Publications

Journal Publications

1. R. Miller and Q.F. Stout, Geometric algorithms for digitized pictures on a mesh-connected computer, IEEE Transactions on Pattern Analysis and Machine Intelligence, PAMI-7 (1985), pp. 216-228. Abstract
2. R. Miller and Q.F. Stout, Data movement techniques for the pyramid computer, SIAM Journal on Computing, vol. 16, no. 1, Feb. 1987, pp. 38-60. Abstract
3. R. Miller and Q.F. Stout, Simulating essential pyramids, IEEE Transactions on Computers, vol. 37, no. 12, Dec. 1988, pp. 1642-1647. Paper.pdf
4. R. Miller and Q.F. Stout, Efficient parallel convex hull algorithms, IEEE Transactions on Computers, vol. 37, no. 12, Dec. 1988, pp. 1605-1619. Abstract Paper.pdf
5. E. Cohen and R. Miller, Hypercube algorithms for the multiprocessor scheduling problem, Supercomputer Journal 27, vol. V, no. 5, September, 1988, pp. 17-32.
6. R. Miller and Q.F. Stout, Mesh computer algorithms for computational geometry, IEEE Transactions on Computers, vol. 38, no. 3, March 1989, pp. 321-340. Abstract Paper.pdf
7. L. Boxer and R. Miller, Parallel dynamic computational geometry, The Journal of New Generation Computer Systems 2 (1989) 3, pp. 227-246.
8. R. Miller and S.E. Miller, Convexity algorithms for digitized pictures on an Intel iPSC hypercube, Supercomputer Journal 31, vol. VI, no. 3, May 1989, pp. 45-53.
9. L. Boxer and R. Miller, A parallel circle-cover minimization algorithm, Information Processing Letters 32, July 1989, pp. 57-60.
10. L. Boxer and R. Miller, Dynamic computational geometry on meshes and hypercubes, Journal of Supercomputing, vol. 3, no. 3, September, 1989, pp. 161-192.
11. L. Boxer and R. Miller, Common intersections of polygons, Information Processing Letters 33, February 1990, pp. 249-254.
12. R. Miller and Q.F. Stout, Seymour: A portable parallel programming language, Structured Programming (1990), vol. 11, no. 4, pp. 157-171. Abstract
13. R. Miller and Q.F. Stout, Computing convexity properties of images on a pyramid computer, Algorithmica, vol. 6, no. 5, 1991, pp. 658-684. Abstract
14. F. Dehne, R. Miller, and A. Rau-Chaplin, Optical clustering on a mesh-connected computer, International Journal on Parallel Programming, Vol. 20, No. 6, 1991, pp. 475-486. Paper.pdf
15. E. Cohen, R. Miller, E. Sarraf, and Q.F. Stout, Efficient convexity and domination algorithms for fine- and medium-grain hypercube computers, Algorithmica, vol. 7, no. 1, 1992, pp. 51-75. Abstract
16. C.M. Weeks, G.T. DeTitta, R. Miller, and H.A. Hauptman, Applications of the minimal principle to peptide structures, Acta Crystallographica D49, 1993, pp. 179-181. Paper.pdf
17. L. Boxer, C.-S. Chang, R. Miller, and A. Rau-Chaplin, Polygonal approximation by boundary reduction, Pattern Recognition Letters 14 (1993), pp. 111-119. Paper.pdf
18. L. Boxer and R. Miller, Parallel algorithms for all maximal equally-spaced collinear sets and all maximal regular coplanar lattices, Pattern Recognition Letters 14 (1993), pp. 17-22. Paper.pdf
19. R. Miller, G.T. DeTitta, R. Jones, D.A. Langs, C.M. Weeks, and H.A. Hauptman, On the application of the minimal principle to solve unknown structures, Science, vol. 259, March, 1993, pp. 1430-1433. Paper.pdf
20. C.-S. Chang, G. DeTitta, H. Hauptman, R. Miller, P. Thuman, and C. Weeks, Using parallel computers to solve the phase problem of x-ray crystallography, The International Journal of Supercomputer Applications, vol. 7, no. 1, Spring 1993, pp. 25-49. Abstract.pdf
21. R. Miller, V.K. Prasanna Kumar, D. Reisis, and Q.F. Stout, Parallel computations on reconfigurable meshes, IEEE Transactions on Computers, vol. 42, no. 6, June 1993, pp. 678-692. Abstract Paper.pdf
22. R. Miller, N.M. Galitsky, W.L. Duax, D.A. Langs, V.Z. Pletnev, and V.T. Ivanov, Molecular structures of two crystalline polymorphs of the cyclic heptapeptide antibiotic ternatin: cyclo [-$\beta$-OH-D-Leu-D-Ile-(N Me)Ala-(N Me)Leu-Leu-(N Me)Ala-D-(N ME)Ala-], International Journal of Peptide & Protein Research 42, 1993, pp. 539-549.
23. M.J. Atallah, F. Dehne, R. Miller, A. Rau-Chaplin, and J.-J. Tsay, Multisearch techniques for implementing data structures on a mesh-connected computer, Journal of Parallel and Distributed Computing 20, 1994, pp. 1-13. Abstract Paper.pdf
24. S. Hambrusch, X. He, and R. Miller, Parallel algorithms for gray-scale digitized picture component labeling on a mesh-connected computer, Journal of Parallel and Distributed Computing 20, 1994, pp. 56-68.
25. G.T. DeTitta, C.M. Weeks, P. Thuman, R. Miller, and H.A. Hauptman, Structure solution by minimal function phase refinement and Fourier filtering. I. Theoretical basis, Acta Crystallographica A50, 1994, pp. 203-210. Paper.pdf
26. C.M. Weeks, G.T. DeTitta, H.A. Hauptman, P. Thuman, and R. Miller, Structure solution by minimal function phase refinement and Fourier filtering. II. Implementation and applications, Acta Crystallographica A50, 1994, pp. 210-220. Abstract Paper.pdf
27. R. Miller, S.M. Gallo, H.G. Khalak, and C.M. Weeks, SnB: Crystal structure determination via Shake-and-Bake, Journal of Applied Crystallography (1994), 27, pp. 613-621. Paper.pdf
28. R. Miller, The status of parallel processing education, Computer, August, 1994, pp. 40-43.
29. S.L. Tanimoto and R. Miller, Mesh algorithms for finding repetitions and partial symmetries in arrays, International Journal of Pattern Recognition and Artificial Intelligence, Vol. 8, No. 2, 1994, pp. 465-483.
30. D.A. Langs, R. Miller, H.A. Hauptman, and G.W. Han, Use of the minimal function for partial structure development in direct methods, Acta Crystallographica A51, 1995, pp. 81-87.
31. C.M. Weeks, H.A. Hauptman, G.D. Smith, R.H. Blessing, M.M. Teeter, and R. Miller, Crambin: a direct solution for a 400 atom structure, Acta Crystallographica D51, 1995, pp. 33-38. Paper.pdf
32. M.P. McCourt, N. Li, W.A. Pangborn, R. Miller, C.M. Weeks, and D.L. Dorset, Crystallography of linear molecule binary solids. X-ray structure of a cholesteryl myristate/cholesteryl pentadecanoate solid solution, J. Phys. Chem., vol. 100, no. 23, 1996, pp. 9842-9847.
33. M.P. McCourt, K. Ashraf, R. Miller, C.M. Weeks, N. Li, W. Pangborn, and D.L. Dorset, X-ray crystal structure of cytotoxic, oxidized cholesterols: 7-ketocholesterol and 25-hydroxycholesterol, Journal of Lipid Research, vol. 38, 1997, pp. 1014-1021.
34. C.-S. Chang, C.M. Weeks, R. Miller, and H.A. Hauptman, Incorporating tangent refinement in the Shake-and-Bake formalism, Acta Crystallographica A53, 1997, pp. 436-444. Paper.pdf
35. G.D. Smith, R.H. Blessing, S.E. Ealick, J.C. Fontecilla-Camps, H.A. Hauptman, D. Housset, D.A. Langs, and R. Miller, The ab initio structure determination and refinement of a scorpion protein toxin, Acta Crystallographica D53, 1997, pp. 551-557.
36. P.J. Loll, R. Miller, C.M. Weeks, and P.H. Axelsen, A ligand-mediated dimerization mode for vancomycin, Chemistry and Biology 5, 1998, pp. 293-298. Abstract Paper.pdf
37. A. Deacon, C.M. Weeks, R. Miller, and S.E. Ealick, The Shake-and-Bake structure determination of triclinic lysozyme, Proceedings of the National Academy of Sciences, U.S.A., 95, August 1998, pp. 9284-9289. Abstract Paper.pdf
38. S.-H. Hu, M. Loughnan, R. Miller, C.M. Weeks, R.H. Blessing, P.F. Alewood, R.J. Lewis, and J.L. Martin, The 1.1A Crystal Structure of [Tyr^{15}]-EpI, A novel $\alpha$--conotoxin from Conus Episcopatus, solved by direct methods, Biochemistry 37, 1998, pp. 11425-11433.
39. L. Boxer, R. Miller, and A. Rau-Chaplin, Scaleable parallel algorithms for lower envelope with applications, Journal of Parallel and Distributed Computing 53, 1998, pp. 91-118. Paper.pdf
40. C.M. Weeks and R. Miller, Optimizing Shake-and-Bake for proteins, Acta Crystallographica D55, 1999, pp. 492-500. Paper.pdf
41. C.M. Weeks and R. Miller, The design and implementation of SnB v2.0, Journal of Applied Crystallography 32, 1999, pp. 120-124. Paper.pdf
42. L. Boxer, R. Miller, and A. Rau-Chaplin, Scalable parallel algorithms for geometric pattern recognition, Journal of Parallel and Distributed Computing 58, 1999, pp. 466-486. Abstract Paper.pdf
43. H.A. Hauptman, H. Xu, C.M. Weeks, and R. Miller, Exponential Shake-and-Bake: theoretical basis and applications, Acta Crystallographica A55, 1999, pp. 891-900.
44. M. Egli, V. Tereshko, M. Teplova, G. Minasov, A. Joachimiak, R. Sanishvilli, C.M. Weeks, R. Miller, M.A. Maier, H. An, P.D. Cook, and M. Manoharan, X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution, Biopolymers (Nucleic Acid Sciences) 48, 2000, pp. 234-252.
45. H. Xu, H.A. Hauptman, C.M. Weeks, and R. Miller, P1 Shake-and-Bake: Can success be guaranteed?, Acta Crystallographica D56, 2000, pp. 238-240.
46. H. Xu, C.M. Weeks, A.M. Deacon, R. Miller, and H.A. Hauptman, Ill-conditioned Shake-and-Bake: The trap of the false minimum, Acta Crystallographica A56, 2000, pp. 112-118. Paper.pdf
47. L. Boxer and R. Miller, Efficient computation of the Euclidean distance transform, Computer Vision and Image Understanding 80, 2000, pp. 379-383. Paper.pdf
48. Y. Vekhter and R. Miller, An improved phase-extension procedure for isomorphous-replacement phases, Acta Crystallographica D57, 2001, pp. 1048-1051.
49. L. Boxer and R. Miller, A parallel algorithm for approximate regularity, Information Processing Letters 80, 2001, pp. 311-316. Paper.pdf
50. J. Rappleye, M. Innus, C.M. Weeks, and R. Miller, SnB v2.2: An Example of Crystallographic Multiprocessing, Journal of Applied Crystallography 35, 2002, pp. 374-376. Paper.pdf
51. C.M. Weeks, R.H. Blessing, R. Miller, R. Mungee, S.A. Potter, J. Rappleye, G.D. Smith, H. Xu, and W. Furey, Towards automated protein structure determination: BnP, the SnB-PHASES interface, Z. Kristallogr. 217, 2002, pp. 686-693. Paper.pdf
52. M.L. Green and R. Miller, Grid computing in Buffalo, New York, Annals of the European Academy of Sciences, 2003, pp. 191-218. Paper.pdf
53. M.L. Green and R. Miller, A client-server prototype for application grid-enabling template design, Parallel Processing Letters, Vol. 14, No. 2 (2004), pp. 241-253. Paper.pdf
54. M.L. Green and R. Miller, Molecular structure determination on a computational & data grid, Parallel Computing Journal 30 (2004), pp. 1001-1017. Paper.pdf
55. M.L. Green and R. Miller, Evolutionary molecular structure determination using grid-enabled data mining, Parallel Computing Journal 30 (2004), pp. 1057-1071. Paper.pdf
56. L. Boxer and R. Miller, Coarse Grained Gather and Scatter Operations with Applications, Journal of Parallel and Distributed Computing 64 (2004), pp. 1297-1310. Paper.pdf
57. M.M. Eshaghian-Wilner and R. Miller, The Systolic Reconfigurable Mesh, Parallel Processing Letters, Vol. 14, Nos. 3&4 (2004), pp. 335-350. Paper.pdf
58. C.L. Ruby, M.L. Green, and R. Miller, The Operations Dashboard: A Collaborative Environment for Monitoring Virtual Organization-Specific Compute Element Operational Status, Parallel Processing Letters, Vol. 16, No. 4 (2006), pp. 485-500. Paper.pdf
59. R. Miller, N. Shah, M. Green, W. Furey, and C. Weeks, Shake-and-Bake on the grid, Journal of Applied Crystallography 40, 2007, pp. 938-944. Paper.pdf
60. L. Boxer and R. Miller, Efficient coarse grained data distributions and string pattern matching, International Journal of Information and Systems Sciences, vol. 6, no. 4, 2010, pp. 424-434. Journal.pdf
61. L. Boxer and R. Miller, Efficient coarse grained data distributions and string pattern matching, International Journal of Information and Systems Sciences, vol. 7, nos. 2-3, 2011, pp. 214-224. Journal.pdf
62. R. Miller, Integrating Modern Computing Systems into the Computer Science Curriculum at SUNY-Buffalo: A 30-Year Case Study, International Journal of Teaching and Case Studies, 2016, Vol.7, No.2, pp. 105-117.
63. R. Miller, A Modern Approach to Discrete Structures, International Journal of Teaching and Case Studies, 2018, Vol. 9, No. 1, pp. 33-47.
    

    Book Chapters
    

64. R. Miller, Image processing on reconfigurable meshes, From Pixels to Features II: Parallelism in Image Processing, J.C. Simon, ed., pp. 377-394, 1990. (From Pixels to Features II: Parallelism in Image Processing, H. Burkhardt, Y. Neuvo, and J.C. Simon, eds., North Holland, 1991, pp. 85-101.)
65. R. Miller, V.K. Prasanna Kumar, D. Reisis, and Q.F. Stout, Efficient parallel algorithms for intermediate-level vision analysis on the reconfigurable mesh, Parallel Architectures and Algorithms for Image Understanding, V.K.P. Kumar, ed., Academic Press, New York, 1991, pp. 185-208.
66. R. Miller, Parallel Processing Architectures, Encyclopedia of Computer Science, 3rd edition, A. Ralston and E. Reilly, eds., Van Nostrand Reinhold Company, Inc., New York, 1993, pp. 1015-1025.
67. R. Miller, Parallel Processing Algorithms, Encyclopedia of Computer Science, 3rd edition, A. Ralston and E. Reilly, eds., Van Nostrand Reinhold Company, Inc., New York, 1993, pp. 1025-1028.
68. M.M. Eshaghian, R. Miller, and C. Weems, Multimode System Heterogeneous Computing, Heterogeneous Computing, M.M. Eshaghian, ed., Artech House Publishers, Mass., 1996, pp. 67-100.
69. C.M. Weeks and R. Miller, SnB: applying Shake-and-Bake to proteins, Crystallographic Computing 7: Proceedings of the International Macromolecular Crystallography Computing Summer School, P. Bourne & K. Watenpaugh (Eds.), Bellingham, Washington, August 1996, pp. 138-147. Paper.pdf
70. R. Miller and C.M. Weeks, Shake-and-Bake: Applications and Advances, Direct Methods for Solving Macromolecular Structures, S. Fortier, ed., Erice, Sicily, May-June, 1997, Kluwer Academic Publishers, 25th Course, International School of Crystallography, NATO ASI Series, 1998, pp. 389-400.
71. C.M. Weeks, R. Miller, and H.A. Hauptman, Extending the resolving power of Shake-and-Bake, Direct Methods for Solving Macromolecular Structures, S. Fortier, ed., Erice, Sicily, May-June, 1997, Kluwer Academic Publishers, 25th Course, International School of Crystallography, NATO ASI Series, 1998, pp. 463-468.
72. C.M. Weeks, H.A. Hauptman, C.-S. Chang, and R. Miller, Structure determination by Shake-and-Bake with tangent refinement, Likelihood, Bayesian, Inference and Their Application to the Solution of New Structures, G. Bricogne and C.W. Carter, eds., Transactions of the American Crystallographic Association Transactions, vol. 30, 1994 (1996), pp. 153-161.
73. R. Miller and Q.F. Stout, Algorithmic Techniques for Networks of Processors, CRC Handook of Algorithms and Theory of Computation, M.J. Atallah, ed., 1999, pp. 46-1 — 46-19. Abstract Paper.pdf
74. G.M. Sheldrick, H.A. Hauptman, C.M. Weeks, R. Miller, and I. Us\'{o}n, Ab Initio Phasing, International Tables for Macromolecular Crystallography, Vol. F, M. Rossman and E. Arnold, Eds., Kluwer Academic Publishers, Dordrecht, The Netherlands, 2001, pp. 333-351.
75. C.M. Weeks, G.M. Sheldrick, R. Miller, I. Us\'{o}n, and H.A. Hauptman, Ab initio phasing by dual-space direct methods, Bulletin of the Czech and Slovak Crystallographic Association, 2001, pp. 37-64. Paper.pdf
76. R. Miller, Parallel Processing Architectures, Concise Encyclopedia of Computer Science, E.D. Reilly, ed., John Wiley & Sons, Ltd., New Jersey, 2004, pp. 598-601.
77. R. Miller, Parallel Processing Algorithms, Concise Encyclopedia of Computer Science, E.D. Reilly, ed., John Wiley & Sons, Ltd., New Jersey, 2004, pp. 601-602.
78. R. Miller and M.L. Green, Molecular Structure Determination on a Computational and Data Grid, Parallel Computing in Bioinformatics and Computational Biology, A. Zomaya, ed., John Wiley & Sons, Ltd., New Jersey, 2006, pp. 583-621. Paper.pdf
79. C.L. Ruby and R. Miller, Effectively Managing Data on a Grid, Handbook of Parallel Computing: Models, Algorithms, and Applications, S. Rajasekaran and J. Reif, eds., CRC Press, 2007, pp. 46-1 — 46-36. Paper.pdf
80. R. Miller, Grid Case Study: Grid in New York State, The Grid Technology Cookbook, M. Yafchak and M. Trauner, eds., 2007. Book Link; Section Link
81. R. Miller and Q.F. Stout, Algorithmic Techniques for Regular Networks of Processors, CRC Handook of Algorithms and Theory of Computation, 2nd edition, M.J. Atallah, ed., 2009, 46-1 - 46-33. Paper.pdf
82. J.J. Bednasz, K. Chiu, S.M. Gallo, M. Govindaraju, M. Lewis, R. Miller, C.L. Ruby, and C.M. Weeks, Cyberinfrastructure in New York State, Grid Computing: Infrastructure, Service, and Application, L. Wang and W. Jie, eds., CRC Press, 2009, pp. 31-54.
83. R. Miller and C.M. Weeks, Molecular Structure Determination on the Grid, Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare, M. Cannataro, ed., IRI Press, 2009, pp. 327-345. Paper.pdf

    Books
    

84. R. Miller and Q.F. Stout, Parallel Algorithms for Regular Architectures: Meshes and Pyramids, The MIT Press, Cambridge, Mass., 1996. Additional Information
85. R. Miller and L. Boxer, Algorithms Sequential and Parallel: A Unified Approach, Prentice-Hall, Upper Saddle River, New Jersey, 2000. (Translated into Russian in 2007.) Additional Information
86. R. Miller and L. Boxer, Algorithms Sequential and Parallel: A Unified Approach, Second Edition, Charles River Media, Hingham, Mass., 2005.
87. R. Miller and L. Boxer, Algorithms Sequential and Parallel: A Unified Approach, Third Edition, Cengage Learning, Boston, Mass., 2013.

    Additional Book Information

    • Parallel Algorithms for Regular Architectures

    • Algorithms Sequential and Parallel: A Unified Approach, Third Edition

      • Delmar Cengage Learning Web Site.

        • The third edition of Algorithms Sequential and Parallel, A Unified Approach s available (2013). In addition to a complete rewrite and modernization of the text, a solution manual is available that includes detailed solutions for all problems in the text. A complete set of powerpoint slides for all chapters is also available.

        • Errata for Algorithms Sequential and Parallel, A Unified Approach 2E, Charles River Media.

      • Amazon.com: includes reviews for the third edition.

      • Amazon.com: includes reviews for the second edition.

      • Barnes and Noble: includes reviews for the second edition.

      • SIGACT News Review, Anthony Widjaja, June 2003, pp. 3-5. Professional review of the first edition.

    Philosophy and Music
88. Escher's Enigma
    • From Me to There, 2013.
      • Choice, Drowning in Time, Ideally, Such a Disgrace, Green Candy Eyes
    • Piece of Mind, 2014.
      • Here for the Last Time, The Write Words, Keep Reaching, Safety Net, Backstreet Boy
    • For a Moment, 2015.
      • Should Have Known, When Your Heart, Bonfire Rings and Heated Pools, My Guitar, Hide Behind the Text, Life of Solitude, Bixby Canyon Bridge, Beauty in the Flames, Beginnings, Sweet Child O' Mine
    • Interpretations, Vol. 1, 2016.
      • Kryptonite, Baba O'Riley / Let My Love Open the Door, Invincible, Come to Me, Enter Sandman, Missed the Boat