[Pipet Devel] Job interviews, etc

deanne at density.biop.umich.edu deanne at density.biop.umich.edu
Thu Apr 27 09:52:17 EDT 2000

> > 
> > "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.


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. 

 Present: 	 Ph.D. candidate,  Biophysics Graduate Program
 		 University of Michigan, Ann Arbor, MI.
  		Expected date of Ph.D. Degree Completion: July/August
 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.


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

* 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

May-August 1992   			Wellesley College  
Dr. R. Berg  				Physics

 Synopsis: Installation/Design of a Solar Zeeman Effect spectroscopy

* 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
 * 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
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
* 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
* Provided college student questions online with excellent reviews.  
*  Crafted extensive expert knowledge database trees in several science
* 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
 				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,
* 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
*  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
*  Delivery and customization of materials for various University courses
involved in the project, including adaptation for Chemistry and
*  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
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
*  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.

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