Publications Refereed Publications




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Curriculum Vita


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Zhijun Wu


Phone: 515-294-8165

Email: zhijun@iastate.edu

Website: http://www.math.iastate.edu/wu

Education



Ph.D., Computational and Applied Mathematics, Rice University, 1991

M.A., Computer Science / Computational Linguistics, Wuhan University, China, 1985

B.Eng., Computer Science, Huazhong University of Sci. and Tech., China, 1982


Professional Experience


Professor, Department of Mathematics, Program on Bioinformatics and Computational Biology, Iowa State University, 2008 --


Associate Professor, Department of Mathematics, Program on Bioinformatics and Computational Biology, Iowa State University, 2000 -- 2008


New Direction Research Professor, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, Minnesota, September 2007 – June 2008


Visiting Professor, Mathematical Biosciences Institute, Ohio State University, Columbus, Ohio, January 2005 – May 2005


Visiting Professor, Laboratory for Scientific and Engineering Computing, Chinese Academy of Sciences, Beijing, China, summer 2005


Visiting Professor, Department of Mathematics, National Institute of Applied Sciences, Rouen, France, summer 2001


Research Scientist, Keck Center for Computational Biology, Rice University, Houston, Texas, January 1999 – August 2000


Staff Scientist, Applications and Benchmarking Group, Tera/Cray Computer Company, Seattle, Washington, September 1997 – December 1998


Senior Research Associate, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, April 1994 – September 1997


Postdoctoral Associate, Advanced Computing Research Institute, Cornell University, Ithaca, New York, June 1991 – April 1994

Research Interests



Computational Biology: Molecular distance geometry, protein structure refinement, simulation of transition of protein conformation, constrained molecular dynamics, potential energy minimization, protein geometry databases, multiscale protein modeling, metabolic network simulation and optimization


Computational Mathematics: Numerical linear algebra, nonlinear optimization, linear programming, integer and combinatorial optimization, numerical solution of ordinary and partial differential equations, parallel high-performance computing

Publications




Refereed Publications:



1. Enhancement of Torsion Angle Constraints in NMR Structure Refinement via Database Derived Distance Constraints, to appear in Journal of Bioinformatics and Computational Biology, 2008 (with Feng Cui and Robert Jernigan)


2. A Penalty-Function Method for Constrained Molecular Dynamics Simulation, to appear in Numerical Analysis and Modeling, 2008 (with Ajith Gunaratne)


3. A Multiple Shooting Algorithm for Solving the Boundary Value Problems in Molecular Dynamics Simulation, to appear in Numerical Analysis and Modeling, 2008 (with Peter Vedell)


4. Dual Stepsize Explicit Numerical Integration Method and Applications, to appear in the Proceedings of the IEEE Power Engineering Society General Meeting, 2008 (with Dan Yang, Tao Jin, and Hengfu Zou)


5. The Solution of the Distance Geometry Problem for Protein Modeling via Geometric Buildup, to appear in BIOMAT 2007 -- International Symposium on Mathematical and Computational Biology, Rubem Mondaini, ed., 2007 (with Di Wu and Yaxiang Yuan)


6 PRTAD: A Protein Residue Torsion Angle Distribution Database, Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, 2007, pp. 24-31 (with Xiaoyong Sun, Di Wu, and Robert Jernigan)


7. Improvement of Under-Determined Loop Regions of Human Prion Protein by Database Derived Distance Constraints, Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, 2007, pp. 14-23 (with Feng Cui, Kriti Mukhopadhyay, Wonbin Young, and Robert Jernigan)


8. Generating Rigid Protein Structures with Sparse Sets of Inter-Atomic and Inter-Residual Distances, Optimization Letters (published online in 2007: DOI: 10.1007/s11590-007-0060-7), 2007 (with Di Wu and Yaxiang Yuan)


9. Solving Large Scale Double Digestion Problems for DNA Restriction Mapping by Using Branch and Bound Integer Linear Programming, in Lecture Notes on Operations Research, Dingzhu Du and Xiangsun Zhang, eds., 2007, pp. 267-279 (with Yin Zhang)


10. Refinement of NMR-Determined Protein Structures with Database Derived Mean Force Potentials, Proteins: Structure, Function, Bioinformatics (published online in 2007: DOI: 10.1002/prot.21358), Vol. 68, 2007, pp. 232-242 (with Di Wu and Robert Jernigan)


11. PIDD: A Protein Inter-atomic Distance Distribution Database, Journal of Nucleic Acid Research (published online in 2006: DOI: 10.1093/nar/gkl802), Vol. 35, 2007, pp. D202-D207 (with Di Wu, Feng Cui, and Robert Jernigan)


12. An Updated Geometric Buildup Algorithm for Solving the Molecular Distance Geometry Problem with Sparse Distance Data, Journal of Global Optimization (published online in 2006: DOI 10.1007/s10898-006-9080-6), Vol. 37, No. 4, 2007, pp. 661-673 (with Di Wu)

13. Refinement of NMR-Determined Protein Structures with Database Derived Distance Constraints, Journal of Bioinformatics and Computational Biology, Vol. 3, 2005, pp. 1315-1330 (with Feng Cui and Robert Jernigan)


14. A Matlab Toolbox for Macromolecular Modeling, in Advances in Bioinformatics and Its Applications, Mathew He, Giri, Narasimhan, and Sergei Petoukhov, eds., 2004, pp. 319-328 (with Feng Cui and Tauqir Bibi)


15. Mathematical Modeling of Protein Structure with Distance Geometry, in Numerical Linear Algebra and Optimization, Y. Yuan, ed., Scientific Press, 2003, pp. 68-80 (with Jeong-Mi Yoon and Yash Gad)


16. A Geometric Buildup Algorithm for Solving the Molecular Distance Geometry Problem with Sparse Distance Data, Journal of Global Optimization, Vol. 26, 2003, pp. 321-333 (with Qunfeng Dong)


17. A Linear-Time Algorithm for Solving the Molecular Distance Geometry Problem with Exact Inter-Atomic Distances, Journal of Global Optimization, Vol. 22, 2002, pp. 365-375 (with Qunfeng Dong)


18. A Fast Newton’s Algorithm for Entropy Maximization in Phase Determination, SIAM Review, Vol. 43, 2001, pp. 623-642 (with George Phillips, Richard Tapia, and Yin Zhang)


19. A Fast Newton’s Method for Entropy Maximization in Statistical Phase Estimation, ACTA Crystallographica, A, Vol. 57, 2001, pp. 681-685 (with George Phillips, Richard Tapia, and Yin Zhang)


20. Distance Geometry Optimization for Protein Structures, Journal of Global Optimization, Vol. 15, 1999, pp. 219-234 (with Jorge Moré)


21. Crash Analysis on the Tera Multi-threaded Architectures, IEEE Journal on Computational Science and Engineering, October-December, 1998, pp. 53--59 (with John Feo and Simon Kahan)


22. Global Continuation for Distance Geometry Problems, SIAM Journal on Optimization, Vol. 7, 1997, pp. 814-836 (with Jorge Moré)


23. Issues in Large Scale Global Molecular Optimization, in IMA Series on Mathematics and Its Applications, Vol. 94, Large Scale Optimization with Applications, L. Biegler, T. Coleman, A. Conn and F. Santosa, eds., Springer-Verlag, 1997, pp. 99-122 (with Jorge Moré)


24. -Optimal Solutions to Distance Geometry Problems via Global Continuation, in Global Minimization of Non-convex Energy Functions: Molecular Conformation and Protein Folding, P. M. Pardalos, D. Shalloway, and G. Xue, eds., American Mathematical Society, 1996, pp. 151-168 (with Jorge Moré)


25. Smoothing Techniques for Macromolecular Global Optimization, in Nonlinear Optimization and Applications, G. Di Pillo and F. Gianessi, eds., Plenum Press, 1996, pp. 297-312 (with Jorge Moré)


26. The Effective Energy Transformation Scheme as a Special Continuation Approach to Global Optimization with Application to Molecular Conformation, SIAM Journal on Optimization, Vol. 6, 1996, pp. 748-768


27. Parallel Continuation-Based Global Optimization for Molecular Conformation and Protein Folding, Journal of Global Optimization, Vol. 8, 1996, pp. 49-65 (with Thomas Coleman)


28. Solving Nonlinear Integer Programs with a Sub-gradient Approach on Parallel Computers, in Applications on Advanced Architecture Computers, Greg Astfalk, ed., SIAM, 1996, pp. 277-286 (with Robert Bixby and John Dennis)


29. A Parallel Buildup Algorithm for Global Energy Minimization of Molecular Clusters Using Effective Energy Simulated Annealing, Journal of Global Optimization, Vol. 4, 1994, pp. 171-185 (with Thomas Coleman and David Shalloway)


30. Isotropic Effective Energy Simulated Annealing Searches for Low Energy Molecular Cluster States, Journal of Computational Optimization and Applications, Vol. 2, 1993, pp. 145-170 (with Thomas Coleman and David Shalloway)

Non-Refereed Publications:



31. (book) Lecture Notes on Computational Structural Biology, to be published by World Scientific Publishing Co., 2008, (250 pages)


32. (book chapter) Linear Algebraic Computing in Biomolecular Modeling, in Encyclopedia of Linear Algebra, Leslie Hogben, ed., Chapman/Hall CRC Press, 2006, pp. 60.1-60.15

33. (book chapter) Parallel Continuous Optimization, in Sourcebook for Parallel Computing, Jack Dongarra, Ian Foster, Geoffrey Fox, Ken Kennedy, Linda Torczon, and Andy White, eds., Morgan Kaufmann, 2002, pp. 640-670 (with John Dennis)

Papers Submitted: (expected to be published in one year)



34. A Geometric Buildup Algorithm for the Solution of the Distance Geometry Problems with the Least-Squares Approximation, 2007, (with Atilla Sit and Yaxiang Yuan)


35. Computation of Thermodynamic Fluctuations of Proteins, 2007 (with Di Wu, Steve Smith, Hanna Mahan, and Robert Jernigan)


36. A Subgradient Algorithm for Nonlinear 0-1-Integer Programming, 2007 (with John Dennis and Robert Bixby)


Papers in Preparation: (expected to be submitted in one year)


37. A Geometric Buildup Algorithm for the Solution of the Generalized Distance Geometry Problem with Distance Intervals, 2006 (with Yaxiang Yuan and Hongchao Zhang)


38. Multiple Protein Structure Alignment and Comparison, 2006 (with Hanna Mahan, Steve Smith, Kyongming Roh, Di Wu)


39. Weighted RMSD with Mean-Square Fluctuations for Protein Structure Alignment and Comparison, 2007, (with Di Wu and Robert Jernigan)


40. A Parallel High-Performance System for Protein Structure Refinement, 2007, (with Rahul Ravindrudu, Ajith Gunaratne, and Di Wu)


Technical Reports:


41. Solving the Molecular Distance Geometry Problem as a Bound-Constrained Minimization Problem, Technical Report, Laboratoire LMI, Département Génie Mathématiques, Institut National Des Sciences Appliquees De Rouen, France, 2002 (with Le Thi Hoai An and Pham Dihn Tao)


42. SMV – An Object-Oriented Sparse Matrix-Vector Computation Class Library – A Programming Manual, Technical Report, TR00-20, Department of Computational and Applied Mathematics, Rice University, 2000 (with Yin Zhang)


43. The Bayesian Statistical Approach to the Phase Problem in Protein X-ray Crystallography, Technical Report, TR99-13, Department of Computational and Applied Mathematics, Rice University, 1999 (with George Phillips, Richard Tapia, and Yin Zhang)


44. Newton's Method for Large Scale Optimization, Technical Report MCS-P635-0197, Mathematics and Computer Science Division, Argonne National Laboratory, 1997 (with Ali Bouaricha and Jorge Moré)


45. Configuration of Large, Confined Ionic Systems by Potential Energy Minimization, Technical Report, Mathematics and Computer Science Division, Argonne National Laboratory, 1996 (with Jorge Moré and Brian Walenz)


46. A Parallel Row Distributed Linear Algebra System -- PRDLA Users' Guide, Technical Report, Advanced Computing Research Institute, Cornell University, 1992 (with Thomas Coleman)

Software Developed



1. PRTAD – A Protein Residue Torsion Angle Distribution Database, Department of Mathematics, Iowa State University, 2007 (with Xiaoyong Sun, Di Wu, and Robert Jernigan, available online: http://www.math.iastate.edu/prtad/)


2. PIDD – A Protein Inter-Atomic Distance Distribution Database, Department of Mathematics, Iowa State University, 2005 (with Di Wu and Robert Jernigan, available online: http://www.math.iastate.edu/pidd/)


3. MTMM – A Matlab Toolbox for Macromolecular Modeling, Department of Mathematics, Iowa State University, 2003 (with Tauqir Bibi and Feng Cui, documented with users’ manual).

4. SMV – An Object-Oriented Sparse Matrix-Vector Computation Class Library, Department of Computational and Applied Mathematics, Rice University, 2000 (with Yin Zhang, documented with users’ manual)


5. DGSOL – A Parallel Molecular Distance Geometry Optimization Package, Mathematics and Computer Science Division, Argonne National Laboratory, 1997 (with Jorge Moré, available in public domain: http://www.mcs.anl.gov/)


6. PRDLA – A Parallel Row Distributed Linear Algebra System, Cornell Theory Center, Cornell University, 1992 (with Thomas Coleman, documented with users’ manual)


Recent Invited Lectures


1. Geometric Approaches to Protein Modeling, Plenary Speaker, BIOMAT International Symposium on Mathematical and Computational Biology, Armacao dos Buzios, RJ, Brazil, November 2007


2. Improvement of Under-Determined Loop Regions of Human Prion Protein by Database Derived Distance Constraints, IEEE Workshop on Computational Structural Biology, San Fracisco, California, October 2007


3. A Geometric Buildup Algorithm for the Solution of the Distance Geometry Problems with the Least-Squares Approximation, International Conference on Numerical Linear Algebra and Optimization, Urumuqi, China, September 2007


4. Applications of Optimization in Computational Biology (lecture series), International Workshop on Optimization and Applications, Beijing, China, October 2006


5. Distance Based Protein Modeling, The 19th International Symposium on Mathematical Programming, Rio De Janeiro, Brazil, August 2006


6. Refinement of Protein Structures with Database Derived Distance Constraints and Mean-Force Potentials, The 32nd Steenbock Symposium on Dynamics of Proteins and Macromolecular Assemblies, University of Wisconsin, Madison, Wisconsin, May 2006

7. Modeling and Simulation of Protein Folding, Scientific Computing Center, Peking University, Beijing, China, June 2005

8. Fast Newton Method for Entropy Maximization, Mathematical Biosciences Institute, Ohio State University, Columbus, Ohio, January 2005


9. Bio-molecular Modeling and Simulation, International Workshop on Perspective of Computational Biology, organized by Chinese Academy of Science and German Max-Planck Society, Shanghai, China, June 2004


10. A Novel Geometric Buildup Algorithm for Solving the Molecular Distance Geometry Problem and Its Application to Multidimensional Scaling, DIMACS Workshop on Multidimensional Scaling, Tallahassee, FL, June 2003


11. A Geometric Buildup Approach to Molecular Distance Geometry Problem, The 4th International Conference on Global Optimization, Santorini, Greece, June 2003

12. Distance Geometry, Graph Embedding, and Structure Determination, University of Iowa and Iowa State University Joint Workshop on Bio-Informatics, Iowa City, Iowa, April 2003


13. Mathematical and Computational Challenges in Protein Structure Prediction and Determination, Laboratory of Mathematics, National Institute of Applied Sciences – Rouen, France, June 2001


14. Macromolecular Modeling: Problems, Approaches, and Challenges, Institute of Engineering and Scientific Computing, Chinese Academy of Sciences, Beijing, China, May 2001


15. A Fast Newton’s Algorithm for Entropy Maximization in Phase Determination, International Conference on Numerical Linear Algebra and Optimization, Dunhuang, China, May 2001


16. Entropy Maximization, Phase Determination, and Convex Programming, The International Conference on Convex Analysis and Global Optimization, Samos, Greece, June 2000


PhD Students Directed


1. Feng Cui, PhD in Bioinformatics; graduated in summer 2005 and joined the NIH National Cancer Institute as a research fellow. Thesis Topics: Distance Based Protein Structure Determination and Refinement. Two papers are published, and two more submitted.


2. Ajith Gunaratne, PhD in Applied Math; graduated in summer 2006 and joined the faculty in Department of Mathematics, Florida A & M University. Thesis Topics: A Penalty Function Method for Constrained Molecular Dynamics. A paper is accepted by Numerical Analysis and Modeling.


3. Di Wu, PhD in Applied Math & Bioinformatics; graduated in summer 2006 and joined the faculty in Department of Mathematics, Western Kentucky University. Thesis Topics: Distance Based Protein Modeling. Three papers are published, one accepted, and one submitted.


4. Peter Vedell, PhD in Applied Math & Bioinformatics; graduated in spring 2007 and joined the Jackson Lab as a postdoctoral associate. Thesis Topics: Multiple Shooting Approaches to Boundary-Value Problems in Molecular Dynamics Simulation. A paper is accepted by Numerical Analysis and Modeling.


5. Rahul Ravindrudu, PhD in Computer Science; expected to graduate in summer 2008. Thesis Topics: A Parallel High-Performance System for Protein Structure Refinement.


6. Vladimir Sukhoy, PhD in Applied Math; expected to graduate in 2010. Thesis Topics: Parallel Schemes for Protein Structure Determination and Dynamics Simulation.


7. Atilla Sit, PhD in Applied Math; expected to graduate in 2010. Thesis Topics: Geometric Approaches to Protein Modeling.


8. Jun-Koo Park, PhD in Applied Math, expected to graduate in 2010. Thesis Topics: Multiscale Modeling for Protein Structure Determination and Dynamics Simulation.




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