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REFERENCES
Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.
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BURKERT, U., AND ALLINGER, N.L. Molecular Mechanics. ACS Monograph 177, American Chemical Society, 1987.
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2
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DEMBO, R. S., AND STEIHAUG, T. Truncated-Newton algorithms for large-scale unconstrained optimization. Math. Program. 26, (1983), 190-212.
|
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3
|
EISENSTAT, S. C., GURSKY, M. C., SCHULTZ, M. H., AND SHERMAN, A.H. Yale sparse matrix package, I. The symmetric codes. Intl. J. Num. Met. Eng. 18, (1982), 1145-1151.
|
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4
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EISENSTAT, S. C., SCHULTZ, M. H., ANn SHERMAN, A.H. Algorithms and data structures for sparse symmetric Gaussian elimination. SIAM J. Sci. Stat. Comput. 2, (1981), 225-237.
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5
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EISENSTAT, S C., SHULTZ, M. H., ANn SHERMAN, A. H Application of sparse matrix methods to partial differential equations. In Advances in Computer Methods for Partial Differential Equations, R. Vichnevetsky, Ed., AICA, New Brunswick, New Jersey, 1975, 40-45.
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6
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EmENSTAT, S. C., SHULTZ, M. H., AND SHERMAN, A. H. Efficient implementation of sparse symmetric Gaussian elimination In Advances tn Computer Methods for Partial Differential Equations, R. Vichnevetsky, Ed., AICA, New Brunswick, New Jersey, 1975, 33-39
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7
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FAUCI, L., AND FOGELSON, A. Truncated Newton methods and the modeling of complex immersed elastic structures. Comm. Pure Appl. Math. In press.
|
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8
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FOGELSON, A. L. A mathematical model and numerical method for studying platelet adhesion and aggregation during blood clotting. J. Comput. Phys. 56, (1984), 111-134.
|
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9
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|
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10
|
GILL, P. E., MURRAY, W., SAUNDERS, M. A., AND WRIGHT, M. H. Computing Forward- Difference Intervals for Numerical Optimization. SIAM J. Sci. Stat. Comput. 4, (1983), 310-321.
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11
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GILL, P. E., MURRAY, W., AND WRIGHT, M.H. Practlcal Opttmization. Academic Press, New York, 1983.
|
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12
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LIFSON, S. Potential energy functions for structural molecular biology. In Supramolecular Structure and Function, G. Pifat and J. N. Herak, Ed., Plenum Press, New York and London, 1983, 1-44.
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13
|
|
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14
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McCAMMON, J. A., AND HARVEY, S.C. Dynamics of Proteins and Nucleic Acids. Cambridge Univ. Press, New York, 1987.
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15
|
MOR~, J., AND THUENTE, D. J. On line search algorithms with guaranteed sufficient decrease. Mathematics and Computer Science Division Preprint MCS-P153-0590, Argonne National Lab., Argonne, Ill., 1990.
|
 |
16
|
|
 |
17
|
|
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18
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NASH, S. G. Preconditioning of truncated-Newton methods. SIAM J. Sci. Stat. Comput. 6, (1985), 599-616.
|
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19
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NASH, S. G., AND SOFER, A. Assessing a search direction within a truncated Newton method. Oper. Res. Lett. 9, (1990), 219-221.
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20
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NOCEDAL, J. Updating quasi-Newton matrices with limited storage. Math. Comput. 35, (1980), 773-782.
|
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21
|
OPPE, T. C., JOUBERT, W. D., AND KINCAID, D. R. NSPCG User's Guide. Version 1.0: A package for solving large sparse linear systems by various iterative methods. Tech. Rep. CNA-216, Center for Numerical Analysis, The Univ. of Texas at Austin, 1988.
|
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22
|
SCHLICK, T. Modeling and minimization techniques for predicting three-dimensional structures of large biological molec, ules. Ph.D. thesis, New York Univ., Dept. of Mathematics, 1987. Available through Uniw~rsity Microfilm International.
|
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23
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24
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SCHLICK, T. New approaches to potential energy minimization and molecular dynamics algorithms. Comput. Chem. 15, (1991), 251-260.
|
 |
25
|
|
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26
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SCHLICK, T., AND OVERTON, M. A powerful truncated Newton method for potential energy minimization. J. Comput. Chem. 8, (1987), 1025-1039.
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27
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SCHLICK, T., AND OVERTON, M.L. A study of limited-memory quasi-Newton and truncated Newton methods. In progress.
|
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28
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SCHLICK, T., FIGUEROA, S., AND MEZEI, M. A molecular dynamics of a water droplet by the Langevin/Implicit-Euler scheme. J. Chem. Phys. 94, (1991), 2118-2119.
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29
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SCHLICK, T., HINGERTY, B. E., PESKIN, C. S., OVERTON, M. L., AND BROYDE~, S. Search strategies, minimization algorithms, and molecular dynamics simulations tbr exploring conformational spaces of nucleic acids. In Theoretical Biochemistry and Molecular Biophysics, Volume l: Nucleic Acids, D. L. Beveridge and R. Lavery, Eds. Adenine Press, Guilderland, N.Y., 1991, 39-58.
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30
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Zou, X., NAVON, I. M., BERGER, M., PHUA, P. K. H., LE DIMET, F. X., NOUAILLER, A., AND SCHLICK, T. Numerical experience with hmited-memory quasi-Newton and truncated Newton methods. SIAM J. Optim. To appear.
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