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<H1><A NAME="top"></A>Robert Fraczkiewicz</H1>
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<H3><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Job Objective</H3>
<DL>
<DD>Research position related to molecular modelling where creative
approach to problem solving and strong programming skills are required.
</DL>
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<H4>Table of contents</H4>
<DL>
<DT><A HREF="#education">Education</A>
<DT><A HREF="#awards">Awards</A>
<DT><A HREF="#computer">Computer Skills</A>
<DT><A HREF="#languages">Languages</A>
<DT><A HREF="#research">Research Experience</A>
<DT><A HREF="#industrial">Industrial Experience</A>
<DT><A HREF="#teaching">Teaching Experience</A>
<DT><A HREF="#publications">List of Publications</A>
<DT><A HREF="#references">References</A>
<DT><A HREF="#contact">Contact</A>
<DT><A TARGET="_top" HREF="cv_grace.html">My wife's resume</A>
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<H3><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Immigration Status</H3>
<DL>
<DD>Authorized to work in the United States; based on the approved
National Interest Waiver. Permanent residence case in progress.
</DL>
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<H3><A NAME="education"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Education</H3>
<DL>
<DT><I>1991 - 1996</I>
<DD>Ph.D. degree in Computational Chemistry and Raman Spectroscopy of
Biological Molecules, University of Houston, Houston, Texas, U.S.A.
GPA = 3.91/4.0.
<DT><I>1995</I>
<DD>Inorganic Biochemistry Summer Workshop, University of Georgia, Athens, Georgia,
U.S.A.
<DT><I>1995</I>
<DD>Molecular Modeling and Drug Design Workshop, North Carolina Supercomputing
Center, Research Triangle Park, North Carolina, U.S.A.
<DT><I>1988 - 1989</I>
<DD>Graduate Computer Study: Computer Applications in Chemistry, Technical
University of Wroclaw, Wroclaw, Poland. GPA = 5.0/5.0.
<DT><I>1982 - 1988</I>
<DD>M.Sc. degree in Theoretical Chemistry and Spectroscopy, Wroclaw
University, Wroclaw, Poland. Overall GPA =4.5/5.0, major GPA = 4.9/5.0.
</DL>
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<H3><A NAME="awards"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Awards</H3>
<DL>
<DT><I>1995</I>
<DD>The Pennzoil Company Graduate Fellowship.
<DT><I>1995</I>
<DD>Sigma Xi Graduate Student Research Achievement Award.
<DT><I>1994</I>
<DD>Chemistry Alumni at Shell Development Scholarship.
<DT><I>1993</I>
<DD>R.B. Seymour Outstanding First Year Teaching Assistant.
<DT><I>1993</I>
<DD>Dow Chemical Company Foundation Scholarship.
<DT><I>1992 - 1993</I>
<DD>Welch Research Fellowship.
<DT><I>1983 - 1988</I>
<DD>Outstanding Student Scholarship, Wroclaw University, Poland.
<DT><I>1982</I>
<DD>Laureate of The XXX-th Polish Physics Olympiad.
<DT><I>1981</I>
<DD>Laureate of The XXVII-th Polish Chemistry Olympiad.
</DL>
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<H3><A NAME="computer"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Computer Skills</H3>
<DL>
<DT><I>Languages</I>
<DD>FORTRAN,C, Turbo Pascal, BASIC, HTML,
<A TARGET="_top" HREF="http://www.scsb.utmb.edu/getarea/area_form.html">CGI</A>,
PostScript, OOGL, LaTeX, shell scripting, learning C++. 11 years of experience
in computer programming.
<DT><I>Operating Systems</I>
<DD>Unix (SGI IRIX and CRAY UNICOS), VMS, DOS, Windows 3.1 and 95,
Macintosh OS, Nuclear Data.
<DT><I>Platforms</I>
<DD>Various Silicon Graphics workstations, CRAY J90, VAX, IBM PC,
Apple Macintosh.
<DT><I>System Administration</I>
<DD>Unix (four years of experience), system security, WWW server.
<DT><I>Networking</I>
<DD>TCP/IP (socket programming), Ethernet, AppleTalk.
<DT><I>Software</I>
<DD>Experienced user of a wide variety of molecular simulations, modeling
and graphics packages, word processing, spreadsheets, programming tools,
system tools, etc. Too numerous to count :).
</DL>
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<H3><A NAME="languages"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Languages</H3>
<DL>
<DT>
<DD>Polish, English, Russian.
</DL>
<HR>
<H3><A NAME="research"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Research Experience</H3>
<DL>
<DT><I>1996-present</I>
<DD><B>Research Associate</B>, University of Texas Medical Branch,
Galveston, Texas, U.S.A. Computer modeling of protein folding and
structure prediction, protein energy refinement and Monte Carlo
simulations with hydrophobic surface area potentials. Continuum models
of protein-solvent interactions.
<P>
<UL>
<LI>Maintained and developed program
<A TARGET="_top" HREF="http://www.scsb.utmb.edu/fantom/fm_home.html">
FANTOM</A> designed for molecular modeling of proteins
[<A HREF="#publications">12,14,24</A>].
<LI>Created a novel <A TARGET="_top" HREF="http://www.scsb.utmb.edu/comp_biol.html/poster1/">
efficient algorithm</A> of calculating the exact
<A TARGET="_top" HREF="http://www.scsb.utmb.edu/getarea/area_form.html">
solvent accessible surface area</A> of proteins and its analytical
derivatives based on the Gauss-Bonnet theorem
[<A HREF="#publications">12,19,20</A>]. This <U>exact</U> algorithm matched
the best <U>approximate</U> numerical methods in terms of computational
speed.
<LI>Performed diverse studies on structure prediction of a number of
proteins, including the HIV Rev protein (regulator of the expression of
virion) [<A HREF="#publications">19</A>] and inhibitors of apoptosis:
Bcl-X<sub>L</sub> and Bcl-2 [<A HREF="#publications">22</A>].
<LI>Studied the role of protein-solvent interaction energy terms in the
structure prediction and refinement of small globular proteins based on
Monte Carlo simulations [<A HREF="#publications">20,21,23,24</A>].
</UL>
<P>
<DT><I>1991-1996</I>
<DD><B>Research Assistant</B>, University of Houston, Houston, Texas, U.S.A.
Theoretical vibrational spectroscopy of biological molecules, normal
mode analysis, Raman spectroscopy, structure and dynamics of metalloproteins
and metalloporphyrins.
<P>
<UL>
<LI>Created original algorithms for (a) regularized least-squares
optimization immune to numerical ill-conditioning, (b) automatic
elimination of coordinate redundancies and (c) force constant selection
[<A HREF="#publications">6,7</A>]. These tools were implemented into a
novel method for harmonic force field refinement.
<LI>Wrote a new and complete software package RAMVIB for normal
coordinate analysis (7000+ lines of code)
[<A HREF="#publications">6,9</A>].
<LI>Solved a number of important, previously intractable vibrational
problems of oxyhemocyanins [<A HREF="#publications">2</A>], heme
proteins [<A HREF="#publications">8</A>], blue copper proteins [<A
HREF="#publications">3,4,6,10</A>], the cytochrome oxidase
Cu<sub>A</sub> subunit [<A HREF="#publications">5</A>], and
Fe<sub>2</sub>O<sub>2</sub> core of iron proteins
[<A HREF="#publications">11</A>].
<LI>Wrote a software package for Fourier analysis of molecular dynamics
trajectories produced by program CHARMM
[<A HREF="#publications">18</A>].
</UL>
<P>
<DT><I>1989-1991</I>
<DD><B>Staff Scientist</B>, Radioisotope Laboratory, Technical
University of Wroclaw, Wroclaw, Poland. Nuclear physics, chemistry and
electronics. Gamma-ray spectrometry of naturally occuring radionuclides.
<P>
<UL>
<LI>Proficient in nuclear electronics. Set up a complete gamma spectrometry
system; designed a novel sample holding and shielding equipment.
<LI>Designed and developed an original gamma-spectrometric method for
quantitative analysis of samples containing natural radioactive elements;
wrote data analysis software [<A HREF="#publications">1</A>].
<LI>Generated an automatic technique of time-dependent gamma photon counting.
Used to study kinetics of ion flotation with radioactive tracers.
<LI>Taught a computer course for chemistry teachers. Designed and developed
educational software.
</UL>
</DL>
<HR>
<H3><A NAME="industrial"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Industrial Experience</H3>
<DL>
<DT><I>1988</I>
<DD><B>Practical Trainee</B>, Chemitex-Viscoplast, Wroclaw, Poland.
<P>
<UL>
<LI>Received an extensive industrial experience in medical supplies company;
supervised groups of people (6-8); performed market research concerning
self-adhesive tapes for industry.
</UL>
<P>
<DT><I>Summer 1987</I>
<DD><B>Hourly Worker</B>, Polifarb, Wroclaw, Poland (paint industry).
</DL>
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<H3><A NAME="teaching"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Teaching Experience</H3>
<DL>
<DT><I>1991-1993</I>
<DD><B>Teaching Assistant</B>, University of Houston, Houston, Texas, U.S.A.
<P>
<DT><I>1990-1991</I>
<DD><B>Lecturer</B>, Technical University of Wroclaw, Wroclaw, Poland.
Computer course for chemistry teachers.
<P>
<DT><I>1986-1988</I>
<DD><B>Practical Trainee</B>, Wroclaw, Poland. Taught chemistry and physics
at the level of middle and high school.
</DL>
<HR>
<H3><A NAME="publications"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">List of Publications</H3>
<OL>
<B>Articles</B>
<P>
<LI>Fraczkiewicz, R. and Walkowiak, W. (1992) "Calculations of an
Effective Solid Angle Including Self-Absorption Correction Applied to
Gamma-Ray Spectrometry Analysis of Natural Samples" <I>Nucl. Instr. Meth.
Phys. Res.</I>, <B>B71</B>, 434.
<P>
<LI>Ling, J.; Nestor, L.P.; Czernuszewicz, R.S.; Spiro, T.G.; Fraczkiewicz, R.;
Sharma, K.D.; Loehr, T.M. and Sanders-Loehr, J. (1994) "Common Oxygen Binding Site
in Hemocyanins from Arthropods and Mollusks. Evidence from Raman
Spectroscopy and Normal Coordinate Analysis" <I>J. Am. Chem. Soc.</I>, <B>116</B>,
7682.
<P>
<LI>Czernuszewicz, R.S.; Fraczkiewicz, G.; Fraczkiewicz, R.; Dave, B.C. and
Germanas, J.P. (1995) "Ground and Excited State Dynamics of Blue Cu Active Site
from Resonance Raman Spectroscopy of Azurin" in <I>Spectroscopy of Biological
Molecules</I>, Ed. Merlin, J.C.; Kluwer Academic Publishers, Dordrecht; The
Netherlands, p 273.
<P>
<LI>Fraczkiewicz G.; Fraczkiewicz, R.; Germanas, J. and Czernuszewicz, R.S. (1996)
"Vibrational Mode Mixing in Azurin" in <I>Proceedings of the XV-th
International Conference on Raman Spectroscopy</I>, August 11-16,
Pittsburgh, PA, U.S.A.; Ed. Asher, S.A.; Stein, P.; John Wiley & Sons,
New York, p. 404.
<P>
<LI>Andrew, C.R.; Fraczkiewicz, R.; Czernuszewicz, R.S.; Lappalainen,
P.; Saraste, M. and Sanders-Loehr, J. (1996) "Identification and
Description of Copper-Thiolate Vibrations in the Dinuclear
Cu<sub>A</sub> Site of Cytochrome <I>c</I> Oxidase" <I>J. Am. Chem.
Soc.</I>, <B>118</B>, 10436.
<P>
<LI>Fraczkiewicz, R. (1996) "Methods for Theoretical Vibrational Analysis of
Biological Molecules Containing Transition Metal Ions. Development and
Applications." Ph.D. Thesis, University of Houston, Houston, TX, U.S.A.
<P>
<LI>Fraczkiewicz, R. and Czernuszewicz, R.S. (1998) "A New Algorithm for
Solving an Inverse Eigenvalue Problem in Vibrational Spectroscopy. I.
Theory" (submitted for publication).
<P>
<LI>Fraczkiewicz, R. and Czernuszewicz, R.S. (1998) "A New Algorithm for
Solving an Inverse Eigenvalue Problem in Vibrational Spectroscopy. II.
Metalloporphyrins" (in preparation).
<P>
<LI>Fraczkiewicz, R. and Czernuszewicz, R.S. (1997) "
<A TARGET="_top" HREF="ftp://ccl.osc.edu/pub/chemistry/software/SGI/ramvib/">RAMVIB</A>
: A New Flexible Normal Mode Analysis Software for Biological Spectroscopists"
<I>J. Mol. Struct.</I>, <B>435</B>, 109-121.
<P>
<LI>Fraczkiewicz, R.; Fraczkiewicz, G. and Czernuszewicz, R.S. (1998)
"Description of Normal Modes of Vibration in the Mononuclear Blue
Copper Site of <I>Pseudomonas aeruginosa</I> Azurin" (submitted for
publication).
<P>
<LI>Wilkinson, E.C.; Dong, Y.; Zang, Y.; Fujii, H.; Fraczkiewicz, G.;
Fraczkiewicz, R.; Czernuszewicz, R.S. and Que, L. Jr. (1998) "The Raman
Signature of the Fe<sub>2</sub>O<sub>2</sub> 'Diamond' Core" <I>J. Am. Chem.
Soc.</I>, <B>120</B>, 955-962.
<P>
<LI>Fraczkiewicz, R. and Braun, W. (1998) "Exact and Efficient Analytical
Calculation of the Accessible Surface Areas and Their Gradients for
Macromolecules" <I>J. Comp. Chem.</I>, <B>19</B>, 319-333.
<P>
<LI>Fraczkiewicz, R. and Braun, W. (1998) "Exploring Energy Landscapes
of Globular Proteins With and Without Solvation" (in preparation).
<P>
<LI>Fraczkiewicz, R. and Braun, W. (1998) "Homology Modeling
with Program FANTOM Using Multiple Templates" (in preparation).
<P>
<B>Posters</B>
<P>
<LI>Fraczkiewicz, R. and Czernuszewicz, R.S. "Vibrational Inverse
Eigenvalue Problem of Macromolecules" presented at <I>The Fourth Annual
Retreat on Computational Biology</I>; W.M. Keck Center for Computational
Biology; November 12, 1993; Houston, TX, U.S.A.
<P>
<LI>Fraczkiewicz, R. and Czernuszewicz, R.S. "A New Method of Force
Field Refinement Applied to Spectroscopically Large Molecules" presented
at <I>The Sigma Xi Research Day</I>; University of Houston; April 1995;
Houston, TX, U.S.A.
<P>
<LI>Fraczkiewicz, R. and Czernuszewicz, R.S. "Resonance Raman Spectrocsopy
of Azurin from <I>Pseudomonas aeruginosa</I> and Normal Mode Analysis Reveal
Complex Dynamics of Blue Copper Proteins" presented at the <I>Inorganic Biochemistry
Summer Workshop</I>; University of Georgia; July 29, 1995; Athens, GA,
U.S.A.
<P>
<LI>Fraczkiewicz, R.; Pettitt, B.M. and Czernuszewicz, R.S. "Extracting
Vibrational Modes from Molecular Dynamics Simulations: A Review of Some
FT-Based Methods" presented at <I>The Fifth Annual Retreat on Computational
Biology</I>; W.M. Keck Center for Computational Biology; September 15,
1995; Galveston, TX, U.S.A.
<P>
<LI>Fraczkiewicz, R. and Braun, W. "A New Efficient Algorithm for
Calculating Solvent Accessible Surface Areas of Macromolecules" presented
at the <I>1996 Retreat on Computational Biology</I>; W.M. Keck Center for
Computational Biology; September 13, 1996; Galveston, TX, U.S.A.
<P>
<LI>Fraczkiewicz, R. and Braun, W.
<A TARGET="_top" HREF="http://www.scsb.utmb.edu/comp_biol.html/poster1/">
"A New Efficient Algorithm for
Calculating Solvent Accessible Surface Areas of Macromolecules"</A>
presented at the
<A TARGET="_top" HREF="http://hackberry.chem.niu.edu/ECCC3/"><I>
Third Electronic Computational Chemistry Conference</I></A>; Northern
Illinois University; November 1996; World Wide Web.
<P>
<LI>Zhu, H.; Fraczkiewicz, R. and Braun, W. "Combining Secondary Structure
Prediction with Self-Correcting Distance Geometry Calculations: Application
to HIV-1 Rev Protein Modeling" presented at the <I>41st Annual Meeting of
Biophysical Society</I>; March 2-6, 1997; New Orleans, LA, U.S.A. Abstract
in <I>Biophys. J.</I>, <B>72</B>, A74 (1997).
<P>
<LI>Fraczkiewicz R. and Braun, W. "Use of Atomic Solvation Energy Terms
in the Refinement of Protein Structures. A New Algorithm Applied to Avian
Pancreatic Polypeptide (APP)" presented at the <I>Texas Protein Folders
Meeting '97</I>; March 21-23, 1997; Camp Allen, TX, U.S.A.
<P>
<LI>Fraczkiewicz R. and Braun, W. "Use of Atomic Solvation Energy Terms
in the Refinement of Protein Structures" presented at the <I>1997 Structural
Biology Symposium</I>; April 11-13, 1997; Galveston, TX, U.S.A.
<P>
<LI>Fraczkiewicz, R. and Braun, W. "The Program
<A TARGET="_top" HREF="http://www.scsb.utmb.edu/fantom/fm_home.html">
FANTOM</A> for Monte Carlo
Simulations and Energy Refinement of Polypeptides and Proteins" presented
at the <I>Annual Research Conference on Computational Biology</I>; September
12, 1997; Galveston, TX, U.S.A.
<P>
<LI>Fraczkiewicz, R. and Braun, W. "The Application of Different
Solvation Models in Monte Carlo Simulations of Small Globular
Proteins: How Well Can They Discriminate Native Structures?" presented
at the <I>Computational Biomedicine Symposium</I>; December 5-7, 1997;
Baylor College of Medicine, Houston, TX, U.S.A.
<P>
<LI>Fraczkiewicz, R. and Braun, W. "Does an Atomic Force Field Distinguish
Native Protein Structures?" presented at the <I>42nd Annual Meeting of
Biophysical Society</I>; February 22-26, 1998; Kansas City, Missouri, U.S.A.
Abstract in <I>Biophys. J.</I>, <B>74</B>, A282 (1998).
<P>
<LI>Fraczkiewicz, R. and Braun, W. "Exploring Energy Landscapes of
Globular Proteins" presented at <I>The Third Annual Structural Biology
Symposium</I>; April 3-5, 1998; Galveston, TX, U.S.A.
</OL>
<HR>
<H3><A NAME="references"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">References</H3>
<DL>
<DT>
<DD>References are available upon request.
</DL>
<HR>
<H3><A NAME="contact"></A><IMG SRC="blueball.gif" WIDTH="14"
HEIGHT="14" ALIGN="BOTTOM" NATURALSIZEFLAG="3">Contact</H3>
<DL>
<DT><I>Mail:</I>
<DD> University of Texas Medical Branch<BR>
Dockside Building R#1157<BR>
Galveston, TX 77555, U.S.A.
<DT><I>E-mail:</I>
<DD><A HREF="mailto:robert@simulations-plus.com">robert@simulations-plus.com</A>
<DT><I>Phone:</I>
<DD>(409) 747-6806
<DT><I>Web:</I>
<DD><A TARGET="_top" HREF="http://www.scsb.utmb.edu/comp_biol.html/robert/">
http://www.scsb.utmb.edu/comp_biol.html/robert/</A>
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