Assistant High School

Andrew J. Rader ******.*****@*****.*** 317-***-****

Profile

Interdisciplinary researcher desiring to apply analytical skills to solve real-world problems. Over 10 years of experience in developing, testing and implementing computer models of biological systems. Uncovered trends in physiochemical properties and protein structure-function relationships. Excellent computational and analytical skills are complemented by an ability to succinctly and clearly explain technical material to a variety of audiences. A synthesizer of ideas who enjoys working within a team to develop a better solution. Director of university research group and physics instructor for the past 6 years. Strengths include creating models and simulations of physical systems as well as statistical analysis of large datasets.

Professional Accomplishments & Qualifications

Research

Developed and applied novel network-based models of proteins to quantitatively characterize function in terms of their structures (QSAR).

Created coarse-grained, multi-scale models of proteins, RNA and DNA, drawing on polymer physics and classical mechanics to develop effective force fields.

Performed molecular dynamics, Monte Carlo, atomistic and coarse-grained simulations of systems containing hundreds of thousands of components representing over one million atoms.

Identified the role of structural flexibility and motion in the context of ligand binding, conformational changes and thermodynamics.

Routinely generated and distilled gigabytes of data from simulations into meaningful trends and physical insights about the system using statistics (PCA, support vector machines, clustering, t-tests, etc.).

Constructed and queried large databases containing hundreds of thousands of relationships of genomics and proteomics data.

Performed bioinformatics analysis of protein, DNA and RNA structures and sequences (searches, alignment, homology modeling, etc.) identifying common features and mechanisms.

Inferred stability trends in homologous thermophile-mesophile pairs. Simulated amino acid mutations and calculated their effect on thermodynamic parameters.

Experienced in various laboratory techniques including vacuum chambers, chemical vapor deposition, photolithography and spectroscopy.

Co-author of 25 scientific articles and 2 book chapters. Presented work at more than 20 local, national and international conferences.

Computational Skills

Highly adaptable software user experienced in numerous software for simulation and visualization of biomolecules such as VMD, PyMOL, MODELLER, Rosetta, Amber, BioPerl and Gromacs as well as those for mathematical and statistical analysis of data such as Matlab, and R.

Fluent in many programming languages including C/C++, FORTRAN77, SQL, perl, python and bash.

Developed source code and web-server interfaces for two coarse-grained biomolecular simulation methods: the GNM elastic network model and the rigidity analysis of FIRST.

Set-up and administered small (8 node) linux computer cluster and ran simulations on BigRed (512 node) HPC cluster.

Experienced user in linux/UNIX and Windows operating systems along with most Microsoft and Adobe software.

Management

Delegated pieces of research projects to different team members and synthesized these independent results into a meaningful product.

Set deadlines and worked on multiple projects simultaneously. Made hiring and purchasing decisions.

Worked on many collaborative, team projects with researchers from many different backgrounds in both support and supervisory roles.

Teaching

Taught undergraduate and graduate courses covering mechanics, optics, electromagnetism, thermodynamics, statistical mechanics and biophysics.

Mentored 13 post-doctoral, graduate, undergraduate and high school students in various projects leading to completed studies, publications, and degrees.

Employment, Education & Awards

Positions

• Assistant Professor (08/2005 – present)

Department of Physics, Indiana University-Purdue University Indianapolis

• Research Associate (01/2003 – 08/2005)

Department of Computational Biology, University of Pittsburgh

• Research Assistant (08/1996 – 12/2002)

Department of Physics, Michigan State University

• Undergraduate Research Assistant (08/1994 – 05/1996)

Department of Physics and Space Vacuum Epitaxy Center, University of Houston

• Undergraduate Research Assistant (Summer 1994)

NSF-REU, Indiana University Cyclotron Facility

Education

Ph.D. Physics and Biochemistry, Michigan State University (2002)

Thesis: “Protein Rigidity and Flexibility: Applications to Folding and Thermostability”

M.S. Physics, Michigan State University (1998)

B.S. Physics and Mathematics, University of Houston (1996)

Graduated summa cum laude with Honors in Major and University Honors

Thesis: “Improved Efficiencies in InP/InGaAs Solar Cells by an Antireflection Coating Process.”

Awards

IU OVPIA Overseas Conference Fund Grant to attend PepCon 2010, Beijing, China. (2010).

IUPUI Jaguars Favorite Professor Award (2008,2009)

Pacific Symposium in Biocomputing Travel Award (2008)

Young Investigator's Scholarship, U Buffalo-SUNY Frontiers in Bioinformatics Symposium. (2003)

Thomas Kaplan Award, MSU Physics Dept. (2001-2002)

Center for Biological Modeling Graduate Award, MSU (2000,2001)

Arete Award for outstanding senior thesis, UH (1996)

National Merit Scholar, UH (1992-1996)

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