott. Computer Modeling of Acetylcholinesterase and Acetylcholinesterase-Ligand Complexes. In "Enzymes of the Cholinesterase Family," D.M. Quinn, et al., eds., Plenum, pp. 97-104, 1995.

27

Clark, T.W., L.R. Scott, S.T. Wlodek, and J.A. McCammon. I/O Limitations in Parallel Molecular Dynamics. In "Proceedings of the 1995 ACM/IEEE Supercomputing Conference" (refereed), F. Baker and J. Wehmer, eds., IEEE Computer Society Press, pp. 1-15, 1995.

28

Jürgen K . Singer, Parallel Implementation of the Fast Multipole Method with Periodic Boundary Conditions (East-West Journal of Numerical Mathematics, Vol. 3, No. 3, pp 199-216, October 1995) compressed postscript (84 kB)

29

Jürgen K . Singer, The Parallel Fast Multipole Method in Three Dimensions, Research Report UH/MD-193, Department of Mathematics, University of Houston, February 1995 compressed postscript (120 kB)

30

Jürgen K . Singer, The Parallel Fast Multipole Method in Molecular Dynamics, Dissertation, August 1995, University of Houston. compressed postscript (565 kB)

31

R. Glowinski, T. W. Pan, and J. Periaux. Fictitious domain/domain decomposition methods for partial differential equations., Chapter 11 of Domain-Based Parallelism and Problem Decomposition Methods in Computational Science and Engineering, D. E. Keyes, Y. Saad, D. G. Truhlar, eds., SIAM, Philadelphia, 1995, pp. 177-192.

32

R. Glowinski, T. W. Pan, and J. Periaux. A one shot domain decomposition/fictitious domain method for the solutions of elliptic equations. In Parallel Computational Fluid Dynamics: New Trends and Advances, A. Ecer, J. Hausen, P. Leca, J. Periaux, eds., North-Holland, Amsterdam, 1995, pp. 317-324.

33

B. Bagheri, A. Ilin, and L. R. Scott. A comparison of distributed and shared memory scalable architectures. 1. KSR shared memory. In Proceedings of the Scalable High Performance Computing Conference, pages 9-16, Knoxville, TN, May 1994.

34

T. W. Clark, R. v. Hanxleden, J. A. McCammon, and L. R. Scott. Parallelizing molecular dynamics using spatial decomposition. In Proceedings of the Scalable High Performance Computing Conf erence, Knoxville, TN, May 1994.

35

B. Bagheri, A. Ilin, and L. R. Scott. Parallel 3-d MOSFET simulation. In Proceedings of the Twenty-Seventh Annual Hawaii International Conference on System Sciences, Maui, HI, January 1994.

36

J. A. McCammon, B. M. Pettitt, and L. R. Scott. Ordinary differential equations of molecular dynamics. Comp. Math., 1994. (in press).

37

P. Bala, B. Lesyng, and J. A. McCammon. Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes. Chemical Physics, 180, 1994.

38

Valère Lounnas and B. M. Pettitt. A connected-cluster of hydration around myoglobin: Correlation between molecular dynamics simulations and experiment. Proteins: Structure, Function and Genetics, 18:133-147, 1994.

39

Valère Lounnas, B. M. Pettitt, and George N. Phillips. A global model of the protein-solvent interface. Biophysical Journal, 66:604-614, 1994.

40

M. K. Gilson, T. P. Straatsma, J. A. McCammon, D. R. Ripoll, C. H. Faerman, P. H. Axelsen, I. Silman, and J. L. Sussman. Open ``back door'' in a molecular dynamics simulation of acetylcholinesterase. Science, 263:1276-1278, March 1994.

41

B. Lesyng and J. A. McCammon. Basic molecular modeling methods. Techniques and challenging problems. Pharmac. Ther., 1994. (to appear).

42

J. Antosiewicz, J. A. McCammon, and M. K. Gilson. Prediction of pH-dependent properties of proteins. J. Mol. Biol., 1994. (to appear).

43

M. O. Bristeau, J. Ehrel, R. Glowinski, and J. Perriau. Parallelization of an exact solvability method for the Helmholtz equation. Implementation on a KSR1. Int. J. of Supercomputing, 1994. (accepted).

44

L. Ridgway Scott, B. Bagheri, A. Ilin, and D. Xie. Parallel solution of elliptic boundary value problems. In Proceedings of the International Workshop on Computational Electronics, Portland, OR, May 1994.

45

Babak Bagheri, Mircea Draghicescu, and L. Ridgway Scott. Functional objects for finite element computation. In Proceedings of the Second Annual Object-Oriented Numerics Conference, Sunriver, OR, April 1994.

46

B. Bagheri, A. Ilin, J. A. McCammon, L. R. Scott and Dexuan Xie. Parallel Algorithms for Biomolecular Modeling. In Proceedings of the Workshop on Algorithms for Macromolecular Modeling, pages 77-82, Lawrence, KA, September, 1994.

47

Babak Bagheri. Parallel Programming with Guarded Objects, The Pennsylvania State University, August 1994. Thesis.

48

L. Ridgway Scott. Elliptic preconditioners using fast summation techniques. In Proceedings of the 7th International Symposium on Domain Decomposition Methods, Penn. State, November 1993. Providence, RI, Contemporary Mathematics, AMS.

49

B. Bagheri, A. Ilin, and L. R. Scott. Parallel 3-d MOSFET simulation . Research Report UH/MD 169, Department of Mathematics, the University of Houston, 1993.

50

B. Bagheri, A. Ilin, and L. R. Scott. Parallelizing UHBD. Research Report UH/MD 167, Department of Mathematics, the University of Houston, 1993.

51

B. Bagheri, A. Ilin, and L. R. Scott. Parallelizing UHBD for iPSC-860. In Proceedings of the Intel Supercomputer Users' Group 1993 Annual Users' Conference, pages 295-299, St. Louis, MO, October 1993.

52

J. A. McCammon, B. M. Pettitt, and L. R. Scott. Ordinary differential equations of molecular dynamics. Research Report UH/MD 168, Department of Mathematics, the University of Houston, 1993.

53

B. A. Luty, S. El Amrani, and J. A. McCammon. Simulation of the bimolecular reaction between superoxide and superoxide dismutase: Synthesis of the encounter and reaction steps. J. Amer. Chem. Soc., 115(25), 1993.

54

Y. T. Wong, T. W. Clark, J. Shen, and J. A. McCammon. Molecular dynamics simulation of substrate-enzyme interactions in the active site channel of superoxide dismutase. Journal of Molecular Simulation, 10(2-6), 1993.

55

Gail E. Marlow, John Perkyns, and B. M. Pettitt. Salt effects in peptide solutions: Theory and simulations. Chemical Reviews, 93:2503-2521, 1993.

56

R. Glowinski, T. W. Pan, and J. Periaux. A one shot domain decomposition/fictitious domain method for the Navier-Stokes equations. In Proceedings of the 7th International Symposium on Domain Decomposition Methods, Penn. State, November 1993. Providence, RI, Contemporary Mathematics, AMS.

57

R. Glowinski, T. W. Pan, and J. Periaux. A one shot domain decomposition/fictitious domain method for the Stokes problem. In M. N. Dhaubhadel, M. S. Engelman, and W. G. Habash, editors, Advances in Finite Element Analysis in Fluid Dynamics-1993, pages 115-124, Fairfield, NJ, 1993.

58

Terry W. Clark, Reinhard v. Hanxleden, J. Andrew McCammon, and L. Ridgway Scott. Irregular structures in molecular dynamics computations. In Proceedings of the Intel Supercomputer Users' Group 1992 Annual Users' Conference, Dallas, TX, October 1992.

59

Clark, T.W., Reinhard von Hankleden, J. Andrew McCammon, and L. Ridgway Scott. Parallelization Strategies for a Molecular Dynamics Program. In "Technology Focus Conference proceedings" April 5-7, 1992.

60

B.Bagheri, T.W.Clark and L.R.Scott, Pfortran: A Parallel Dialect of Fortran, Fortran Forum, ACM Press, 11, pp. 3-20, 1992.

61

T.W.Clark, R.von Hanxleden, K.Kennedy, C.Koelbel, and L.R.Scott, Evaluating Parallel Languages for Molecular Dynamics Computations, Proceedings of the Scalable High Performance Computing Conference, Williamsburg, VA, April, pp. 98-105, 1992.

62

T.W.Clark, J.A.McCammon, and L.R.Scott, Parallel Molecular Dynamics, Proceedings of the Fifth SIAM Conference on Parallel Processing for Scientific Computing, J.Dongarra, et al., editors, Philadelphia: SIAM, March, 1991, pp.338-344.