D. References 1. T. S. Rahman, A. Kara, A. Karim, and A. Al-Rawi, “Paths, Barriers and Prefactors for Adatom Descent from Ag clusters onAg(111)'', in Collective Diffusion on urfaces:Correlation Effects and Adatom Interactions, edts M.C.Tringides and Z. Chvoj (Kluwer 2001), p327. 2. M. Rusanen, I. T. Koponen, T. Ala-Nissila, C. Ghosh, and T. S. Rahman, “Morphology of ledge patterns during step flow growth of metal surfacesvicinal to fcc(001)," Phys. Rev. B(Rapid Comm.) 65, 041404, (2002). 3. A. Karim, T. S. Rahman, M. Rusanen, I. T. Koponen, and T. Ala-Nissila, “Evolution of Step Morphology in Thermal equilibrium,” Surf. Sci. Lett (2004), in press. 4. C. Ghosh, A. Kara, and T. S. Rahman, “Diffusion of small 2-dimensional Cu clusters on Cu(111), to be published; C. Ghosh, PhD Thesis, KSU, 2003. 5. M. Tringides, Z. Chvoj, C. Ghosh, and T. S. Rahman, “Prefactors for interlayer diffusion: Ag/Ag(111),” J. Phys.: Condensed Matter 15, 5223 (2003). 6. A. Al-Rawi, A. Kara and T. S. Rahman, “Molecular dynamics study of the diffusion of small Cu clusters on Cu(111): role of multi-atom processes and anharmonic effects,” to be published. 7. A Al-Rawi, C. Ghosh, P. Staikov, A. Kara, and T. S. Rahman, “Validity of the Quasiharmonic Analysis for Surface Thermal Expansion of Ag(111),"'Phys. Rev. Lett. 86, 2074 (2001). 8. A. Al-Rawi and T. S. Rahman, “Comparative Study of Anharmonic Effects on Ag(111), Cu(111), and Ni(111),” Phys. Rev. B 66, 165439 (2002). 9. T. S. Rahman, “Simulations of Surface Phenomena,” in Methods in Materials Research, Ed. J. M. Sanchez, J. Wiley, NY (2000). 10. T. S. Rahman, J. D. Spangler, and A. Al-Rawi, “Temperature Variation of Surface Phonon Linewidth: low Miller index surfaces of Ag and Cu,” Surf. Sci. 502-503, 429 (2002) 11. S. Stolbov, T. S. Rahman, Role of long range interaction in oxygen superstructure formation on Cu(001) and Ni(001), Phys. Rev. Lett. 89, 11601 (2002). 12. S.V. Stolbov, A. Kara, and T. S. Rahman, “Electronic Structure of the c(2x2)O/Cu(001) System,” Phys. Rev. B. 66, 245405 (2002). 13. S. Stolbov, T. S. Rahman, Relationship between electronic and geometric structures of the O/Cu(001) system, J. Chem. Phys. 117, 18 (2002). 14. S. Hong, A. Kara, T. S. Rahman, and K. P. Bohnen, “Adsorbate Induced Stress on Ni(100): ab initio Calculations for Oxygen and Carbon Overlayers,” Phys. Rev. B, in press. 15. S. Hong, K. P. Bohnen, R. Heid, and T. S. Rahman, “Ab initio Calculations of Surface Phonons of Clean and Oxygen Chemisorbed Ni(100),” to be published. 16. I. Makkonen, P. Salo, M. Alatalo, and T. S. Rahman, “Ab initio studies of stepped Pd surfaces with and without S”, Phys. Rev. B, 67, 165415 (2003). 17. R. Heid, A. Kara, K. P. Bohnen, and T. S. Rahman,” Ab initio Calculations of Multilayer Relaxations of Stepped Cu Surfaces,” Phys. Rev. B 65, 115405 (2002). 18. A. Kara, P. Staikov, T.S. Rahman, J. Radnik, R. Biage and H.J. Ernst, “High Frequency Phonon Modes on Stepped and Kinked Cu Surface: Experiment and Theory,'' Phys. Rev. 61, 5714 (2000). 19. A. Kara and T.S. Rahman, “Vibrational Properties of Metallic Nanocrystals,”Phys. Rev. Lett. 81, 1453 (1998). 20. S. Durukanoglu, and T.S. Rahman, “Atomic Relaxations of Stepped Cu(410),” Surf. Sci. 409, 395(1998). 21. U. Kurpick and T. S. Rahman, “Diffusion Processes Relevant to Homoepitaxial Growth on Ag(100), Phys. Rev. B57, 2482 (1998). 22. U. Kuerpick and T.S. Rahman, “Diffusion Processes and Pre-Exponential Factors in Homoepitaxial Growth on Ag(100)," in Vol. 492, MRS Symposium Proceedings Series, (Fall 1997, Boston, MA). Editors S.R. Phillpot, P.D. Bristowe, D.G. Stroud and J.R. Smith, 1998. 23. U. Kuerpick and T.S. Rahman, “Monovacancy Diffusion on Ag(100),Cu(100), and Ni(100): Prefactor and Activation Barriers,” Phys. Rev. B 59, 11014 (1999). 24. U. Kuerpick and T.S. Rahman, “The Role of Vibrational Entropy in Surface Diffusion: Adatoms and Vacancies of Ag(100), Cu(100), and Ni(100),” Surf. Science 427, 15 (1999). 25. U. Kuerpick and T.S. Rahman, “Tip Induced Motion of Adatoms on Metal Surfaces,” Phys. Rev. Lett. 83, 2765 (1999). 26. W. Fei, A. Kara, and T.S. Rahman, “Contributions of Vibrational Dynamics to the Local and Excess Thermodynamic Properties of Cu3Au Surfaces," Phys. Rev. B. 61, 16105 (2000). 27. P. Staikov, and T. S. Rahman,”Multilayer Relaxations of Mg Surfaces”, Phys. Rev. B60, 15613 (1999). 28. S. Stolbov, T. S. Rahman, “Giant increase in isoelectronic reactivity of transition and noble metal surfaces upon alkali metal adsorption”, to be published. 29. P. Hohenberg and W. Kohn, “Inhomogeneous Electron Gas,” Phys. Rev. B136, 864 (1964). 30. W. Kohn and L.J. Sham, “Self-consistent Equations Including Exchange and Correlation Effects”, Phys. Rev. A140, 1133 (1965). 31. For a review see: M.C. Payne, M.P. Teter, D.C. Allen, T.A. Arias and J.D. Joannopoulos, “Iterative Minimization Techniques for ab-initio Total-Energy Calculations: Molecular Dynamics and Conjugate Gradients,'' Rev. Mod. Phys. 64, 1045 (1992). 32. N. Chetty, M. Weinert, T.S. Rahman, J.E. Pasciak and J.W. Davenport, “Vacancies and impurities in aluminum and magnesium”, Phys. Rev. B 52, 6313 (1995). 33. D. Alfe, S. de Gironcoli, and S. Baroni, Surf. Sci. 437, 18 (1999). 34. J. P. Perdew, K. Burke, and M. Ernzerhof, “Generalized Gradient Approximation Made Simple” Phys. Rev. Lett. 77, 3865 (1996). 35. R. Heid and K. P. Bohnen, “Linear response in a density-functional mixed-basis approach”, Phys. Rev. B 60, R3709 (1999). 36. Y Wang, G. M. Stocks, W. A. Shelton, D. M. Nicholson, Z. Szotek, W. M. Temmerman, “Order-N Multiple Scattering Approach to Electronic Structure Calculations”, Phys. Rev. Lett.75, 2867 (1995). 37. P. Blaha, K. Schwarz, G. K. H. Madsen, D. Kvasnicka, and J. Luitz, WIEN2k, An Augmented Plane Wave + Local Orbitals Program for Calculating Crystal Properties (Karlheinz Schwarz, Techn. Universität Wien, Austria) 2001. ISBN 3-9501031-1-2. 38. G. Kresse and J. Hafner, “Ab initio molecular dynamics for liquid metals”,Phys. Rev. B 47, 558 (1993). 39. Jianguo Yu and Jacques G. Amar , "Short-range Attraction, Surface Currents, and Mound formation in Metal (111) Epitaxial Growth", Physical Review B 69, 045426 (2004). 40. Jianguo Yu, Jacques G. Amar, and Alexander Bogicevic, "First-Principles Calculations of Steering in Cu(100) Growth", Physical Review B (in press). 41. Jianguo Yu and Jacques G. Amar, “Effects of Short-Range Attraction in Metal Epitaxial Growth”, Physical Review Letters 89, 286013 (2002). 42. Jacques G. Amar and Mihail N. Popescu, "Asymptotic Capture-Number and Island-Size Distributions for One-Dimensional Irreversible Submonolayer Growth", Physical Review B 69, 033401 (2004). 43. A Noreyan, J.G. Amar, and I. Marinescu, "Molecular Dynamics Simulation of Nanoindentation of beta-SiC by a Diamond Tip", submitted to Physical Review B. 44. Yunsic Shim and Jacques G. Amar , "Synchronous sublattice algorithm for parallel kinetic Monte Carlo", to be submitted. 45. Yunsic Shim and Jacques G. Amar, "Synchronous relaxation algorithm for parallel kinetic Monte Carlo", (in preparation). 46. Leach, J. E. & Hsu, W. H. (2003). REU supplement to: Inducible Ac elements for activation-tagging and PCR-based detection of deleted genes in rice. NSF Plant Scientific Data Research Program. Distributed from URL: http://www.kddresearch.org/REU/Summer2003. 47. Welge, M. et al., (2003). Data to Knowledge (D2K) v3.0. National Center for Supercomputing Applications (NCSA) Automated Learning Group (ALG). Distributed from URL: http://alg.ncsa.uiuc.edu. 48. Hsu, W. H., Harmon, S. J., Johanes, R., & Thornton, J. A. (2003). Bayesian Network Tools in Java (BNJ) v2.. Kansas State University Laboratory for Knowledge Discovery in Databases. Distributed from URL: http://sourceforge.net/projects/bndev 49. A. F. Voter, F. Montalenti, T. C. Germann, “Extending the time scale in atomistic simulation of materials”, Annu. Rev. Mater.Res. 32, 321 (2002). 50. A.B. Bortz, M.H. Kalos, and J.L. Lebowitz, "A New Algorithm for Monte Carlo Simulation of Ising Systems", J. Comp. Phys. 17, 10 (1975). 51. A.F. Voter, "Classically exact overlayer dynamics: Diffusion of rhodium clusters on Rh(100)", Phys. Rev. B 34, 6819 (1986). 52. P.A. Maksym, "Fast Monte Carlo simulation of MBE growth", Semicond. Sci. Technol. 3, 594 (1988). 53. J.Y. Tsao, Materials Fundamentals of Molecular Beam Epitaxy, World Scientific, Singapore, (1993) 54. A.-L. Barabasi and H.E. Stanley, Fractal Concepts in Surface Growth, Cambridge University Press, New York, 1995 55. N.C. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, and E. Teller, “Equation of State Calculations by Fast Computing Machines," J. Chem. Phys. 21, 6 (1953). 56. O.S. Trushin, P. Salo, T. Ala-Nissila,PRB, {\bf 62}, p.1611 (2000). 57. P. Salo, J. Hirvonen, I.T. Koponen, O.S. Trushin, J. Heinonen, T. Ala-Nissila , PRB, {\bf 64} , p. 161405-I (2001). 58. S.C. Wang, U. Kurpick, G. Ehrlich, Surface diffusion of compact and other clusters: Ir on Ir(111), Phys. Rev. Lett., 81, p.4923 (1998). 59. S.C. Wang, G. Ehrlich, Diffusion of large surface clusters: direct observations on Ir(111), Phys. Rev. Lett. 79, p. 4234 (1997). 60. A. F. Voter, Phys. Rev. B 57, 13985 (1998). 61. A. F. Voter, J. Chem. Phys. 106, 4665 (1997). 62. M. R. Sørensen, A. F. Voter, J. Chem. Phys. 112, 9599 (2000). 63. G. Henkelman, H. Jonsson, J. Chem. Phys. 115, 9657 (2001). 64. G. Henkelman, H. Jonsson, Phys. Rev. Lett. 90, 116101 (2003). 65. G. T. Barkema, N. Mousseau, Phys. Rev. Lett. 77, 4358 (1996). 66. G. T. Barkema, N. Mousseau, Comput. Mater. Sci. 20, 285 (2001). 67. S.M. Foiles, M.I. Bakes, and M.S. Daw, Phys. Rev. B 33, 798 (1986). 68. O. Trushin, E. Granato, S.C. Ying, P. Salo, T. Ala-Nissila, Phys. Rev. B, 65, p. 241408 (2002). 69. H. Jónsson, G. Mills and K. W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase simulations, ed. by B. J. Berne et al. (World Scientific, Singapore, 1998). 70. Neal, Radford. (1996). Bayesian Learning in Neural Networks. Berlin: Springer-Verlag. 71. Y. Shim and J. G. Amar, “Synchronous Sublattice Algorithm for Parallel Kinetic Monte Carlo Simulations”, submitted to Physical Review E. 72. Y. Shim and J.G. Amar, “Scaling Behavior of Parallel Kinetic Monte Carlo Simulations of Epitaxial Growth Using Synchronous Relaxation”, (in preparation). 73. http://www.beowulf.org/ 74. http://www.stephenwolfram.com/publications/articles/ca. 75. I. Foster. Designing and Building Parallel Programs. Addison-Wesley, 1995. 76. J. Butler and V. Wallentine. A Performance Study of the RPE Mechanism for PDES, In Proceedings of the 1994 International Workshop on Modeling, Analysis and Simulation of Computer and Telecommunications Systems, Edited by Madisetti, Gelenbe and Walrand, IEEE Computer Society Press, Jan., 1994. 77. J. Butler and V. Wallentine. Vignettes: A Distributed Discrete Event Simulation System, Proceedings of IEEE IPCCC-91, Phoenix, AZ, March, 1991. 78. J. Butler and V. Wallentine. Message Bundling in Time-Warp, Proceedings of the Workshop on Parallel and Distributed Simulation, Anaheim, CA., Jan. 1991. 79. B. Shirazi, A. Hurson, and K. Kavi. Scheduling and Load Balancing in Parallel and Distributed Systems, Wiley, 2003. 80. M. Mizuno, L. Chen, and V. Wallentine. Synchronization in a Thread-Pool Model and its Application in Parallel Computing. Submitted to: 2004 International Conference on Application of Concurrency to System Design. 81. M. Dwyer and V. Wallentine. A Framework for Parallel Adaptive Grid Simulations. Concurrency: Practice and Experience, 9(11), pp. 1293-1310, November, 1997 82. Object-oriented coordination abstractions for parallel software. In Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA97), June 1997. 83. G. Andrews. Foundations of Multithreaded, Parallel, and Distributed Programming. Addison-Wesley, 2000.