Selected Publications
(For a complete publication list, please refer to my
CV.)
Journal Publications

R. Miller and Q.F. Stout, Geometric algorithms for digitized pictures on a
meshconnected computer,
IEEE Transactions on Pattern Analysis and Machine Intelligence,
PAMI7 (1985), pp. 216228.
Abstract

R. Miller and Q.F. Stout, Data movement techniques for the pyramid computer,
SIAM Journal on Computing,
vol. 16, no. 1, Feb. 1987, pp. 3860.
Abstract

R. Miller and Q.F. Stout, Simulating essential pyramids,
IEEE Transactions on Computers, vol. 37, no. 12, Dec. 1988,
pp. 16421647.
Paper.pdf

R. Miller and Q.F. Stout, Efficient parallel convex hull algorithms,
IEEE Transactions on Computers, vol. 37, no. 12, Dec. 1988,
pp. 16051619.
Abstract
Paper.pdf

E. Cohen and R. Miller, Hypercube algorithms for the multiprocessor
scheduling problem,
Supercomputer Journal 27, vol. V, no. 5,
September, 1988, pp. 1732.

R. Miller and Q.F. Stout, Mesh computer algorithms for computational geometry,
IEEE Transactions on Computers,
vol. 38, no. 3, March 1989, pp. 321340.
Abstract
Paper.pdf

L. Boxer and R. Miller,
Parallel dynamic computational geometry,
The Journal of New Generation Computer Systems 2 (1989) 3,
pp. 227246.

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. 4553.

L. Boxer and R. Miller,
A parallel circlecover minimization algorithm,
Information Processing Letters 32, July 1989,
pp. 5760.

L. Boxer and R. Miller,
Dynamic computational geometry on meshes and hypercubes,
Journal of Supercomputing,
vol. 3, no. 3, September, 1989, pp. 161192.

L. Boxer and R. Miller,
Common intersections of polygons,
Information Processing Letters 33, February 1990,
pp. 249254.

R. Miller and Q.F. Stout,
Seymour: A portable parallel programming language,
Structured Programming (1990), vol. 11, no. 4, pp. 157171.
Abstract

R. Miller and Q.F. Stout,
Computing convexity properties of images on a pyramid computer,
Algorithmica, vol. 6, no. 5, 1991, pp. 658684.
Abstract

F. Dehne, R. Miller, and A. RauChaplin,
Optical clustering on a meshconnected computer,
International Journal on Parallel Programming,
Vol. 20, No. 6, 1991, pp. 475486.
Paper.pdf

E. Cohen, R. Miller, E. Sarraf, and Q.F. Stout,
Efficient convexity and domination algorithms for
fine and mediumgrain hypercube computers,
Algorithmica, vol. 7, no. 1, 1992, pp. 5175.
Abstract

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. 179181.
Paper.pdf

L. Boxer, C.S. Chang, R. Miller, and A. RauChaplin,
Polygonal approximation by boundary reduction,
Pattern Recognition Letters 14 (1993), pp. 111119.
Paper.pdf

L. Boxer and R. Miller,
Parallel algorithms for all maximal equallyspaced collinear sets and
all maximal regular coplanar lattices,
Pattern Recognition Letters 14 (1993), pp. 1722.
Paper.pdf

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. 14301433.
Paper.pdf

C.S. Chang, G. DeTitta, H. Hauptman, R. Miller, P. Thuman, and C. Weeks,
Using parallel computers to solve the phase problem of xray
crystallography,
The International Journal of Supercomputer Applications,
vol. 7, no. 1, Spring 1993, pp. 2549.
Abstract.pdf

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. 678692.
Abstract
Paper.pdf

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 [$\beta$OHDLeuDIle(N Me)Ala(N Me)LeuLeu(N Me)AlaD(N ME)Ala],
International Journal of Peptide & Protein Research 42,
1993, pp. 539549.

M.J. Atallah, F. Dehne, R. Miller, A. RauChaplin, and J.J. Tsay,
Multisearch techniques for implementing data structures on a
meshconnected computer,
Journal of Parallel and Distributed Computing 20,
1994, pp. 113.
Abstract
Paper.pdf

S. Hambrusch, X. He, and R. Miller,
Parallel algorithms for grayscale digitized picture component labeling on
a meshconnected computer,
Journal of Parallel and Distributed Computing 20,
1994, pp. 5668.

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. 203210.
Paper.pdf

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. 210220.
Abstract
Paper.pdf

R. Miller, S.M. Gallo, H.G. Khalak, and C.M. Weeks,
SnB: Crystal structure determination via ShakeandBake,
Journal of Applied Crystallography (1994), 27, pp. 613621.
Paper.pdf

R. Miller, The status of parallel processing education,
Computer, August, 1994, pp. 4043.

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. 465483.

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. 8187.

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. 3338.
Paper.pdf

M.P. McCourt, N. Li, W.A. Pangborn, R. Miller, C.M. Weeks, and D.L. Dorset,
Crystallography of linear molecule binary solids. Xray structure
of a cholesteryl myristate/cholesteryl pentadecanoate solid solution,
J. Phys. Chem., vol. 100, no. 23, 1996, pp. 98429847.

M.P. McCourt, K. Ashraf, R. Miller, C.M. Weeks, N. Li, W. Pangborn,
and D.L. Dorset,
Xray crystal structure of cytotoxic, oxidized cholesterols:
7ketocholesterol and 25hydroxycholesterol,
Journal of Lipid Research, vol. 38, 1997, pp. 10141021.

C.S. Chang, C.M. Weeks, R. Miller, and H.A. Hauptman,
Incorporating tangent refinement in the ShakeandBake formalism,
Acta Crystallographica A53, 1997, pp. 436444.
Paper.pdf

G.D. Smith, R.H. Blessing, S.E. Ealick, J.C. FontecillaCamps,
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. 551557.

P.J. Loll, R. Miller, C.M. Weeks, and P.H. Axelsen,
A ligandmediated dimerization mode for vancomycin,
Chemistry and Biology 5, 1998, pp. 293298.
Abstract
Paper.pdf

A. Deacon, C.M. Weeks, R. Miller, and S.E. Ealick,
The ShakeandBake structure determination of triclinic lysozyme,
Proceedings of the National Academy of Sciences, U.S.A.,
95, August 1998, pp. 92849289.
Abstract
Paper.pdf

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. 1142511433.

L. Boxer, R. Miller, and A. RauChaplin,
Scaleable parallel algorithms for lower envelope with applications,
Journal of Parallel and Distributed Computing 53, 1998, pp. 91118.
Paper.pdf

C.M. Weeks and R. Miller,
Optimizing ShakeandBake for proteins,
Acta Crystallographica D55, 1999, pp. 492500.
Paper.pdf

C.M. Weeks and R. Miller,
The design and implementation of SnB v2.0,
Journal of Applied Crystallography 32, 1999, pp. 120124.
Paper.pdf

L. Boxer, R. Miller, and A. RauChaplin,
Scalable parallel algorithms for geometric pattern
recognition,
Journal of Parallel and Distributed Computing 58, 1999,
pp. 466486.
Abstract
Paper.pdf

H.A. Hauptman, H. Xu, C.M. Weeks, and R. Miller,
Exponential ShakeandBake: theoretical basis and applications,
Acta Crystallographica A55, 1999, pp. 891900.

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,
Xray crystallographic analysis of the hydration of A and Bform
DNA at atomic resolution,
Biopolymers (Nucleic Acid Sciences) 48, 2000, pp. 234252.

H. Xu, H.A. Hauptman, C.M. Weeks, and R. Miller,
P1 ShakeandBake: Can success be guaranteed?,
Acta Crystallographica D56, 2000, pp. 238240.

H. Xu, C.M. Weeks, A.M. Deacon, R. Miller, and H.A. Hauptman,
Illconditioned ShakeandBake: The trap of the false minimum,
Acta Crystallographica A56, 2000, pp. 112118.
Paper.pdf

L. Boxer and R. Miller,
Efficient computation of the Euclidean distance transform,
Computer Vision and Image Understanding 80, 2000, pp. 379383.
Paper.pdf

Y. Vekhter and R. Miller,
An improved phaseextension procedure for isomorphousreplacement phases,
Acta Crystallographica D57, 2001, pp. 10481051.

L. Boxer and R. Miller,
A parallel algorithm for approximate regularity,
Information Processing Letters 80, 2001, pp. 311316.
Paper.pdf

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. 374376.
Paper.pdf

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
SnBPHASES interface,
Z. Kristallogr. 217, 2002, pp. 686693.
Paper.pdf

M.L. Green and R. Miller, Grid computing in Buffalo, New York,
Annals of the European Academy of Sciences, 2003, pp. 191218.
Paper.pdf

M.L. Green and R. Miller, A clientserver prototype for application
gridenabling template design, Parallel Processing Letters, Vol. 14,
No. 2 (2004), pp. 241253.
Paper.pdf

M.L. Green and R. Miller, Molecular structure determination on a
computational & data grid,
Parallel Computing Journal 30 (2004), pp. 10011017.
Paper.pdf

M.L. Green and R. Miller, Evolutionary molecular structure determination using gridenabled data mining,
Parallel Computing Journal 30 (2004), pp. 10571071.
Paper.pdf

L. Boxer and R. Miller,
Coarse Grained Gather and Scatter Operations with Applications,
Journal of Parallel and Distributed Computing
64 (2004), pp. 12971310.
Paper.pdf

M.M. EshaghianWilner and R. Miller,
The Systolic Reconfigurable Mesh,
Parallel Processing Letters,
Vol. 14, Nos. 3&4 (2004), pp. 335350.
Paper.pdf

C.L. Ruby, M.L. Green, and R. Miller,
The Operations Dashboard: A Collaborative Environment
for Monitoring Virtual OrganizationSpecific Compute Element
Operational Status,
Parallel Processing Letters,
Vol. 16, No. 4 (2006), pp. 485500.
Paper.pdf

R. Miller, N. Shah, M. Green, W. Furey, and C. Weeks,
ShakeandBake on the grid,
Journal of Applied Crystallography 40, 2007, pp. 938944.
Paper.pdf

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. 424434.
Journal.pdf

L. Boxer and R. Miller,
Efficient coarse grained data distributions and string pattern matching,
International Journal of Information and Systems Sciences, vol. 7, nos. 23, 2011, pp. 214224.
Journal.pdf
 R. Miller, Integrating Modern Computing Systems into the Computer Science Curriculum at SUNYBuffalo: A 30Year Case Study, International Journal of Teaching and Case Studies, 2016, Vol.7, No.2, pp. 105117.
 R. Miller, A Modern Approach to Discrete Structures, International Journal of Teaching and Case Studies, 2018, Vol. 9, No. 1, pp. 3347.
Book Chapters

R. Miller, Image processing on reconfigurable meshes,
From Pixels to Features II: Parallelism in Image Processing,
J.C. Simon, ed., pp. 377394, 1990.
(From Pixels to Features II: Parallelism in Image Processing,
H. Burkhardt, Y. Neuvo, and J.C. Simon, eds., North Holland, 1991, pp. 85101.)

R. Miller, V.K. Prasanna Kumar, D. Reisis, and Q.F. Stout,
Efficient parallel algorithms for
intermediatelevel vision analysis on the reconfigurable mesh,
Parallel Architectures and Algorithms for Image
Understanding,
V.K.P. Kumar, ed.,
Academic Press, New York, 1991, pp. 185208.

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. 10151025.

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. 10251028.

M.M. Eshaghian, R. Miller, and C. Weems,
Multimode System Heterogeneous Computing,
Heterogeneous Computing,
M.M. Eshaghian, ed., Artech House Publishers,
Mass., 1996, pp. 67100.

C.M. Weeks and R. Miller,
SnB: applying ShakeandBake to proteins,
Crystallographic Computing 7: Proceedings of the International
Macromolecular Crystallography Computing Summer School,
P. Bourne & K. Watenpaugh (Eds.), Bellingham, Washington,
August 1996, pp. 138147.
Paper.pdf

R. Miller and C.M. Weeks,
ShakeandBake: Applications and Advances,
Direct Methods for Solving Macromolecular Structures,
S. Fortier, ed., Erice, Sicily, MayJune, 1997, Kluwer Academic Publishers,
25th Course, International School of Crystallography, NATO ASI Series, 1998,
pp. 389400.

C.M. Weeks, R. Miller, and H.A. Hauptman,
Extending the resolving power of ShakeandBake,
Direct Methods for Solving Macromolecular Structures,
S. Fortier, ed., Erice, Sicily, MayJune, 1997, Kluwer Academic Publishers,
25th Course, International School of Crystallography, NATO ASI Series, 1998,
pp. 463468.

C.M. Weeks, H.A. Hauptman, C.S. Chang, and R. Miller,
Structure determination by ShakeandBake 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. 153161.

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. 461 — 4619.
Abstract
Paper.pdf

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. 333351.

C.M. Weeks, G.M. Sheldrick, R. Miller, I. Us\'{o}n, and H.A. Hauptman,
Ab initio phasing by dualspace direct methods,
Bulletin of the Czech and Slovak Crystallographic Association,
2001, pp. 3764.
Paper.pdf

R. Miller, Parallel Processing Architectures, Concise Encyclopedia of
Computer Science, E.D. Reilly, ed., John Wiley & Sons, Ltd., New Jersey,
2004, pp. 598601.

R. Miller, Parallel Processing Algorithms, Concise Encyclopedia of
Computer Science, E.D. Reilly, ed., John Wiley & Sons, Ltd., New Jersey,
2004, pp. 601602.

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. 583621.
Paper.pdf

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. 461 — 4636.
Paper.pdf

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

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, 461  4633.
Paper.pdf

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. 3154.

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. 327345.
Paper.pdf
Books

R. Miller and Q.F. Stout,
Parallel Algorithms for Regular Architectures: Meshes and Pyramids,
The MIT Press, Cambridge, Mass., 1996.
Additional Information

R. Miller and L. Boxer,
Algorithms Sequential and Parallel: A Unified Approach,
PrenticeHall, Upper Saddle River, New Jersey, 2000.
(Translated into Russian in 2007.)
Additional Information

R. Miller and L. Boxer,
Algorithms Sequential and Parallel: A Unified Approach,
Second Edition, Charles River Media, Hingham, Mass., 2005.

R. Miller and L. Boxer,
Algorithms Sequential and Parallel: A Unified Approach,
Third Edition, Cengage Learning, Boston, Mass., 2013.
Additional Book Information
Philosophy and Music
 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
