Job Objective

Software R&D in molecular simulations and drug discovery which requires strong programming skills, extensive experience of macromolecular structures, and solid background in mathematical physics and chemistry.

Education

1992.7,  Ph.D. Computational Chemistry, Jilin University, China
1989.7,  M. S. Computational Chemistry, Jilin University, China
1982.7,  B. S. Chemistry, Wuhan University, China

Computer Skill

• Languages:
• Proficient in C, Java, Fortran, and Tcl/Tk scripting.


• Skilled in GUI and CGI applications, HTML, LaTeX, PostScript, and shell scripting.


• Knowledge of C++ and Perl.


• Operating Systems:
• UNIX (IBM AIX, SGI IRIX, and CRAY UNICOS); LINUX.
• VAX/VMS; DOS, Windows.


• Platforms:
• Silicon Graphics, IBM RISC/6000, CRAY J90, VAX, PC, and Macintosh.


• Networking:
• TCP/IP, Socket programming in Tcl.


• Softwares:
• Experienced user of application packages in semiempirical and ab initio quantum chemistry, molecular simulations, modeling, and molecular graphics; e.g., Gaussian, Mopac, X-plor, Diana, Molmol, Quanta, GCG, Methematica, and tools for bioinformatics.

Research Experience

• 1999.5 - present, College of Pharmacy, University of Texas, Austin.

Development of novel theory and software for computer-assisted drug design (CADD).
• 1996.6 - 1999.4, Postdoc fellow, Sealy Center for Structure Biology, University of Texas Medical Branch.
  Development of software tools and 3D structure modeling of important protein drug targets.
• Design and development of program MASIA (Multiple Aligned Sequences Investigation and Analysis) based on pattern recognition with GUI;
• Improvement and develepment of program DIAMOD (DIstance geometry Algorithm for MODelling): implementation of Quasi-Newton method and different optimization protocols in variable target function algorithm to improve the performance and convergence;
• Residue-specific-pairing propensities in -sheet of proteins;
• 3D modeling and molecular dynamics simulations of UV glycoslase PBCV-1 complexed with photodamaged DNA.
• 1993.6 - 1996.5, Postdoc Fellow, Theoretical Chemical Physics, Texas A&M University at Galveston.
• Fullerenes and nano-tubes: 3D structures and their computational chemistry;
• Structural classification and isomer identification via graphs, topology, and groups;
• Structure-property and structure-activity correlations.

References

References are available upon request.

Publications

• ZHU H, Schein CH, Braun W. Homology Modeling and Molecular Dynamics Simulations of PBCV-1 Glycosylase Complexed with UV-damaged DNA. J.Mol.Model. 5, 302 (1999).
• ZHU H, Braun W. Sequence specificity, statistical potentials, and 3D structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins. Protein Sciences 8, 326 (1999).
• Klein DJ, ZHU H. Distances and volumina for graphs. J. Math. Chem. 23, 179 (1998).
• ZHU H, Klein DJ, March NH, Rubio A. Small band-gap graphitic CBN layers. J. Phys. Chem. Solids 59, 1303 (1998).
• ZHU H, Klein DJ, Schmalz TG, Rubio A, March NH. Geometric boundary effects on the electronic properties of finite carbon nanotubes. J. Phys. Chem. Solids 59, 417 (1997).
• Klein DJ, ZHU H, Garcia-Bach MA, Valenti R. Many-body valence-bond theory. Int. J. Quantum Chem. 65, 421 (1997).
• ZHU H, Klein DJ. Buckyball super-polyhedra. Croat. Chim. Acta 70, 519 (1997).
• ZHU H, Schmalz TG, Klein DJ. Alternate boron nitride cages: a theoretical study. Int. J. Quantum Chem. 63, 393 (1997).
• ZHU H, Klein DJ. Graph-geometric invariants for molecular structures. J. Chem. Inf. Comput. Sci. 36, 1067 (1996).
• Balaban AT, Schmalz TG, ZHU H, Klein DJ. Generalizations of the Stone-Wales rearrangement for cage compounds, including fullerenes. J. Mol. Strucut. 363, 291 (1996).
• ZHU H, Klein DJ, Lukovits I. Extensions of the Wiener number. J. Chem. Inf. Comput. Sci. 36, 420 (1996).
• Klein DJ, ZHU H. Resonance in elemental benzenoids. Disc. Appl. Math. 67, 157 (1996).
• ZHU H, Klein DJ. Tetrahedral-symmetry tetrahydrofullerenes. J. Mol. Strucut. 338, 11 (1995).
• Balaban AT, ZHU H, Klein DJ. Fullero-polycoronands. Fullerene Sci. Tech. 3, 133 (1995).
• ZHU H, Klein DJ, Seitz WA, March NH. BN alternants: boron nitride cages and polymers. Inorg. Chem. 34, 1377 (1995).
• Zivkovic T, Randic M, Klein DJ, ZHU H, Trinajstic N. Analytical approach to very large benzenoid polymers. J. Comput. Chem. 16, 517 (1995).
• Randic M, Klein DJ, ZHU H, Trinajstic N, Zivkovic T. Comparative study of large molecules. Highly accurate calculation of a limit for infinit systems from data on finite. Theor. Chim. Acta 90, 1 (1995).
• Randic M, Klein DJ, ZHU H, Trinajstic N, Zivkovic T. Aromatic properties of fully benzenoid polymers. Fizika A3, 61 (1994).
• ZHU H, Balaban AT, Klein DJ, Zivkovic T. Conjugated-circuit computations on two-dimensional carbon networks. J. Chem. Phys. 101, 5281 (1994).
• Jiang Y, ZHU H. Evaluation of level pattern indices. J. Chem. Inf. Comput. Sci. 34, 337 (1994).
• Jiang Y, Xu J, ZHU H. A pictorial evaluation on bonding and antibonding molecular orbitals. Acta Chim. Sin. 51, 527 (1993).
• Jiang Y, ZHU H, Wang G. Spin-correlation orderings and their applications in benzenoid hydrocarbons. J. Mol. Struct. 297, 327(1993).
• ZHU H, Jiang Y. Cluster-Bethe-lattice model for simple lattice systems. Acta Phys. Chim. Sin. 9, 437 (1993).
• ZHU H, Jiang Y. On Huckel-Hubbard correlation diagrams. Acta Chim. Sin. 51, 527 (1993).
• ZHU H, Jiang Y. Localized structure of conjugated hydrocarbons based on spin-spin correlation analysis. Acta Chim. Sin. 50, 772 (1992).
• ZHU H, Peng X, Jiang Y. Analytical formulae of the expansion of total pi-energy. Bull. Chin. Sci. 7, 605 (1992).
• ZHU H, Jiang Y. Clar's structure of benzenoid hydrocarbons and six-electron spin correlation ordering in hexagons. Chem. Phys. Letters 446, 193 (1992).
• Jiang Y, ZHU H, Zhang H, Gutman I. Moment expansion of Huckel molecular energies. Chem. Phys. Letters 159, 159 (1989).

Book Chapter

• Klein DJ, ZHU H. All-conjugated elemental carbon species. in From Chemical Topology to Three-Dimensional Structure, Plenum Press, New York, 1997, pp 297-341.

Conference Presentations

• ZHU H, Klein DJ. Conjugated circuits for polymers. Southwest Theoretical Chemistry Conference, 1993, Austin, Texas.
• ZHU H, Klein DJ, Seitz WA. Buckytubes: correspondences between carbon phase and boron-nitrogen alternants. Southwest Theoretical Chemistry Conference, 1994, Houston, Texas.
• ZHU H, Schmalz TG, Klein DJ. Understading the stabilities for high fullerene: strain and resonances. Southwest Theoretical Chemistry Conference, 1995, Galveston, Texas.
• ZHU H, Fraczkiewicz R, Braun W. Combining Secondary Structure Prediction with Self-Correcting Distance Geometry Calculation: Application to HIV-1 Rev Protein Modelling. Biophysical Society Forty-first Annaul Meeting, 1997, New Orleans, Louisiana.
• ZHU H, Braun W. Folding globular proteins with self-correcting distance geometry calculations. Second Structural Biology Symposium, 1997, Galveston, Texas.
• ZHU H, Braun W. The propensity of -strand-pairing of proteins: statistical studies for pairing potential energy functions. Annual Research Conference on Computational Biology, 1997, Galveston, Texas.
• ZHU H, Braun W. Cross strand interactions on -sheet formation in proteins: sequence specificity, statistical potential and 3D structure prediction with distance geometry calculations. Computational Biomedicine Symposium, Baylor College of Medicine, 1997, Houston, Texas.
• ZHU H, Braun W. Homology modeling and molecular dynamics simulations of PBCV-1 UV glycoslase complexed with damaged DNA. Third Structural Biology Symposium, 1998, Galveston, Texas.
• ZHU H, Schein CH, Braun W. Homology modeling and molecular dynamics simulations of PBCV-1 UV glycoslase complexed with DNA containing a thymidine dimer, Biophysical Society Forty-third Annaul Meeting, 1999, Baltimore, Maryland.