> > > > "Pure" biologists are such snobs when it comes to the allied fields. I can > > attest to that in my many failed attempts to cross over from chemistry. But > > don't get me going on that...I want to keep people ON this list :-) > > Sorry you've had negative experiences. BTW I'll only tolerate 2, maybe 3 > hundred more disparaging remarks about 'pure' biologists before leaving in > a huff :) What kind of cross overs were you attempting? > Hi again. Running late. Slow laundry. :) Me, I'm trying to "cross over" from structural/quantum/physical biochemistry into bioinformatics. If there's such a thing as "cross over" there. Baxevanis himself started off as a physical biochemist, so I don't understand the cliquishness I'm experiencing in the field. I have publications, a solid reference group, a nice pedigree as far as education and research experience. What I don't have is the "bioinformatics stamp of approval". Even postdoctoral jobs are being weird. I'm putting my resume below so you can see what I mean about everything I just said. The only thing I can see that I'm lacking is some development package (software) but I'm someone who programs to solve problems lately, so I've been working in FORTRAN. But my experience is pretty far-reaching overall. ---------------------------------------------------------- Objective Biophysical scientist with extensive computing, technical, administration, teaching, and communication experience seeks challenging position in structural bioinformatics, computational biology, and/or other interface between molecular biology, biological sciences, and computing. Education Present: Ph.D. candidate, Biophysics Graduate Program University of Michigan, Ann Arbor, MI. Expected date of Ph.D. Degree Completion: July/August 2000 April 1997 Masters of Science in Biophysics University of Michigan, Ann Arbor MI June 1995 Bachelor of Arts, Double Major: Physics, Astronomy Wellesley College, Wellesley, MA June 1991 Associate of Arts (Honors) North Shore Community College, Lynn, MA. High School: Our Lady of Nazareth Academy, Wakefield, MA. Publications D. M. Taylor and A. Ramamoorthy "Analysis of Dipolar-Coupling Mediated Coherence Transfer in a Homonuclear Two-Spin-1/2 Solid-State System." Journal of Magnetic Resonance, 141, 18-28 (1999) D. M. Taylor and A. Ramamoorthy "Analysis of Dipolar-Recoupled Coherence Transfer in MAS experiments of a Homonuclear Two-Spin-1/2 Solid-State System " (in review) J. Brender, D. Taylor and A. Ramamoorthy "Optimization of Ab Initio Calculations for NMR Tensor Orientations in Peptides" (in review) Research Experience 1/97-present University of Michigan Dr. A Ramamoorthy Chemistry/Biophysics Synopsis: Solid-state NMR theory of dipolar coherence transfer among multiply-labeled spin sites in membrane proteins, and quantum chemical calculations of NMR parameters. Membrane proteins, whose structures are notoriously difficult to study using normal structural biology techniques (solution NMR, x-ray crystallography), can be studied using NMR in the solid state (SSNMR). SSNMR has several challenges which need to be addressed before successful experimental algorithms can be developed to yield useful protein structural information without prohibitive cost or time investment. My research is directed towards using quantum physics and information theory to develop optimal experimental conditions and analytical solutions for information transfer between two or more atoms of the same element (carbon-carbon, for example). The strongest exchange process in SSNMR which both prevents finely resolved spectra yet at the same time provides distance information (r) is the dipolar interaction, which is a strong coupling interaction that acts as 1/r3 . One of the biggest obstacles to the use of SSNMR to solve complex structural biology problems is the understanding, at the quantum level, of how atoms exchange distance information, in our case, carbon-13 atoms in a peptide backbone. This research is particularly relevant to protein samples that have some limited or extensive aspect of diffusional and spatial randomness, such as experienced in proteins integrated into artificial membrane planes, or those in bicelles (small elliptical "pieces" of bilayer membrane). Before this work, it was not known how information exchange would travel through space between carbon backbone atoms in a randomly aligned population of proteins to other spatially proximate but not necessarily directly bonded peptide carbons. After solving the quantum-mechanics equations for information exchange between the peptide carbons, I have simulated, using computer programs, models of the transfer of distance information among peptide backbone carbon atoms. The programs' outputs give the coherent evolution of information exchange over time, frequency, and distance in the quantum spin operators under various experimental conditions for both oriented (crystalline) and unoriented (powder) samples of small proteins and peptides. During the course of my investigations, I have discovered a significant deviation from the simplest predicted models by including scalar coupling effects previously thought insignificant within the peptide unit, as their effects are only two percent of the total coupling, but convoluted over the experimental time of milliseconds, evolution frequency patterns deviate twenty percent or more in phase (and therefore in immediate magnitude). This means that it may be possible to isolate out directly-bonded carbon atoms in a two-dimensional spectrum by examining the phase behavior. It has been established experimentally that high-resolution spectra can be gained by using a method called magic angle sample spinning (MAS) which removes the strong coupling of the dipolar interaction, but loses the distance information as well. However, application of certain multipulse sequences can recouple some of that distance information (dipolar recovery experiments). I have derived the average Hamiltonian for several dipolar-recovery experiments published by other groups (DRAMA, USEME, DRAWS, SEDRA) and worked on solving their particular dipolar coherence transfer. I have determined how the distance information is transferred in the unoriented population in each experiment and have solved the equations of maximal magnetization transfer velocity (distance versus time) as well as sample-dependent transfer (dipolar coupling constant versus time), and established the effects of intra- as well as inter-peptide information exchange, the effects of bonding on distance exchange, and am currently finishing work on adding offset parameters to account for deviation in chemical shifts between the carbons of the peptide plane. At that point, I am confident I can match my results with experimental structure, obtaining, for the first time, analytical equations that can accurately predict the information exchange among the proximate carbons of a folded membrane protein. My secondary project is again interested in solving structures of proteins using NMR, this time calculating the orientations of the peptide plane in respect to the laboratory frame, gathering information in this way on the absolute orientation of the planes to one another. This is done through simulation of chemical shift (NMR) tensor orientations of small proteins on several platform ab initio (quantum chemistry) packages such as Dalton, deMON, Gaussian98, and NWChem. However, modeling NMR experimental constraints must also take into account special factors, such as the contribution of the magnetic field within the magnet to the behavior of the electron orbitals, the accuracy of our basis sets and methods, and our choice of compounds and initial conditions. We have a paper in review which will publish optimized methods for calculation of these experimental constraints so that protein structure or protein-ligand interaction can be solved. 5/96-12/96 University of Michigan Dr. Noemi Mirkin Physics/Biophysics. Synopsis: Ab initio calculations of dipeptide structure and bond energies * Calculations of minimum energy conformers of pentane and various conformations of a blocked glycine dipeptide, * Creation of peptide bond rotation energy curves/surfaces. * Established benchmarks for computational efficiency for various GAUSSIAN ab initio computational routines on available hardware * Determined relative energies of glycine dipeptide in several conformations found in larger proteins. 01/96-05/96 University of Michigan Dr. W. Richard Dunham Biophysics Synopsis: study of cobalt-ligand electronic bonding in wildtype vitamin B12-dependent methionine synthase and mutants using EPR and quantum mechanics. * Using software developed in the Dunham Lab, I matched experimental EPR spectra of cobalt in B12-dependent methionine synthase and mutants with software-generated models to establish symmetric changes around the cobalt atom between the mutants and the wildtype. * Discovered significant deviations in the A-tensor strain from the spectral parameters, proving that there exists a difference from the traditional models of the symmetric structure of fifth and sixth ligands and possibly of the corrin ring. * Discovered indications that chemical bonding may occur between the cobalt atom and the fifth and sixth ligands through an s-orbital rather than a d-orbital, by establishing that a significant change exists in the Fermi contact term between the cases of base-on and base-off (fifth ligand) mutants of methionine synthase. * Performed associated molecular biology/biochemistry laboratory experiments, including expression and purification of protein and mutants. 9/94-5/95 Wellesley College Dr. Wendy Bauer Astronomy Synopsis: Characterization of a binary star's unusual emission/absorption UV spectra. * Using data obtained from the International Ultraviolet Explorer satellite, the unusual dynamic behavior of the spectrum of VV Cephei, a long-period binary system, was studied. * Utilized off-site spectroscopic databases by authoring FORTRAN routines to process the raw IUE satellite data into useable format. * Wrote programs to process and analyze spectra, including addition, multiplication, subtraction and division of UV satellite spectra. * Helped determine that the anomalous spectra are a convolution of two spectral effects not previously encountered, due to emission from the smaller hot secondary and molecular absorption of a cooler dust cloud from the cooler primary giant. 5/93-8/93 Stanford Linear Accelerator Dr. Elliot Bloom USA satellite project. Synopsis: Determination of surface reflection properties of a satellite copper collimator. * Tested copper material sample using a single X-ray wavelength. * Was able to establish the non-reflectivity of the copper foil at low angles to all X-ray wavelengths based on Maxwell's equations, proving its suitability for use in the satellite experiment. * Produced an official report to the records of the government-funded project, establishing that the material was suited for the satellite system. May-August 1992 Wellesley College Dr. R. Berg Physics Synopsis: Installation/Design of a Solar Zeeman Effect spectroscopy system. * Designed an on-board photon counting system as well as a cooling/refrigeration system to be used with a high-resolution 1-meter optical spectrometer. * Designed and installed optics at a nearby observatory to be used with a fiber optic network running between the solar collector and the spectrometer. * Built circuit boards and programmed photon counting system in BASIC over IEEE interface between a lock-in amplifier and a personal computer. 1991-1993 Massachusetts Institute of Technology Dr. Wade Sapp Bates Linear Accelerator Synopsis: Optimization and installation work on a new electron beam storage ring. * Large dipole magnet placement and dipole/quadrupole/octupole magnet field mapping, survey work, test equipment design, computational calculations of higher field moments of magnets. * Optimization calculations for beam placement. after higher moments were determined on the Linac's VAX system . Awards, Fellowships 2000 University of Michigan Outstanding Graduate Student Instructor Award 1999 Graduate Student Instructor Award , University of Michigan Chemistry Dept. 1998 1999 Sloan Foundation Fellowship, U of M 1997 Margaret Dow Towsley Scholarship, U. of Michigan 1995 Sigma Xi Science Honors Fraternity 1991 Henry Cabot Lodge Scholarship 1991 Association of American University Women Scholarship 1991 USA Today All-American Academic Team Award 1990 Phi Theta Kappa Honors Fraternity Significant Coursework * Mathematics: Complex Variables. Calculus 1, 2, 3. Group Theory. Linear Algebra. Differential Equations. Analysis. * Biophysics: Principles of Magnetic Resonance. Advanced Topics (crystallography, NMR, Thermodynamics, Protein Folding). Microscopy. Dynamic Processes in Biophysics. Protein Structure & Dynamics. Physics of Macromolecules . * Physics: Quantum Mechanics. Quantum Theory. Applied Quantum Laboratory. Electrodynamics. Nonlinearity/Chaos/Complex Systems. Mechanics. Thermodynamics and Statistical Mechanics. Waves and Vibrations. Electronics and Circuit Design. * Chemistry: Organic Chemistry I, II. General Chemistry I, II. * Astronomy: Observational Techniques I+II. Advanced Astrophysics I+II. Stellar Astronomy. Planetary Astronomy. * Biochemistry and Molecular Biology: Protein Trafficking. Signal Transduction. Metabolic Regulation. Molecular Cell Biology. Protein/Nucleic Acid Interactions. Nucleic Acids. Gene Expression. Biochemistry. Methods in Molecular Biology . * Pharmacology: Methods of Computational Chemistry . Associated Skills * Programming: FORTRAN, C++, some familiarity with Perl, and some Java. * WWW: HTML, JavaScript, and php3 * Software (high proficiency): Adobe PhotoShop, Adobe Illustrator, MS Word and various other WP, MS Excel, Mathematica, Maple V, Gaussian, various quantum chemistry packages, many GNU packages (gnuplot, gcc, gnu make, etc.), GNOME, XFREE86, exposure to programming with message passing for parallel computing libraries (MPICH), scientific libraries (BLAS, etc), many others. * Database: mySQL, FileMaker, Microsoft Access, some FoxPro * Operating systems Linux, IRIX, Unix, Solaris, MacOS, Windows95, 98, NT, X windows, some VMS. * Molecular Biology/wetlab: Protein Expression protocols, Purification (HPLC, gels, columns), PCR, training in ELISA, Northern, Eastern. Protein crystallization. Also inorganic lab experience. Employment Outside of Research 9/97-Present University of Michigan Biophysics Program Systems Administrator * Systems Administrator for a physical chemistry/biophysics laboratory specializing in computer modeling, molecular simulation, quantum chemistry calculations, and quantum computing. * Management of a 20-machine networked cluster of multi-user machines, including SGI (Octane, O2), PC-clones (single and multi-processor), Macintosh, and Suns, with the following OS: Irix, Solaris, Linux, MacOS, Windows 9X/NT and Unix. * Starting from scratch, built an integrated and smoothly functioning computer simulation and scientific support laboratory environment over three years, much of which is multiuser Linux, NT, Win98 and Irix. * Assembled inexpensive but powerful Linux multiprocessor servers from components to run quantum mechanical simulations using MPI libraries. * Installed, supported, and utilized several proprietary software packages as well as freeware/shareware/commercial packages for quantum chemical calculations (such as DALTON, deMON, Gaussian98, GAMESS). * Performed analyses of quantum-chemistry software performance cross-platform and cross-package. * Installed and supported software and upgrades for applications on all platforms such as web servers and associated engines (apache, php3), database programs (mySQL), gnu and other freeware applications (GAMMA, make, Tex, gnuplot, XFREE86, GIMP, etc). * Maintained programming libraries and compilers (gcc/g77, libc, tk, various scientific libraries, etc), operating systems and kernel upgrades, multi-processor programming libraries (mpich), commercial applications (Mathematica, Maple, Adobe, Microsoft), security (ssh, system security optimization). * Supplied ready user support for all software packages. * Performed scheduled hardware and network maintenance/swapouts, such as for disk drive, memory, and processor upgrades, tape backups, troubleshooting, diagnosis and repair. 5/99 - Present Versity.com Expert Consultant Astronomy and Chemistry knowledge Expert. * Provided college student questions online with excellent reviews. * Crafted extensive expert knowledge database trees in several science fields. * Performed helpful quality control on student note submissions. * Researched nationwide college programs and textbooks for inclusion in student help center. * Provided web links and scientific definitions for databases. * Strengthened the company's intellectual product. 5/99-10/99 University of Michigan Educational and Tech Consultant Office of the VP for Student Affairs Curriculum Infusion Project * Co-designer and creator of a program teaching Teamwork and Leadership to professionally-bound college students (engineers, scientists, etc) in areas such as: Active Listening, Effective Meetings, Communication, Accountability, Stages of Team Development, Team Building, Self-Awareness, Multiple Perspectives, Goal-setting, Being Proactive, Time Management, Trust-Building. * Part of team that designed the Michigan Team System that utilized these skills in a set format for the introduction of a sample, standard operating agreement for group meetings across the University of Michigan. * Co-author of student and faculty manuals on teamwork and students' personal development, especially in the areas of Accountability, Multiple Perspectives, Self Awareness, Team Building, Being Proactive; also wrote faculty research documents on "Effective Assessment of Student Team Performance" and "Establishing Accountability Among Members of Student Teams." * Development of self-assessment and faculty assessment tools to be used in classrooms. * Development of web tools for knowledge delivery with php3 and mySQL. * Design and creation of all of the project's PowerPoint presentations, graphics, slides, and plots to be presented to University officials and administrators. * Delivery and customization of materials for various University courses involved in the project, including adaptation for Chemistry and Mathematics. * Provided leadership and work ethic which served as a major impetus for the project. * Acted in a leadership position to bring the project's products to completion within 4 months including a 80-page student manual and a 100-page instructor's manual, as well as presentations and teaching material designed specifically for participating instructors. 9/98-present coLABnet Project, funded by National Science Foundation Tech and Education Consultant University of Michigan * Team member on an National Science Foundation funded project that assists first year chemistry students by allowing them to collaborate in gathering and analyzing individual laboratory observations on a inter-lab system of 18 iMacs networked to a Macintosh G3 server and printers. * Creation of software report outputs and data-seeding system using advanced Excel database analysis and FoxPro. * Configured experiments for student use. * Troubleshooting of new modules and interface, diagnosis and bug repair. * Technical support and instructor training, software installation, system/software interface support, and system/network support. * Contributions of new ideas to enhance the collaborative environment. * Took major role in installation and system implementation. * The coLABnet Project won a Smithsonian Innovation Network Award. Teaching Experience/Employment 9/96-Present University of Michigan Graduate Student Administrator/Manager Chemistry Department * Supervised a team of graduate students teaching a large Chemistry laboratory course at the University of Michigan. * Programmed and administered a course-wide gradebook for up to 20 instructors and 40 course sections using advanced Excel macros and database analysis. * Analyzed and normalized grading curves and grading trends, held review sections, assisted professors and developed new materials to enhance the coursework. * Oversaw other administrative details such as web posting of answer keys, worksheets, and the smooth functioning of course software. 9/96-1/99 University of Michigan Graduate Student Instructor Physics and Chemistry Departments * Taught introductory physics laboratory and chemistry laboratory to college-aged students, facilitated student-run discussions, graded coursework, developed experimental procedures, trained students in the use of equipment and computers. * Regularly received high rankings by students for teaching excellence in course evaluations. * Received a Teaching Award through the Chemistry Department. * Honored with the year 2000 University of Michigan Outstanding Graduate Student Instructor Award.