Yuefan Deng

Tel: 1 (631) 877-7979

Email: Yuefan.Deng@StonyBrook.edu
URL: http://www.ams.sunysb.edu/~deng

 

A-135, Physics Tower, Applied Mathematics Department
Stony Brook University, Stony Brook, NY 11794-3600

Center for Computational Sciences

Brookhaven National Lab, Upton, NY 11973

Version 07.02.2008

Education

BS

Physics (with Honor)

Nankai University, China

1983

MA

Physics

Columbia University

1985

M. Phil.

Physics

Columbia University

1986

Ph.D.

Theoretical Physics

Columbia University

1989

Postdoctoral

Applied Mathematics

Courant Institute, NYU

1989

 

Academic Experience

1989--1990

Visiting Assistant Professor

Stony Brook University

 

1991--1994

Assistant Professor

Stony Brook University

 

1994--1998

Associate Professor

Stony Brook University

 

1999-- 

Professor

Stony Brook University

 

1993--2001

Director, Center for Scientific Computing

Stony Brook University

 

1995--1996

Visiting Associate Professor

Hong Kong University of Science and Technology

 

1997--1999

Adjunct Professor

Biomedical Eng., Stony Brook University

 

1999--2000

Researcher

IBM Watson Research Center

 

1998

Visiting Faculty

Los Alamos National Lab

June/July

1999--

Lab Associate

Brookhaven National Lab

 

2001-- 

Advisory Board Member

Institute of Computational Physics, Beijing

 

2002--2006

Special Guest Professor

Nankai University, China

 

2002--2006

Director

Nankai Institute of Scientific Computing

 

Main Research Topics

1.         Parallel Computing

2.         Molecular Dynamics

3.         Monte Carlo Methods

4.         Computational Physics

5.         Computational Biology

Awards

1.         Excellent Student Award of Nankai University, 1983

2.         Engineering Dean's Award for Excellence in Research, 1993

3.         Supervisor of a Westinghouse Award Winner, 1993

4.         Presidential (SUNY-Stony Brook) Award for Innovative Teaching, 1996

5.         Certificate of Service to Mentor Program, (93,94,96,97)

6.         Distinguished Teaching (fall 2004, fall 2005)

Patents

1.         System for Distributing Requests Across Multiple Servers Using Dynamic Metrics; Patent No.: US 6,938,256 B2; Inventors: Y. Deng, S. Engel, J. Guistozzi, and T. O'Brien

2.         Method and System for Providing Dynamic Hosted Service Management Across Disparate Accounts and Sites; Patent No.: US 6,816,905 B1; Inventors: Y. Deng, et al

3.         A Master Processing Unit with Self-consistent Expandable Internal and External Networks. China Patent Application No.: 200610029753.0 (2006); Inventors: Y. Deng and P. Zhang

4.         A Self-Consistent Multi-rank Tensor Expansion Scheme and Multi-MPU Parallel Computing Systems. China Patent Application No.: 200610030472.7 (2006); Inventors: Y. Deng and P. Zhang.

5.         Routing Strategies for Cellular Networks in MPU Architectures. China Patent Application No.:200610117704.2 (2006); Inventors: Y. Deng and P. Zhang

6.         A Mixed Torus and Hypercube Multi-rank Tensor Expansion Method. China Patent Application No.: 200710042397.0 (06/220/2007); Inventors: P. Zhang and Y. Deng

7.         An Ultra-scalable Supercomputer System Based on MPU, China Patent Application No.: 200710044230.8 (07/26/2007); Inventors: Y. Deng, A. Korobka, and P. Zhang

8.         A MPU with Self-consistent Expandable Networks. US Patent Application No.: 11833994 (08/04/2007); Inventors: Y. Deng and P. Zhang

9.         A Tensor Expansion Scheme and Multi-MPU Systems. US Patent Application No.: 11845014 (08/24/2007); Inventors: Y. Deng and P. Zhang.

10.      Routing Strategies for Cellular Networks in MPU Architecture. US Patent Application No.: 11925944 (11/06/2007); Inventors: Y. Deng and P. Zhang.

Research Leadership Experience

1.         NSF. Four Projects (PI for two and Co-PI for two.)

2.         DOE. Two Projects (Co-PI for two.)

3.         ARO. One Project (one of the two Co-PIs.)

4.         NIH. Two Projects (Consultant for both projects.)

5.         New York State. Three Projects (PI for one and Co-PI for two.)

6.         Architect for Galaxy: an 800-Gflops Beowulf Supercomputer Called Galaxy

7.         Chief Architect for NankaiStars Supercomputer (Fastest Computer in China as of Feb 2004, #42 on Top500 when released,)

8.         St. Jude Research Hospital (Award: 26446; 2002-2004)

9.         Brookhaven National Laboratory (Award: 26944; 2002-)

10.      Brookhaven National Laboratory (LDRD; 2003, 2004, 2005)

11.      IBM Shared University Research (SUR) Grant (2005)

12.      Chief Architect for the RedNeurons Supercomputer (China Ministry of Science and Technology, PI, 2006-2007)

13.      Software and Algorithms for the RedNeurons Supercomputer (Shanghai Commission of Science and Technology, PI, 2006-2007)

 

Former and Current Students

    1. Yuxiang Gao, Linear Algebra Library for QCDOC
    2. Zhang Peng (MS 2006 Nankai University, Ph.D. student, Stony Brook U),  Mathematical Analysis and Modeling of Networks for Ultrascalable Supercomputers
    3. Reid Powell, Analysis of Parallel Computing Networks
    4. Zhihao Lou, Parallel Monte Carlo Methods
    5. Dr. Yongzhi Chen (Ph.D., 2008), Task Mapping on Supercomputers with Cellular Networks
    6. Dr. Fang Bin (Ph.D., 2007, now Senior Financial Engineer), Parallel FFT Algorithms and Their Applications to MD
    7. Dr. Xin Chen (Physics, Ph.D., 2007, now Senior Financial Engineer), MD Modeling of a Biotoxin in Various Temperature and pH Environments and Another Protein Interacting with Small Molecules
    8. Dr. Janet Braunstein (Ph.D., 2007, now assistant professor at the US Military Academy at West Point), Analysis of  Task Mapping for Parallel Supercomputers
    9. Wang Fang (MS 2007 Nankai University; now study at Texas A&M), Benchmark Two Applications on Supercomputers of Various Networks
    10. Yang Liang (MS 2007 Nankai University, now at Google China), Benchmark Molecular Dynamics NAMD on MPU
    11. Min Xuebin (MS 2006 at Nankai University, now at IBM China), Analysis and simulation of the MPU Mesh Network
    12. Dr. Peter Rissland (Ph.D. 2006, Postdoc in BME at Stony Brook), MDOC: A Molecular Dynamics Application Framework for the QCDOC Supercomputer (Thesis in PDF)
    13. Dr. Guowen Han (Ph.D. 2006, now working for Financial Analysis), Analysis of Multi-scale Molecular Dynamics Algorithms for Simulating Biomolecules (Thesis in PDF)
    14. Dr. Alex Korobka (Ph.D. 2002, now in Shanghai), Protein-DNA Binding Simulation on Parallel Computers (Thesis in PDF)
    15. Dr. King-Wai Chu (Ph.D. 2001, now at Mt. Sinai Medical School), Optimal Parallelization of Simulated Annealing by State Mixing, Co-supervised with J. Reinitz
    16. Carlos Rivera (MS 1999), Load Balance and Automatic Mesh Refinement
    17. Eric Roman (Now at LLNL), Galaxy Project
    18. Dr. Chung-Chiang Chou (Ph.D. 1996, now at Teacher's University, Taiwan), Comparison of Several Parallel Simulated Annealing Methods
    19. Dr. Yuan Wang (Ph.D. 1996 now at SynQuest Software), Inventory Modeling on Parallel Processors
    20. Dr. R. Alan McCoy (Ph.D. 1995), Parallel MD for Film Deposition
    21. Dr. Jose Gomezva (Ph.D. 1994), Parallel Algorithms for Circulation Models, Co-supervised with D. P. Wang (Stony Brook Marine Science)
    22. Konstantin Strauch (MA 1995), Genetic Linkage Analysis of Complex Diseases, Co-supervised with M. Wigler (Cold Spring Harbor Lab)
    23. Dr. Yue Zhuge (MA 1994; Ph.D. 1998 at Stanford University; now at Microsoft China), Parallel Front Tracking

 

Textbooks

    1. Y. Deng, Ordinary Differential Equations and Laplace Transform, Supplementary material for the Stony Brook AMS361 (Calculus IV) students, Published by the University Book Store/XanEdu  (Jan 23, 2008)
    2. Y. Deng, Applied Parallel Computing, Supplementary material for the Stony Brook AMS530 (Parallel Computing) students, (In preparation for publication, 2008)

 

Publications

    1. Y. Chen and Y. Deng, Detailed analysis of communication load balance on BlueGene supercomputer, Comp. Phys. Comm., Submitted  (July, 2008)
    2. Y. Deng, A. Korobka, Z. Lou, and P. Zhang, Perspectives on Petascale Processing, KISTI Supercomputer, Vol. 31 (2008), pp. 36-59 
    3. Y. Chen and Y. Deng, Task mapping on supercomputers with cellular networks, Comp. Phys. Comm. 179 (2008), pp. 479-485
    4. X. Chen and Y. Deng, Simulations of a specific inhibitor of the disheveled PDZ domain, J. Mol. Modeling, Submitted (Dec 13, 2007); Accepted (Sept, 2008)
    5. P. Zhang and Y. Deng, Design and analysis of new interconnection networks for ultra-scalable supercomputers, IEEE Transactions on Computers. (submitted May 17, 2007)
    6. K. Oh and Y. Deng,  A efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations, Comp. Phys. Comm. 177 (2007), pp. 426-431
    7. B. Fang, G. Martyna, and Y. Deng, A fine grained parallel smooth particle mesh Ewald algorithm for biophysical simulation studies: applications to the 6D torus supercomputer, Comp. Phys. Comm.  177 (2007), pp. 362-377
    8. Y. Chen, X. Chen, and Y. Deng, Simulating Botulinum Neurotoxin with Constant pH Molecular Dynamics in Generalized Born Implicit Solvent, Comp. Phys. Comm.  177 (2007), pp. 210-213
    9. P. Rissland and Y. Deng, Supercomputers and their effects on molecular dynamics, IEEE Potentials, April/May Issue, 9-12 (2005). Chinese Translation appeared in China Computer World Vol. 34 (May 2005)
    10. B. Fang and Y. Deng, and G. Martyna, Parallel FFT on QCDOC supercomputer, Comp. Phys. Comm. 176 (2007) 531-538
    11. Y. Deng, A. Korobka, and B. Xiang, Nankai Stars: A Supercomputer by and for computational scientists, Int. J. High Perf. Comp. App. (Submitted 1/2006)
    12. G. Han, Y. Deng, J. Glimm, G. Martyna, Error and timing analysis of multiple Time Stepping for MD, Comp. Phys. Comm.  176 (2007), pp. 271-291
    13. X. Chen and Y. Deng, Botulinum structures at various temperatures and pH values, J. Mol. Modeling, 13 (5) (2007) 559-572
    14. P. Rissland and Y. Deng, Structure and performance of molecular dynamics package MDoC on QCDOC, Parallel Computing, (Submitted, 2/2006)
    15. P. Rissland and Y. Deng, All-gather on QCDOC, Parallel Computing, (Submitted 09/2006)
    16. Y. Deng, J. Glimm, J. Davenport, X. Cai, and E. Santos, Performance Models on QCDOC for Molecular Dynamics with Coulomb Potentials, Int. J. High Performance Computing Applications. Vol. 18, Num. 2  (2004) 183-198
    17. Y. Deng, J. Glimm, and J. Davenport, Global Communication Schemes on QCDOC, IEEE Transactions on Parallel and Distributed Computing.
    18. B. Li and Y. Deng: Biography of Prof Chen Ning Yang (in Chinese, Word format), Biographies of Contemporary Chinese Scientists, Vol. 3 (1994). English translation (in PDF) appears in "C. N. Yang: A Great Physicist of the 20th Century", Chapter 19, edited by C. S. Liu and S.-T. Yau.
    19. O. Yasar and Y. Deng, D. Saltz, and R. Tuzun: Guest Editors for New Trend in High Performance Computing, Special Issue of Parallel Computing. Vol. 27 Issues 1-2 (2001)
    20. N. Stojic and J. Glimm and Y. Deng and J. Haus, Transverse magnetic modes in two-dimensional triangular photonic crystals Phys. Rev. E, Vol. 64 (2001), pp. 1-7
    21. Y. Deng and A. Korobka, Performance of a supercomputer Built with Commodity Components, Parallel Computing, Vol. 27 Issues 1-2 (2001), pp. 91-108
    22. Y. Deng, J. Glimm, Y. Wang, A. Korobka, M. Eisenberg, and A. P. Grollman, Prediction of Protein Binding to DNA in the Presence of Water-Mediated Hydrogen Bonds, Journal of Molecular Modelling. Vol. 5 (1999) 125-133.
    23. S. Chen, Y. Deng, and X. Nie, Y. Tu Clustering Kinetics of Granular Media in Three Dimensions, Physical Letters, Vol. 269 (2000), pp. 218-223.
    24. K. Chu and Y. Deng, Quick Minimization of Total Energy of Large Lennard-Jones Clusters, Grand Challenges in Computer Simulation, Proceedings of ASTC Conference. Ed. Adrian Tentner, San Diego, CA (1999), pp. 37-42
    25. Y. Deng, R. Peierls, and C. Rivera, An adaptive load balancing method for parallel molecular dynamics simulations (in pdf or ps), Journal of Computational Physics. Vol. 161 (2000), pp. 250-263
    26. K. Chu, Y. Deng, and J. Reinitz, Parallel Simulated Annealing Algorithms by Mixing States, Journal of Computational Physics. Vol. 148 (1999), pp. 646-662
    27. Y. Deng and C. Rivera, Simple energy minimization for huge Lennard-Jones clusters by dramatic parameter reduction, Applied Math Letters Vol. 12, (1999) 119-125. SUNYSB-AMS-97-20
    28. Y. Deng and C. Rivera, Approximate energy minimization for Large Lennard-Jones clusters, Journal Global Optimization. V. 16 (2000) 325-341. or in PDF.
    29. Y. Deng and R. Peierls, An Asynchronous Decomposition Approach to Parallel Global Optimization, Applied Math Letters. Vol. 11 (1998), pp. 55-59.
    30. J. Asvestas, Y. Deng, J. Glimm, and F.Tangerman, Electromagnetic Scattering from large cavities, Communications of Applied Analysis Vol. 2, Num. 1 (1998), pp. 37-48
    31. Y. Qian and Y. Deng, A Lattice BGK Model for Viscoelastic Media, Physical Review Letters. Vol.79 No.14 (1997), pp. 2742-2746
    32. R. Alan McCoy and Y. Deng, Parallel embedded-atom method simulations with delayed electron density approximations, Computer Physics Communications, 100 (1997), pp. 41-46
    33. R. Alan McCoy and Y. Deng, Parallel Particle Simulations of Thin-Film Deposition, Int. J. High Performance Computing Applications, Vol. 13, No. 1 (1999), pp. 16-32
    34. Y. Deng, M. Mu, and C-C Chou, Numerical Methods for Simulating Ginsburg-Landau Vortices, in Proceedings of High Performance Computing 1996, Ed. Adrian Tentner, San Diego, CA (1996) 96-100
    35. Y. Deng and R. A. McCoy, Computing Sticking Coefficients for Cu-Cu by Localized Molecular Dynamics on Parallel Processors, in Proceedings of High Performance Computing 1996, Ed. Adrian Tentner, San Diego, CA (1996) 18-24.
    36. Y. Deng and Y. Wang, A Multi-location Inventory Model and its Parallel Heuristic Optimization, submitted to Advances in Computational Economics, 1996
    37. M. Mu, Y. Deng, and C-C Chou, Ginsburg-Landau Vortices for Type-II Superconductors: A Numerical Study, SIAM J. Sci. Comp. V. 19, No 4, (1998) 1333-1339.
    38. C-C. Chou and Y. Deng, Numerical Solutions of a Nonlinear Evolution System with Small Dissipation on Parallel Processors, J. Sci. Comp. Vol. 13 No. 4 (1998) 405--417.
    39. Y. Wang and Y. Deng, Multi-item stochastic inventory models with constraints and their parallel computation, in Computational Economic Systems: Models. Methods and Econometrics, Advances in Computational Economics, Vol. 5 (1996) 103-122.
    40. C-C Chou and Y. Deng, Decomposing 40 Billion Integers by Four Tetrahedral Numbers, Math. Comp. Vol. 66 N 218 (1997) 893-901.
    41. Y. Deng, J. Glimm, Q. Yu, and M. Eisenberg, Global Minimization for Problems with Multiple Local Minima, Appl. Math. Lett. Vol 6 (1993) 89-90.
    42. C-C Chou, Y. Deng, G. Li, and Y. Wang, Parallelizing Strassen's method for matrix multiplication on distributed- memory MIMD architectures, in International Journal of Computers and Mathematics with Applications, 30 (2) (1995) 49-69.
    43. Y. Deng, A. McCoy, R. Marr, R. Peierls, and O. Yasar, Molecular dynamics on distributed-memory MIMD computers with load balancing, Appl. Math Letters, 8 (3) 1995 (37-41)
    44. Y. Deng, R. A. McCoy, R. B. Marr, R. F. Peierls and O. Yasar, Molecular dynamics for 400 million particles with short-ranged interactions, Proceedings of High Performance Computing 1995, San Diego, CA (1995) 95-100
    45. Y. Deng, R. A. McCoy, R. B. Marr, and R. F. Peierls, An Unconventional Method for Load Balancing, 7th SIAM Conference on Parallel Processing, San Francisco, CA (1995) 645-651.
    46. G. Campbell, Y. Deng, J. Glimm, M. Eisenberg, and A. Grollman, Analysis and prediction of hydrogen bonding of protein-dna complexes on parallel processors, J. Comp. Chem, Vol 17 (15) (1996) 1712-1725.
    47. J. Asvestas, B. Bielefeld, Y. Deng, J. Glimm, and F.Tangerman, Boundary integral methods applied to electromagnetic scattering problems on parallel processors, Proc. Amer. Math. Soc. Vol 122 (1994) 719-726.
    48. Y. Deng and C. N. Yang, Waring's Problem for Pyramidal Numbers, Science in China (Series A), 37 (3), March 1994, 377-383.
    49. Hu Wang, Y. Deng, J. L. Stephenson, and R. Tewarson, An efficient algorithm for solving n-nephron models of the Renal Inner Medilla, International Journal of Computers and Mathematics with Applications, 28 (5) (1994) 1-12.
    50. Y. Deng, J. Glimm, and D. Sharp, Mixing and Chaotic Microstructure, Los Alamos Science November Vol. 21 (1993) 124-132
    51. Y. Chen, Y. Deng, J. Glimm, G. Li, D. Sharp, and Q. Zhang, A renormalization group scaling analysis for compressible two-phase flow, J. Phys. Fluids A 5 (11) (1993) 2929-2937
    52. G. Campbell, Y. Deng, J. Glimm, and Q. Yu, Analysis and prediction of protein binding on dna: pattern recognition of hydrogen bonds, in High Performance Computing and its Applications in the Physical Sciences (1993) 248-256
    53. Romy Hoque and Y. Deng, Frontiers for the Teraflop in the 21st Century in CSI Communications. Vol. 17 Num. 1 (1993) 5-12
    54. Y. Deng and C. N. Yang, Eigenvalues and eigenfunctions of the Huckel Hamiltonian carbon-60, Physical Letters A, Vol. 170 (1992) 116-126.
    55. Y. Deng, J. Glimm, and D. H. Sharp, Perspectives on Parallel Computing, Daedalus Vol 12 (1992) 31-52
    56. Y. Chen, Y. Deng, J. Glimm, and G. Li, Parallel Interface Methods for Multi-phase Flow Problems on iPSC/860, in Intel Supercomputer Systems Conference Proceedings: Technology Focus Conference (1992) 377-391
    57. Y. Deng and J. Glimm, Fluid Dynamics Using Interface Methods on Parallel Processors in Parallel CFD. Implementations and Results Using Parallel Computers Ed. Horst Simon, MIT Press (1992) 257-270.
    58. F. Brown, N. Christ, Y. Deng, T. Woch, and M. Gao, Nature of the deconfining phase transition in SU(3) gauge theory Phys. Rev. Lett. 61 (1988) 2058-2062
    59. Y. Deng, Using Over-relaxed Microcanonical Update to Perform Canonical Average for Lattice Gauge Theory State Univ. of New York at Stony Brook Report No. ITP-SB-88-80 (1988)
    60. Y. Deng, Simulating lattice gauge theory on special-purpose supercomputers, Ph.D. Thesis Columbia University (1989).  Generous reference to my thesis.
    61. Y. Deng, Energy density and pressure in SU(3) Lattice Gauge Theory at Finite Temperature ed. A. S. Kronfeld and P. B. Mackenzie, Nuclear Physics B (Proc. Suppl.) 9 (1989) 334-339, North-Holland.
    62. Y. Deng, The performance of the microcanonical updating algorithm, ed. K. Haller et al. in Proceedings of the Storrs Meeting on Particles and Fields, (1989) 238-241, World Scientific, Singapore