Adam Jared Helman - a Resume

Adam Helman, Ph.D.
E-mail helman@san.rr.com
Website http://www.cohp.org

Education

University of Michigan, Ann Arbor, Michigan
Ph.D., Chemistry - 1989

University of California, Los Angeles, California
B.Sc., Chemistry, B.A., Biology - 1981

Technical Summary

Computer Languages: C, C++, Fortran, Java. SVG, XML, HTML, Javascript and some UNIX scripting, COM, Perl.

Integrated Development Environments: Microsoft Visual C++; Visual J++; Microsoft Foundation Classes (MFC).

Platforms/Operating systems: UNIX - Silicon Graphics, Linux, IBM; Windows 95, 98, 2000.

Internet-related: HTML, Java, client-side Javascript, Java Server Pages, CGI, SVG, XML, web page design and development.

Expert in algorithm development including molecular modeling applications

Professional Experience

Accelrys, Inc.

December 2002 to February 2003

San Diego, California
Contracting consultant

Discovery Studio Structure Based Design Project (DS SBD)

• Worked in a team effort to develop a new product for structure-based design of pharmaceuticals using existing scientific software. This effort required porting to Windows NT, Linux and IBM Linux and IBM said algorithms as well as development of a new UI for the Windows-based client.
• The relevant technologies are numerous - C++, C, Fortran, IDL, COM, HTML, javascript, CORBA, and relational database (Oracle).
• The software was developed to run on a Windows-based client and either a Windows NT or a UNIX-based server (Silicon Graphics, Linux, IBM).

Peregrine Systems, Inc.

July 2000 to June 2002

San Diego, California
Product development engineer

Stacking algorithms project

• Performed background research into, and developed the software for solving the stacking problem using an array of novel algorithms. Quadratic affinity costs, resource availability constraints, and moving costs are considered in any permutation and with any set of weight factors in the construction of acceptable solution vectors.
• The relevant technologies include a thorough knowledge of JAVA programming and linear algebra.
• A novel variant of the simplex method is used when only linear resource constraints are specified and forms the basis for publishable material were it not for the proprietary nature of the product.
• A time-dependent variant of the stacking algorithm was developed that may be used, with some refinement, to solve the (very) difficult move sequencing problem. The time-dependent algorithm relies upon analogies made with (time-dependent) molecular dynamics simulations. The latter are a key computational tool in studies of drug-receptor interactions.

Scheduling algorithms project

• Developed software to solve complicated scheduling problems in the time domain. This includes the consideration of task-task shadowing, and the existence of excluded zones within which tasks are disallowed.
• The relevant technology is JAVA programming involving multiple Java packages and a dozen well-defined, object-oriented Java classes. This is not simply a Java applet running on a web page!
• The underlying algorithms are extremely efficient and are a testimony to the art of scientific programming at its finest.

Scalable Vector Graphics projects (SVG)

• Several small-scale projects receive XML data on input and render it in visually appealing graphic format that is fully interactive using an SVG tree that is generated on-the-fly at run time.
• The relevant technologies are XML; SVG; HTML; and client-side javascript.
• Examples include dynamic generation of ANY year or monthly calendar; a color widget that generates user-defined colors using scrollable, mouse-activated joysticks; a Gantt plot that enables one to translate and dilate along the time-axis to an infinite degree; SVG-based rendering of solutions to the stacking problem (see above); and an automated color gradient generator.
• These SVG projects are among the most advanced uses of this new language to date. I taught myself SVG at Peregrine Systems and completed these projects in three months.

CACI	May 2000 to June 2000

San Diego, California
Principal engineer

FAA False Radar Echo Project

• Developed software to distinguish between true radar returns and false echoes that represent ground clutter at commercial airports.
• The relevant technologies include pattern recognition, image processing, as well as a thorough understanding of radar theory,
  atmospheric propagation, and geometric ray-tracing.
• The software was developed in C++ to run in MS Windows.

NETROLOGIC, Inc.

July 1998 to April 2000

San Diego, California
Senior scientist

Medicinal Plant Project

• Acted in several key roles under an NIH Phase II Grant whose goal was to provide an automated means of identifying flowering plant species based on leaf and vein shapes and patterns.
• The relevant technologies include pattern recognition, image processing, neural networks, as well as a thorough understanding of botanical taxonomic methods and vascular plant morphology.
• As a knowledge engineer, the link was made between expert identification of plant species and the analogous mathematical equivalent. This step was crucial to success of the project - imparting to the computer the steps taken by a botanist in identifying plants based on leaf morphological features.
  As a software developer / integrator the following tasks were accomplished:

• Reverse-engineered and ported to Windows UNIX-based C code designed to implement the above technologies. The new code was written in C++.
• Developed C++ software in Windows and validated its utility to implement the above technologies.
• Statistical methods included feature selection and extraction; cluster analysis; principal components analysis; Fourier analysis; Gabor filters; texture mapping; fractal analysis; and neural networks.
• Novel tools were developed specifically for higher order leaf vein analysis.

Cost Analysis Project

• Conceived and developed a mathematical model for predicting the revenue stream and expenses of the telephone company (to which we had contracted) by developing algorithms for estimating the fraction of blocked telephone calls given a specified telephone traffic intensity and number of available channels.
• Developed and debugged algorithms to generate financial performance scenarios based on the mathematical model using C++ on a platform independent system.
• Documented the models and the resulting financial performance scenarios in a series of technical memoranda.

Speech Recognition Project

• Researched background material for development of speech recognition algorithms.
• Designed and developed a speech recognition multi-platform application utilizing C++ and incorporating wavelet technology.
• Developed and tested the speech recognition algorithms for digit recognition over noisy transmission lines.

Virtual Chemistry, Inc.

March 1998 to May 1998

San Diego, California
Software engineer (subcontractor)

• Debugged and validated the utility of a molecular modeling software package running in Windows, receiving as input a two-dimensional drawing of a molecule and, based upon classical force fields that determine the preferred lowest-energy conformations, results in a three-dimensional structure of potential value for additional development (lead compound generation, etc.).
  1) The original program suffered from severe problems related to chirality, i.e. the fact that some molecules come in pairs that are mirror images of one another. The program often yielded 3-D structures with the wrong "handedness" at up to several chiral atoms (usually carbon).
  2) Documented the errors using a test suite of molecules (53 total) from the Brookhaven PDB (Protein Data Bank). Based upon my knowledge of organic chemistry and computer programming I modified the source code to eventually eliminate all the chirality errors for the test set.

• This work involved C, C++ languages and the Visual C++ IDE (integrated development environment).

Molecular simulations, Inc. (formerly Biosym Technologies, Inc.)

1992 to 1998

San Diego, California
Scientific programmer / Scientist

• Developed product ELF (ElectroStatic Field), a comprehensive software package that efficiently accounts for the aqueous environment around biological macromolecules in vivo. ELF was programmed in the C language.
  detailed ELF description

• Implemented several algorithms in the C language, to efficiently compute molecular energies and forces.
  Replaced Delphi, as marketed by MSI under contract with Columbia University, with an upgraded version, Delphi II. This involved incorporating the Fortran code provided by Columbia, within the C-language framework of both InsightII and the standalone (non GUI-based) DelPhi as available from MSI. This involved an intimate understanding of both Fortran and molecular computations.
  Incorporated the effect of bond conjugation, (e.g. alternating single and double bonds, as manifested in the cff96 force field), into the DISCOVER molecular modeling program. This effort required C programming.
  Incorporation of the Berendsen temperature control algorithm within the molecular dynamics code of DISCOVER. The results were tested and documented on-line.

• Performed sensitivity analysis of molecular forces at the atomic level. This work was performed under contract with Squibb Pharmaceutical.
  Third derivatives of molecular internal coordinates with respect to Cartesian atomic displacements were derived by hand. In a slightly altered form the same algorithm may be used to rapidly optimize forcefield parameters.

California Institute of Technology

1989 to 1992

Pasadena, California
Research fellow - Chemistry Department

• Performed postdoctoral research in quantum dynamics of molecules under Professor R.A. Marcus (Nobel laureate).

• The "channel three" problem regarding the intermolecular vibrational relaxation of S1 excited state benzene was considered.
• Two papers were published with Prof. Marcus with a third being written prior to my employment at Biosym in San Diego.
• This work employed Fortran and the Cray supercomputer at the Jet Propulsion Laboratory.

Awards

• Bantrell Prize Fellowship (California Institute of Technology) - 1989
• Graduate Student of the Year (University of Michigan) - 1988
• Phi Beta Kappa (summa cum laude, UCLA) - 1981
• First Place California in an examination for Chemistry scholarship to UC Santa Barbara.
• First Place Southern California in a contest for rapidly solving mathematical problems in one’s head (for high school students).
• First Place Los Angeles County in chess playing (for junior high students).

Languages

• Fluent in Spanish
• Reading knowledge of French, Hebrew, Russian

Hobbies

• Very active in mountain climbing.
  In addition, I conceived of, developed, and currently maintain a popular website for county highpointers,
  cohp.org - that is visited and used by about 200 climbers for gathering and sharing information.
• Enjoy gourmet food, cooking and baking.

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