Personal Data

Mugshot
Surname Patchkovskii (Cyrillic spelling)
Given name Serguei (Cyrillic spelling)
Birth date October 2, 1968
Birth place Novosibirsk, Russia
Nationality Russian
Civil status Married
Address (office) Dept. of Chemistry, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4 Canada
Address (home) 2905 Unwin Rd. NW apt. 318B, Calgary, Alberta, T2N 4M5
Phone (office) (403)-220-8204
Phone (home) (403)-282-0274
FAX (403)-289-9488
E-mail patchkov@ucalgary.ca
Status in Canada Permanent resident
Languages Russian (fluent), English (fluent), German (with difficulty)

Executive summary

A highly qualified theoretical chemist (M.Sc.(hons.) Novosibirsk 1990, Ph.D.(summa cum laude) Zürich 1997) with 13 years of experience in information technology and strong problem-solving skills is looking for a faculty position in theoretical or physical chemistry or related field. May also consider an industrial placement in chemical research or information technology offering access to cutting-edge facilities and adequate incentives.

Education

02/1997 Awarded Doctor of Philosophy degree (summa cum laude) for the Dissertation Thesis (in English) on Analytical Computation of First-Order Response Properties in MNDO Methods
03/1993-03/1997 Department of Philosophy II (Postgraduate Studies) of the University of Zürich, Switzerland. Supervisor: Prof. Dr. W. Thiel of the Institute for Organic Chemistry of the University of Zürich
06/1990 Awarded Diploma with Honors in Chemistry (Master of Sciences equivalent) for the Diploma Thesis (in Russian) on Effects of solvation on reactivity of pentacoordinated phosphorus in model enzymes (semiempirical study) Supervisor: Dr. A. Voityuk of the Bioorganic Chemistry Institutre, Novosibirsk
09/1985-06/1990 Department of Natural Sciences of the Novosibirsk State University in Novosibirsk, Russia
09/1984-06/1985 Lavrentyev's school for gifted children with specialization in mathematics and physics (FMSh) in Novosibirsk, Russia
09/1975-06/1984 School No 111 in Novosibirsk, Russia

Employment history

03/1998-present Full-time Postdoctoral Research Associate at the Department of Chemistry of the University of Calgary
03/1997-03/1998 Full-time Postdoctoral Research Associate at the Institute for Organic Chemistry of the University of Zürich, Switzerland
03/1993-03/1997 Full-time Ph. D. Candidate at the Institute for Organic Chemistry of the University of Zürich, Switzerland
11/1991-03/1993 Full-time research associate at Institute for Bioorganic Chemistry of the Russian Academy of Sciences
09/1991-01/1993 Half-time Assistant Instructor in Physical Chemistry at the Natural Sciences Department of the Novosibirsk State University
10/1990-11/1991 Full-time research student at the Institute for Bioorganic Chemistry of the Russian Academy of Sciences
07/1988-08/1989 Half-time Computer Programmer at the Laboratory of Automated Education Systems of the Novosibirsk State University
06/1986-05/1988 Half-time Computer Systems Operator at the Computational Center of the Novosibirsk State University

Employment-Related Skills and Qualifications

Computer languages: C, Fortran, Perl, Mathematica, awk, and 80x86 assembler, C++, Java, HTML, Prolog, C shell, Bourne shell, PDP-11 and IBM System/360 assembler language, VRML 1.0
Graphics programming: Low-level IBM PC, Microsoft Windows, X11 Window System (Unix)
Network programming: NetBIOS (IBM PC), TCP/IP (Unix)
Special skills: Low-level device driver programming on MS DOS and MS Windows systems; Near real-time audio signal processing; Embedded systems programming
Project management: Make, RCS (Revision Control System)
Performance analysis: prof, gprof, pixie, SGI Workshop tools, OSF/1 atom (Unix), Borland Turbo Profiler (MS DOS)
Performance tuning: KAP and VAST preprocessors (Unix), cache blocking and dependence elimination, automated code generation and cloning, reduction to BLAS routines
Systems administration: SGI IRIX, IBM AIX, Compaq Tru64 (Unix), MS DOS, MS Windows
Quantum chemistry applications: Gaussian 92 and 94, Turbomole, MOLPRO, ADF (ab initio and density functional); Ampac, Mopac (semiempirical)

Completed major projects

1998-1999 Construction of the COBALT cluster - one of the largest dedicated computational chemistry resources to date. COBALT (Computers On Benches All Linked Together) consists of 94 Compaq Alpha Personal Workstations 500au connected by a dedicated Fast Ethernet switch. All nodes, which together contain more than 21 gigabytes of memory and 300 gigabytes of scratch disk space are controlled by distributed queuing system (DQS) and can be used as a single computational chemistry resource with PVM and MPI parallel programming libraries. With the peak floating point performance on each node of 1 gigaflop per second, the total construction cost (including all hardware and software) is just cdn$3680 (US$2460 at the February 10, 1999 exchange rate) per gigaflop. Configuration and capabilities of the Cobalt cluster are described on the Internet at http://www.cobalt.chem.ucalgary.ca/. http://www.cobalt.chem.ucalgary.ca/cobalt/gallery.html provides a short guided tour of the Cobalt cluster hardware.

1993-1998 Analytical derivatives of the energy for MNDO-type wavefunctions: Computational routines for the evaluation of the energy gradients for variational and non- variational wavefunctions (including CI), second derivatives of the energy for variational wavefunctions, and NMR shielding tensors in the GIAO-SCF approximation. Computationally efficient expressions for the energy derivatives taking into account simplifications arising from MNDO approximation were developed and verified with prototype implementations in C++ and Mathematica. The final high-performance computer program was implemented in portable Fortran-77, and consists of 75,000 lines of human-produced code in addition to 20,000 lines of computer-generated integral routines. The code is tuned for optimal performance on cache-based workstation and vector supercomputers. Compared to previously available numerical techniques, speedups of several orders of magnitude are obtained for large systems. The code is used extensively in the research performed at the Organic Chemistry Institute of the University of Zürich, as well as elsewhere. It is scheduled for inclusion in the next publicly available version of Prof. Dr. W. Thiel MNDO97 program, and in a future version of UniChem quantum chemistry package (distributed by Oxford Molecular Group, http://www.oxmol.com).

1990-1993 MolDemo: Program for visualization of large molecular systems and their properties on IBM PC-compatible computers, implemented for the Bioorganic Chemistry Institute in Novosibirsk. The program, consisting of 30,000 lines of C and IBM PC assembler code, supports near real-time photorealistic display of molecules with up to 5,000 atoms. Other features of the programs include: Editing of the three-dimensional molecular structures; Construction of small molecules from the libraries of pre-existing fragments; Automated generation of the Z-matrix for use with external quantum-chemical programs; Flexible template-controlled conversion from/to external formats; High quality hardcopy output to printers, plotters, and to graphic files, with screen-independent resolution. MolDemo was used extensively in the studies of the structure and reactivity of proteins and nucleic acids at the Institute. MolDemo (including the complete source code) is freely available on the Internet at http://www.cobalt.chem.ucalgary.ca/ps/moldemo/

1988-1989 GOR: Graphics editor for an embedded LSI-11 computer, implemented for the Laboratory of Automated Education Systems (Novosibirsk State University). The program, consisting of 8,000 lines of C and PDP-11 Assembler code, supports basic interactive image editing operations on an embedded LSI-11 microcomputer with 16 kilowords of memory.

Hobby projects

TrueView, which simulates 262144-color video mode on any VGA adapter by real-time mixing of specially designed color palettes. MS-DOS binary executable of TrueView (which accesses hardware at a very low level and will not work inside the DOS box of Windows or Windows NT) is available at http://www.simtel.net/pub/simtelnet/msdos/vga/trueview.zip or http://www.cobalt.chem.ucalgary.ca/ps/hobby/trueview.zip.

NetBIOS Assist (NBA), which provides remote console control for a PC connected to a NetBIOS network. NBA will not be able to control a Windows session. It is available at http://www.simtel.net/pub/simtelnet/msdos/lan/nba102.zip or http://www.cobalt.chem.ucalgary.ca/ps/hobby/nba102.zip.

pfstat, which displays the list of the currently open files on a DOS or Windows computer by accessing undocumented internal tables of the operating system. Pfstat (including the complete C source code) is available at ftp://garbo.uwasa.fi/pc/sysutil/pfstat.zip or http://www.cobalt.chem.ucalgary.ca/ps/hobby/pfstat.zip.

hdbios, which provides a replacement for IDE hard disk ROM BIOS on IBM PC compatible computers capable of supporting a secondary hard disk controller. It is available at http://www.cobalt.chem.ucalgary.ca/ps/hobby/hdbios.zip.

audiochat, which provides an audio connection between Silicon Graphics and Sun workstations over Internet, using audio-specific compression techniques (CCITT G.711 u- and a-law, Fourier codec) to reduce communication bandwidth. Audiochat (including the complete source code) is available at http://www.cobalt.chem.ucalgary.ca/ps/hobby/audiochat/

Emulating Debugger (EDB), which provides a complete software emulation of Intel 8086 and 8088 CPUs (including many undocumented instructions and features) for the purpose of debugging ill-behaved 8086 programs in the MS-DOS environment. EDB, along with the complete C source code, is available at http://www.cobalt.chem.ucalgary.ca/ps/hobby/edb_gnu.zip.

Port of the public domain version of Mopac (a popular semiempirical quantum chemistry program) to the 32-bit MS-DOS platform using f2c and GCC. The executable binaries and the modified source code are available in the archives of the computational chemistry mailing list at ftp://ftp.ccl.net/pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7/, or at http://www.cobalt.chem.ucalgary.ca/ps/hobby/mopac7/.

Scientific Interests

Scientific Publications

  1. S. Patchkovskii and T. Ziegler, Prediction of EPR g-tensors of transition metal complexes using density functional theory: First applications to some axial d1 MEX4 systems, submitted for publication

  2. S. Patchkovskii and W. Thiel, NMR chemical shifts in MNDO approximation: Parameters and results for H,C,N, and O, J. Comput. Chem., in press

  3. S. Patchkovskii and W. Thiel, C60 dimers: A route to endohedral fullerene compounds?, J. Am. Chem. Soc. 120, 556-563 (1998)

  4. S. Patchkovskii and W. Thiel, Analytical first derivatives of the energy for small CI expansions, Theor. Chem. Accounts 98, 1-4 (1997)

  5. M. Bühl, S. Patchkovskii, and W. Thiel, Interaction energies and NMR chemical shifts of noble gases in C60, Chem. Phys. Lett. 275, 14-18 (1997)

  6. S. Patchkovskii and W. Thiel, Equilibrium yield for helium incorporation into buckminsterfullerene: Quantum-chemical evaluation, J. Chem. Phys. 106, 1796-1799 (1997).

  7. S. Patchkovskii and W. Thiel, Radical impurity mechanisms for helium incorporation into buckminsterfullerene, Helv. Chim. Acta, 80, 495-509 (1997)

  8. S. Patchkovskii and W. Thiel, Theoretical Studies of Helium Incorporation by Buckminsterfullerene, In: Fullerenes, vol. 5, Eds: K.M. Kadish and R.S. Ruoff, Electrochemical Society, Pennington, 1997

  9. S. Patchkovskii and W. Thiel, Analytical second derivatives of the energy in MNDO methods, J. Comput. Chem. 17, 1318-1327 (1996)

  10. S. Patchkovskii and W. Thiel, How does helium get into buckminsterfullerene?, J. Am. Chem. Soc. 118, 7164-7172 (1996)

  11. S. Patchkovskii and W. Thiel, Analytical first derivatives of the energy in the MNDO half-electron open-shell treatment, Theor. Chim. Acta 93, 87-99 (1996)

  12. J. Cioslowski, S. Patchkovskii, and W. Thiel, Electronic structures, geometries, and energetics of highly charged cations of the C60 fullerene, Chem. Phys. Lett. 248, 116-120 (1996)

  13. D. Bakowies, M. Bühl, S. Patchkovskii, and W. Thiel, Theoretical studies on giant fullerenes and on endohedral fullerene complexes, In: Fullerenes, vol. 3, Eds: K.M. Kadish and R.S. Ruoff, Electrochemical Society, Pennington, 1996

  14. S. Patchkovskii and A. Voityuk, The source of the exceptional basicity of the 1,8-tetramethyldiaminonaphtalene, Zh. Phys. Khim (Russ.) 64(6), 1592-1597 (1990)