Yuefan Deng

 

A-135, Physics Tower, Applied Mathematics Department

and

Computational Science Lab

358, Center for Excellence in Wireless and Information Technology

 

Stony Brook University, Stony Brook, NY 11794-3600

 

Center for Computational Sciences

Brookhaven National Lab, Upton, NY 11973

 

Tel: +1 (631) 632-8614

E-mail: Yuefan.Deng@StonyBrook.edu

 

Version 04.28.2012

Education

BS

Physics (with honors)

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, New York University

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 (Sabbatical)

Hong Kong University of Science and Technology

 

1997--1999

Adjunct Professor

Biomedical Eng., Stony Brook University

 

1999--2000

Researcher (Sabbatical)

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

 

2009--

Associate Dean

International Academic Programs, Stony Brook University

 

2009--

Deputy Director

Confucius Institute, Stony Brook University

 

2010--2011

Adjunct Professor

Columbia University

 

 

Main Research Topics

Awards

  1. Supervisor of an InStar Award Finalist, 2011
  2. Outstanding Teacher Awards for 2004, 2005, 2009, 2010, Spring 2011, Fall 2011
  3. Supervisor of a James Simons Scholar, 2009
  4. Award of US$1,000,000 for Establishing Confucius Institute at Stony Brook University by the Chinese Ministry of Education. (Jointly with W. Arens) 2008
  5. IBM Shared University Research (SUR) Award, 2005
  6. Presidential (Stony Brook University) Award for Innovative Teaching, 1996
  7. IBM Faculty Award, 1994
  8. Certificate of Service to Mentor Program, 1993,1994,1996,1997
  9. Engineering Dean's Award for Excellence in Research, 1993
  10. Supervisor of a Westinghouse Award Finalist, 1993
  11. Excellent Student Award of Nankai University, 1983

 

Patents

  1. An Ultra-scalable Supercomputer Based on MPU Architecture; Pub No. US 8,159,973; Patent Date: Apr 17, 2012; Inventors: Y. Deng, A. Korobka, and P. Zhang
  2. System for Balance Distribution of Requests Across Multiple Servers Using Dynamic Metrics; Patent No.: US 6,938,256 B2; Pub. No.: US 2006/0036743 A1; Inventors: Y. Deng, S. Engel, J. Guistozzi, and T. O'Brien
  3. Method and System for Providing Dynamic Hosted Service Management Across Disparate Accounts and Sites; Patent No.: US 7,693,9935 B2; Inventors: K. Sheets, Y. Deng, et al
  4. A Mixed Torus and Hypercube Multi-rank Tensor Expansion Method. Patent No.: 2009/0024829 A1, Pub. Date: Jan. 22, 2009; Inventors: Y. Deng and P. Zhang
  5. A Master Processing Unit with Self-consistent Expandable Internal and External Networks. China Patent No.: ZL 2006 1 0029753.0 (Granting date: 5/10/2010); Inventors: Y. Deng and P. Zhang
  6. A Self-Consistent Multi-rank Tensor Expansion Scheme and Multi-MPU Parallel Computing Systems. China Patent No.: ZL 2006 1 0030472.7 (Granting date: 4/7/2010); Inventors: Y. Deng and P. Zhang.
  7. Routing Strategies for Cellular Networks in MPU Architectures. China Patent Application No.: 200610117704.2 (2006); China Patent No.: ZL 2006 1 0117704.2 (Granting date: 10/28/2009); Inventors: P. Zhang and Y. Deng.
  8. 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
  9. An Ultra-scalable Supercomputer System Based on MPU, China Patent No.: 200710044230.8 (Patent date: 10/13/2010); Inventors: Y. Deng, A. Korobka, and P. Zhang
  10. A MPU with Self-consistent Expandable Networks. US Patent Application No.: 11833994 (08/04/2007); Inventors: Y. Deng and P. Zhang
  11. A Tensor Expansion Scheme and Multi-MPU Systems. US Patent Application No.: 11845014 (08/24/2007); Inventors: Y. Deng and P. Zhang.
  12. 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. China’s Ministry of Science and Technology (863 Program) (Co-PI, 2009-, part-time)
  2. Shanghai Commission of Science and Technology (Co-PI, 2009-, part-time)
  3. NIH, R21 (Co-PI, 3/1/2011-2/28/2013)
  4. China’s Ministry of Science and Technology (863 Program) (PI, 2006-2007 during sabbatical)
  5. Shanghai Commission of Science and Technology (PI, 2006-2007 during sabbatical)
  6. NSF. Four Projects (PI for two and Co-PI for two.)
  7. DOE. Two Projects (Co-PI for two.)
  8. ARO. One Project (one of the two Co-PIs.)
  9. NIH. Two Projects (Consultant for both projects.)
  10. New York State. Three Projects (PI for one and Co-PI for two.)
  11. Architect for Galaxy: an 800-Gflops Beowulf Supercomputer Called Galaxy
  12. Chief Architect for Nankai Stars Supercomputer (Fastest Computer in China as of Feb 2004, #42 on Top500 when released,)
  13. St. Jude Research Hospital (Award: 26446; 2002-2004)
  14. Brookhaven National Laboratory (Award: 26944; 2002-)
  15. Brookhaven National Laboratory (LDRD; 2003, 2004, 2005)
  16. IBM Shared University Research (SUR) Grant (2005)

Former and Current Students

  1. Na Zhang (Ph.D. student, starting 1/2012, Stony Brook Univ.), Coarse-grained modeling of platelet activation and parallel computing
  2. Seetha Pothapragada (Ph.D. student, starting 1/2011, Stony Brook Univ.), A new approach for analyzing and improving supercomputer network performances
  3. Dr. Peng Zhang (Ph.D., 2012, now Postdoctoral Fellow, BME at Stony Brook Univ.,), A Methodology for Design and Applications of Parallel Computers
  4. Vijay Viswanathan (Simons Scholar, Summer 2011)
  5. Dr. Riwei Wang (Ph.D., 2011, for Nankai University, now Associate Professor of Tianjin Institute of Technology, China), Efficient Parallel Algorithms for Multi-scale Collocation Physically Realistic Light Rendering
  6. Jonathan Goldman (Simons Scholar, Summer 2010, now at Carnegie Mellon University)
  7. Dr. Yuxiang Gao (Ph.D., 2010, now Dell HPC), An algebraic representation of the task mapping for parallel computing
  8. Dr. Reid Powell (Ph.D., 2010, now Bloomberg R&D), Analysis of supercomputers and development of a novel network
  9. Dr. Yongzhi Chen (Ph.D., 2008, now Scientist III, Life Sciences, San Jose), Task Mapping on Supercomputers with Cellular Networks
  10. Dr. Fang Bin (Ph.D., 2007, now Senior Financial Engineer), Parallel FFT Algorithms and Their Applications to MD
  11. Dr. Xin Chen (Physics, Ph.D., 2007, now Shanghai Jiaotong University, China), MD Modeling of a Biotoxin in Various Temperature and pH Environments and Another Protein Interacting with Small Molecules
  12. Dr. Janet Braunstein (Ph.D., 2007, now Assistant Professor at the US Military Academy at West Point), Analysis of Task Mapping for Parallel Supercomputers
  13. Wang Fang (MS, 2007 Nankai University; now Texas A&M), Benchmark Two Applications on Supercomputers of Various Networks
  14. Yang Liang (MS, 2007 Nankai University, now at Google China), Benchmark Molecular Dynamics NAMD on MPU
  15. Min Xuebin (MS, 2006 at Nankai University, now at IBM China), Analysis and simulation of the MPU Mesh Network
  16. Dr. Peter Rissland (Ph.D., 2006, now senior engineer of a software company), MDOC: A Molecular Dynamics Application Framework for the QCDOC Supercomputer
  17. Dr. Guowen Han (Ph.D., 2006, now Senior Financial Analyst), Analysis of Multi-scale Molecular Dynamics Algorithms for Simulating Biomolecules
  18. Dr. Alex Korobka (Ph.D., 2002, now Chief Technology Official for a financial company at Wall Street), Protein-DNA Binding Simulation on Parallel Computers
  19. 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
  20. Carlos Rivera (MS, 1999), Load Balance and Automatic Mesh Refinement
  21. Dr. Chung-Chiang Chou (Ph.D., 1996, now Associate Professor at Tai-Chong Teacher's University, Taiwan), Comparison of Several Parallel Simulated Annealing Methods
  22. Dr. Yuan Wang (Ph.D. 1996, now at SynQuest Software), Inventory Modeling on Parallel Processors
  23. Dr. R. Alan McCoy (Ph.D., 1995), Parallel MD for Film Deposition
  24. Dr. Jose Gomezva (Ph.D., 1994), Parallel Algorithms for Circulation Models, Co-supervised with D. P. Wang (Stony Brook Marine Science)
  25. Konstantin Strauch (MA, 1995), Genetic Linkage Analysis of Complex Diseases, Co-supervised with M. Wigler (Cold Spring Harbor Lab)
  26. Dr. Yue Zhuge (MA, 1994; Ph.D. 1998 at Stanford University; now at Microsoft China), Parallel Front Tracking

Textbooks

  1. Y. Deng and Z. Lou, Calculus IV with Many Examples, Published by  Copley Custom Textbook/XanEdu  (Edition 1: 7/2009; Edition 2: 1/2011)
  2. Y. Deng, Applied Parallel Computing, Supplementary material for the Stony Brook AMS530 (Parallel Computing).  World Scientific (Accepted for publication, 2009)

Publications

1.     Y. Deng, A. Ramos, and J. Hornos, Group theory insights for design of supercomputer network topologies, Int. J. Mod. Phys. (Submitted 2/2012)

2.     R. Feng, P. Zhang and Y. Deng, Simulated Performance Evaluation of a 6D Mesh/iBT Interconnect, SNPD 2012. (Accepted 5/2/2012)

3.     P. Zhang and Y. Deng, An Analysis of the Topological Properties of the Interlaced Bypass Torus (iBT) Networks, Applied Mathematics Letters. (Submitted 4/2012)

4.     Y. Deng and P. Zhang, Perspectives on Exascale Computing, New Computing Architectures and Applications, Vol.1. pp 8-22 (9/2010)

5.     P. Zhang, Y. Gao, J. Fierson, and Y. Deng, An Eigenanalysis-based Task Mapping on Parallel Computers with Cellular Networks, Math. Comp. (2nd Rev. submitted 10/2011)

6.     Y. Deng, C. Marques, R. Powell and P. Zhang, Analysis of power and Linpack efficiencies of the world's Top 500 supercomputers, J. Parallel Comp. (2nd Rev. in progress)

7.     P. Zhang and Y. Deng, Design and Analysis of Pipelined Broadcast for the All-Port Interlaced Bypass Torus Networks, IEEE Trans. Parallel and Distributed Systems (Accepted 2/2012)

8.     P. Zhang, R. Powell, and Y. Deng, Interlacing Bypass Rings to Torus Networks for Generating more Efficient Networks, IEEE Trans. Parallel and Distributed Systems Vol. 22 Issue 2  (2011) pp. 287-295

9.     F. Feng, M. Xenos, G. Girdhar, J. Davenport, Y. Deng, D. Bluestein, Viscous Flow Simulation in a Stenosis Model Using Discrete Particle Dynamics: A Comparison Between DPD and CFD, Biomechanics and Modeling in Mechanobiology Vol. 11 Issues 1-2  (2012) pp. 119-129

10.  T. Yamaguchi, T. Ishikawa, Y. Imai, N. Matsuki, M. Xenos, Y. Deng, D. Bluestein,  Particle Based Methods for Multiscale Modeling of Blood Flow in the Circulation and in Devices– Challenges and Future Directions, Annals of Biomedical Eng. 2009; 38(3): 1225–1235

11.  Y. Chen and Y. Deng, A Detailed analysis of communication load balance on BlueGene supercomputer, Comp. Phys. Comm., 180 (2009), pp 1251-1258

12.  Y. Deng, A. Korobka, Z. Lou, and P. Zhang, Perspectives on Petascale Processing, KISTI Supercomputer, Vol. 31 (2008), pp. 36-59 

13.  Y. Chen and Y. Deng, Task mapping on supercomputers with cellular networks, Comp. Phys. Comm. 179 (2008), pp. 479-485

14.  X. Chen and Y. Deng, Simulations of a specific inhibitor of the disheveled PDZ domain, J. Mol. Modeling, Vol. 15 (2009), pp. 91-96

15.  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

16.  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

17.  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

18.  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)

19.  B. Fang and Y. Deng, and G. Martyna, Parallel FFT on QCDOC supercomputer, Comp. Phys. Comm. 176 (2007) 531-538

20.  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

21.  X. Chen and Y. Deng, Botulinum structures at various temperatures and pH values, J. Mol. Modeling, 13 (5) (2007) 559-572

22.  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

23.  Y. Deng, J. Glimm, and J. Davenport, Global Communication Schemes on QCDOC, IEEE Transactions on Parallel and Distributed Computing.

24.  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

25.  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)

26.  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

27.  Y. Deng and A. Korobka, Performance of a supercomputer Built with Commodity Components, Parallel Computing, Vol. 27 Issues 1-2 (2001), pp. 91-108

28.  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.

29.  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

30.  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

31.  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

32.  K. Chu, Y. Deng, and J. Reinitz, Parallel Simulated Annealing Algorithms by Mixing States, Journal of Computational Physics. Vol. 148 (1999), pp. 646-662

33.  Y. Deng and C. Rivera, Simple energy minimization for huge Lennard-Jones clusters by dramatic parameter reduction, Applied Math Letters Vol. 12, (1999) pp. 119-125

34.  Y. Deng and C. Rivera, Approximate energy minimization for Large Lennard-Jones clusters, Journal Global Optimization. 16 (2000) pp. 325-341

35.  Y. Deng and R. Peierls, An Asynchronous Decomposition Approach to Parallel Global Optimization, Applied Math Letters. Vol. 11 (1998), pp. 55-59

36.  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

37.  Y. Qian and Y. Deng, A Lattice BGK Model for Viscoelastic Media, Physical Review Letters. Vol.79 No.14 (1997), pp. 2742-2746

38.  R. Alan McCoy and Y. Deng, Parallel embedded-atom method simulations with delayed electron density approximations, Computer Physics Communications, 100 (1997), pp. 41-46

39.  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

40.  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) pp. 96-100

41.  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.

42.  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) pp. 1333-1339

43.  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) pp. 405-417

44.  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) pp. 103-122

45.  C-C Chou and Y. Deng, Decomposing 40 Billion Integers by Four Tetrahedral Numbers, Math. Comp. V. 66 N 218 (1997) pp. 893-901

46.  Y. Deng, J. Glimm, Q. Yu, and M. Eisenberg, Global Minimization for Problems with Multiple Local Minima, Appl. Math. Lett. Vol 6 (1993) pp. 89-90

47.  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) pp. 49-69

48.  Y. Deng, A. McCoy, R. Marr, R. Peierls, and O. Yasar, Molecular dynamics on distributed-memory MIMD computers with load balancing, Appl. Math Letters, V. 8 (3) (1995) pp. 37-41

49.  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) pp. 95-100

50.  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) pp. 645-651

51.  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) pp. 1712-1725.

52.  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) pp. 719-726.

53.  Y. Deng and C. N. Yang, Waring's Problem for Pyramidal Numbers, Science in China (Series A), 37 (3), (March 1994) pp. 377-383

54.  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) pp. 1-12

55.  Y. Deng, J. Glimm, and D. Sharp, Mixing and Chaotic Microstructure, Los Alamos Science November Vol. 21 (1993)  pp.124-132

56.  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) pp. 2929-2937

57.  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) pp. 248-256

58.  Romy Hoque and Y. Deng, Frontiers for the Teraflop in the 21st Century in CSI Communications. Vol. 17 Num. 1 (1993) pp. 5-12

59.  Y. Deng and C. N. Yang, Eigenvalues and eigenfunctions of the Huckel Hamiltonian carbon-60, Physical Letters A, Vol. 170 (1992) pp. 116-126.

60.  Y. Deng, J. Glimm, and D. H. Sharp, Perspectives on Parallel Computing, Daedalus Vol 12 (1992) pp. 31-52

61.  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) pp. 377-391

62.  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.

63.  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

64.  Y. Deng, Simulating lattice gauge theory on special-purpose supercomputers, Ph.D. Thesis Columbia University (1989).  Generous reference to my thesis.

65.  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) pp. 334-339

66.  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) pp. 238-241, World Scientific, Singapore