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Adam W. Van Wynsberghe1063 Science Center Visiting Assistant Research Scientist (Sabbatical Leave from Hamilton College)University of California-San DiegoDepartment of Chemistry and Biochemistry Assistant ProfessorHamilton College, Clinton, NYDepartment of Chemistry NIH Post-Doctoral FellowUniversity of California-San DiegoDepartment of Chemistry and BiochemistryAdvisor: Dr. J. Andrew McCammon Associate LecturerUniversity of Wisconsin-MadisonDepartment of Chemistry Ph.D., BiophysicsUniversity of Wisconsin-MadisonDissertation: Investigation into functional motions of biological macromole-cules from a computational and theoretical perspective.
Advisor: Dr. Qiang Cui B.A. (Summa Cum Laude, Phi Beta Kappa, University Honors)Major: ACS Biochemistry, Minor: MathematicsOhio Wesleyan University, Delaware, OH Primary InvestigatorDirected computational biophysical chemistry laboratory at a primary under-graduate institution. Research activities included investigations into enzymecatalysis, protein-protein interactions, and protein-ligand interactions.
Department of Chemistry, Hamilton College NIH Post-Doctoral FellowSpecialized in Brownian Dynamics simulations of macromolecular assemblies.
Advisor: Dr. J. Andrew McCammon, University of California-San Diego WARF Prize Fellow, NSF Pre-Doctoral Fellow, Graduate Research AssistantDoctoral Research: Used theoretical and computational techniques to studymacromolecular motions over both fast and slow timescales. Specialized inNormal Mode Analysis and Molecular Dynamics simulations.
Advisor: Dr. Qiang Cui, University of Wisconsin-Madison Undergraduate Summer Research InternUsed molecular biology techniques to study the contribution of the internalguidance sequence to substrate binding in the Group I intronAdvisor: Dr. Dan Herschlag, Stanford University Independent Study Undergraduate Research StudentAssigned microwave spectra of environmentally interesting molecules α- andβ-pinene; assisted in construction and setup of a Beowulf cluster for theoret-ical chemistry researchAdvisor: Dr. Dale Brugh, Ohio Wesleyan University NSF-REU Summer Research StudentUsed FT-Mircowave Spectroscopy to determine the structure of 1,2-dichloro-3,3,4,4-tetrafluorocyclobutene in order to investigate the effect of halogena-tion on adjacent chemical bonds.
Advisor: Dr. Robert Kuczkowski, University of Michigan Independent Study Undergraduate Research StudentUsed classical biochemistry techniques to isolate and characterize an enzymewith keratinase activity.
Advisor: Dr. David Lever, Ohio Wesleyan University Assistant ProfessorDepartment of Chemistry, Hamilton College -Instructor of record for lecture and laboratory courses.
Lecture courses taught: Physical Chemistry (Quantum Mechanics), Physical Chemistry (Statistical and Classical Thermodynamics and Kinetics), Laboratory courses taught: General Chemistry, Biological Chemistry, Undergraduate Research MentorDepartment of Chemistry, Hamilton College -Primary supervisor for research lab in computational biophysical chemistry Undergraduate Research MentorChemistry and Biochemistry, University of California-San Diego -Supervised day to day research activities of undergraduates while a Postdoctoral fellow Associate LecturerCHEM 104, General Chemistry, University of Wisconsin-Madison -Instructor of record for second semester general chemistry course.
Teaching AssistantCHEM 109H, General Chemistry, University of Wisconsin-Madison -Responsible for content and oversight of weekly discussion and laboratory section Undergraduate Research MentorChemistry, University of Wisconsin-Madison -Supervised day to day research activities of independent study and summer research undergraduates while a graduate student National Biomedical Computational Resource Summer Institute Scholarship NIH (NIGMS) Ruth L. Kirschstein NRSA Post-Doctoral Fellowship National Science Foundation Pre-Doctoral Fellowship Department of Defense Pre-Doctoral Fellowship (declined) Honorable Mention, Howard Hughes Medical Institute Pre-Doctoral Fellowship University of Wisconsin-Madison WARF Prize Fellowship Slocum Prize in the Sciences (Highest Overall GPA), Ohio Wesleyan University Outstanding Senior Chemistry Major, Ohio Wesleyan University Phi Beta Kappa Honor Society, Ohio Wesleyan University Ernest B. Yeager Award, Society for Applied Spectroscopy, Cleveland Section Ralph E. Hall Chemistry Fellowship, Ohio Wesleyan University Outstanding Junior Chemistry Major, Ohio Wesleyan University Chi Gamma Nu Chemistry Honor Society, Ohio Wesleyan University Phi Sigma Biological Sciences Honor Society, Ohio Wesleyan Univsersity Outstanding Poster, Central Ohio Undergraduate Research Symposium Charles Schafer Chemistry Scholarship, Ohio Wesleyan University Phi Society Sophomore Honor Society, Ohio Wesleyan University Pi Mu Epsilon Mathematics Honor Society, Ohio Wesleyan University Phi Eta Sigma Freshman Honor Society, Ohio Wesleyan University Presidential Scholarship, Ohio Wesleyan University President, Hamilton College chapter of Phi Beta Kappa Vice-President, Hamilton College chapter of Phi Beta Kappa Organizer, Chemistry Department Seminar Series High Performance Computing Advisory Group Other Professonial Activities2012-Present Reviewer, Journal of the American Chemical Society Reviewer, PROTEINS: Structure, Function, and Bioinformatics.
Cover Art Designer, Molecular and Cellular Biophysics, Meyer Jackson, Cam-bridge University Press, Cambridge.
Co-President of Chemistry Student Board, Ohio Wesleyan University Depart-ment of Chemistry Grant ActivityNational Science Foundation: Major Research Instrumentation, $200,000, 2012-2015, Co-PI MRI: Acquisition of a High Performance Computer for the Molecular Education andResearch Consortium in Undergraduate computational chemistRY (MERCURY) Research Corporation: Cottrell College Science Award, $35,000 plus $30,000 Hamilton College match, 2010-2012, PI, Accurate Evaluation of Association Rate Constants of InfluenzaNeuraminidase Inhibitors.
National Science Foundation: Major Research Instrumentation, $177,950, 2010-2012, PI MRI-R2: Acquisition of a High Performance Computing cluster with a fast interconnectto enable shared-use, college-wide computational investigations at Hamilton College.
Teragrid Allocation: TG-MCB090196, 200,000 Service Units, 2009-2010, PI, Investigations Publications (* denotes undergraduate co-author) Tsutakawa, S. E., A. W. Van Wynsberghe, B. D. Freudenthal, C. P. Weinacht, L. Gakhar, M. T. Washington, Z. Zhuang, J. A. Tainer, and I. Ivanov, 2011. Solution X-ray scatter-ing combined with computational modeling reveals multiple conformations ofcovalently-bound ubiquitin on PCNA. Proc. Natl. Acad. Sci. 108(43):17672-17677.
Sinko, W., C. de Oliveira, S. Williams, A. Van Wynsberghe, J. Durrant, R. Cao, E. Oldfield, and J. A. McCammon, 2011. Applying Molecular Dynamics Simulations to IdentifyRarely Sampled Ligand bound Conformational States of Undecaprenyl PyrophosphateSynthase, an Antibacterial Target. Chem. Biol. Drug Des. 77(6):412-420.
Van Wynsberghe, A. W. and Q. Cui, 2010. Conservation and Variation of Structural Flexibility in Protein Families. Structure. 18:281-283.
(Corresponding Author) Sung, J. C.*, A. W. Van Wynsberghe, R. E. Amaro, W. W. Li, and J. A. McCammon, 2010. The role of secondary sialic acid binding sites in influenza N1 neuraminidase.
J. Amer. Chem. Soc. 132(9):2883-2885.
(Corresponding Author) Van Wynsberghe, A. W., L. Ma, X. Chen, and Q. Cui, 2008. Functional Motions in Bio- molecules: Insights from Computational Studies at Multiple Scales. In ComputationalStructural Biology. T. Schwede and M. Peitsch, editors. World Scientific Publishing.
Kondrashov, D., A. Van Wynsberghe, R. M. Bannen, Q. Cui, and G. N. Phillips, Jr., 2007.
Protein Structural Variation in Computational Models and Crystallographic Data.
Structure. 15:169-177.
(Feature Article) Van Wynsberghe, A., and Q. Cui, 2006. Interpreting correlated motions using normal mode analysis. Structure. 14:1647-1653.
Van Wynsberghe, A. W., and Q. Cui. 2005. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys. J. 89:2939-2949.
(Cover Article) Li, G., A. Van Wynsberghe, O. N. A. Demerdash, and Q. Cui. 2005. Normal Mode Anal- ysis of Macromolecules: From Enzyme Active Sites to Molecular Machines. In Nor-mal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Q.
Cui and I. Bahar, editors. CRC Press, Boca Raton.
Felitsky, D. J., J. G. Cannon, M. W. Capp, J. Hong, A. W. Van Wynsberghe, C. F.
Anderson, and M. T. Record. 2004. The exclusion of glycine betaine from anionicbiopolymer surface: Why glycine betaine is an effective osmoprotectant but also acompatible solute. Biochem. 43:14732-14743.
Van Wynsberghe, A., G. H. Li, and Q. Cui. 2004. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase’s functional cycle. Biochem.
43:13083-13096.
(Corresponding Author) Van Wynsberghe, A. W., S. A. Peebles, R. A. Peebles, and R. L. Kuczkowski. 2000.
Rotational spectrum and structure of 1,2-dichloro-3,3,4,4-tetrafluorocyclobutene:Comparison of spectroscopy, diffraction, and ab initio results. J. Phys. Chem. A104:8702-8708.
Invited PresentationsVan Wynsberghe, A. W., 2012. Simulations of ligand binding pathways: directed diffusion with Hamilton College undergraduates.
University of California-San Diego, Modeling Diffusional Encounter and SubsequentEvents Mini-Symposium Van Wynsberghe, A. W., 2012. Hitting the Target: Simulations of the ligand binding pathways of influenza neuraminidase.
Colgate University, Chemistry Department Seminar Series Van Wynsberghe, A. and Q. Cui, 2004. Nucleic acid conformational flexibility and function: Molecular dynamics and normal mode analyses of the hammerhead ribozyme.
228th ACS National Meeting, Philadelphia, PA Van Wynsberghe, A., S. A. Peebles, R. A. Peebles, and R. L. Kuczkowski, 2000. Determining molecular structure with FT-microwave spectroscopy: expectations and surprises.
44th Meeting of the Cleveland Section of the Society for Applied Spectros-copy, Cleveland, OH(Ernest B. Yeager Award lecture) Contributed PresentationsMontagnon, C. M.*, R. B. Clayton*, and A. W. Van Wynsberghe, 2013. Investigation of the effects of electronic desolvation on oseltamivir binding kinetics to N1 influenza neuraminidase.
Poster- 245th ACS National Meeting, New Orlenas, LA Wu, A. R.*, L. Krause*, and A. W. Van Wynsberghe, 2013. Elucidation of the molecular interactions between neuraminidase and sialic acid.
Poster- 245th ACS National Meeting, New Orlenas, LA Krause, L.*, A. Wu*, D. Mermelstein*, J. E. Adelman*, and A. W. Van Wynsberghe, 2012.
The Effect of Starting Location and Orientation on Molecular Dynamics Simulations asApplied to the Influenza Neuraminidase-Sialic Acid System.
Poster- 7th National Biomedical Computation Resource Summer Institute, San Diego, CA Krause, L.*, A. Wu*, D. Mermelstein*, J. E. Adelman*, and A. W. Van Wynsberghe, 2012.
The Effect of Starting Location and Orientation on Molecular Dynamics Simulations asApplied to the Influenza Neuraminidase-Sialic Acid System.
Poster- 11th MERCURY conference on Computational Chemistry, Lewisburg, PA Clayton, R. B.*, C. M. Montagnon*, E. L. Losito*, and A. W. Van Wynsberghe, 2012.
Investigation of Differences in Desolvation Energy Between LigandsPoster- 11th MERCURY conference on Computational Chemistry, Lewisburg, PA Losito, E. L.*, L. D. Leonard*, and A. W. Van Wynsberghe, 2012. Role of influenza A neuraminidase electrostatics in the binding of ligands.
Poster- 243rd ACS National Meeting, San Diego, CA Mermelstein, D. J.*, J. E. Adelman*, and A. W. Van Wynsberghe, 2012. Determination of an Appropriate Surface for the Transition from Brownian Dynamics to Molecular Dyna-mics in Sialic Acid Binding to Neuraminidase.
Poster- 243rd ACS National Meeting, San Diego, CA Montagnon, C. M.*, L. D. Leonard*, E. L. Losito*, and A. W. Van Wynsberghe, 2012. Investigation of Oseltamivir Binding Kinetics to N1 Influenza Neuraminidase.
Poster- 243rd ACS National Meeting, San Diego, CA Wu, A. R.*, R. S. Green*, and A. W. Van Wynsberghe, 2012. Characterization of the Asso- ciation between Neuraminidase and Sialic Acid Using Molecular Dynamics Simulations.
Poster- 243rd ACS National Meeting, San Diego, CA Mermelstein, D. J.*, J. E. Adelman*, and A. W. Van Wynsberghe, 2011. Determination of an Appropriate Surface for the Transition from Brownian Dynamics to Molecular Dyna-mics in Sialic Acid Binding to Neuraminidase.
Poster- 10th MERCURY conference on Computational Chemistry, Lewisburg, PA Montagnon, C. M.*, L. D. Leonard*, E. L. Losito*, J. C. Sung*, and A. W. Van Wynsberghe, 2011. Investigation of Oseltamivir Binding Kinetics to N1 Influenza Neuraminidase.
Poster- 10th MERCURY conference on Computational Chemistry, Lewisburg, PA Wu, A. R.*, R. S. Green*, and A. W. Van Wynsberghe, 2011. Characterization of the Asso- ciation between Neuraminidase and Sialic Acid Using Molecular Dynamics Simulations.
Poster- 10th MERCURY conference on Computational Chemistry, Lewisburg, PA Adelman, J. E.*, J. C. Sung*, and A. W. Van Wynsberghe, 2010. A novel paradigm for finding the kinetics of the the influenza neuraminidase-sialic acid system.
Poster- 9th MERCURY conference on Computational Chemistry, Clinton, NY Losito, E. L.*, J. C. Sung*, C. A. Rico*, and A. W. Van Wynsberghe, 2010. Association rate constants of peramivir and zanamivir to influenza A neuraminidase active andsecondary sites.
Poster- 9th MERCURY conference on Computational Chemistry, Clinton, NY Hagstrom, A. L.*, Sam Ha Eun Cho*, and A. W. Van Wynsberghe, 2010. Analysis of con- formational changes in thrombin mutants and their effects on thrombomodulin binding.
Poster- 9th MERCURY conference on Computational Chemistry Sung, J. C.*, A. W. Van Wynsberghe, R. E. Amaro, W. W. Li, and J. A. McCammon, 2009. The role of secondary sialic acid binding sites in influenza N1 neuraminidase.
Poster- 8th MERCURY Conference on Computational Chemistry, Clinton, NY Sung, J.*, A. W. Van Wynsberghe, R. E. Amaro, and J. A. McCammon, 2009. Theoretical studies on the purpose of the surface binding site of avian influenza neuraminidase.
Poster- 237th ACS National Meeting, Salt Lake City, UT Van Wynsberghe, A. W., I. Ivanov, and J. A. McCammon, 2009. Models of PCNA-monoubiquitin interaction complexes.
Poster- 237th ACS National Meeting, Salt Lake City, UT Van Wynsberghe, A. W., and J. A. McCammon, 2008. Investigation of Thrombin- Thrombomodulin Association Kinetics Using Brownian Dynamics Simulations.
Poster- 52nd Biophysical Society National Meeting, Long Beach, CA Kondrashov, D., A. W. Van Wynsberghe, E. J. Levin, R. M. Bannen, E. Bitto, R. Aranda, J. G. McCoy, Q. Cui, and G. N. Phillips Jr., 2007. Protein dynamics in crystallographicdata and coarse-grained normal mode analysis.
Poster- 234th ACS National Meeting, Boston, MA Van Wynsberghe, A. and Q. Cui, 2006. Identifying important residues through computation- al “Alanine Scanning” and the Kullback-Leibler divergence and a discussion on interpre-ting correlated motion using normal modes.
Poster-32nd Steenbock Symposium, Madison, WI.
Kondrashov, D. A., A. Van Wynsberghe, R. M. Bannen, Q. Cui, and G. N. Phillips, Jr., 2006.
Optimization, validation, and application of coarse-grained models of residue interaction.
Platform- 32nd Steenbock Symposium, Madison, WI.
Bannen, R. M., V. Suresh, D. Kondrashov, A. Van Wynsberghe, Q. Cui, J. C., Mitchell, G. N.
Phillips, Jr., and S. J. Wright., 2006. Probing dynamics and interactions of proteins usingnormal modes.
Poster- 32nd Steenbock Symposium, Madison, WI.
Van Wynsberghe A., G. Li, and Q. Cui, 2003. Structural analysis of protein flexibility in bacterial and viral RNA polymerases.
Poster- FASEB Summer Conference on Transcription Initiation in Prokaryotes, SaxtonsRiver,VT Van Wynsberghe A., G. Li, and Q. Cui, 2003. Structural analysis of protein flexibility in bacterial and viral RNA polymerases.
Poster- 47th Biophysical Society National Meeting, San Antonio, TX Brugh, D. J., A. Van Wynsberghe, and R. D. Suenram, 2000. Application of Fourier Transform Microwave Spectroscopy to Pinene Detection.
Platform- Pittcon 2000, New Orleans, LA Van Wynsberghe, A., S. A. Peebles, R. A. Peebles, and R. L. Kuczkowski, 1999. Structure determination of 1,2-dichloro-3,3,4,4-tetrafluorocycylobutene by FT-microwavespectroscopy.
Poster- Central Ohio Undergraduate Research Symposium, Columbus, OH(Awarded Outstanding Poster) Students Supervised (immediate or current position) Jeremy Adelman, (Barry M. Goldwater Scholar) Mathematics and Physics ’13 Erica Losito, Biochemistry ’12 (graduate student and Carlson Fellow, Biophysics, Johns Hopkins) Rebecca Green, Chemistry and Mathematics ’11 (medical student, University of Pennsylvania School of Medicine) Laura Leonard, Chemistry and Hispanic Studies, ’11 (Clinical Research Coordinator, Division of Genomic Medicine, Sam Cho, Chemistry ’10 (medical student, Michigan State University College of Human Medicine) Tom Morrell, Chemistry ’10 (NSF Pre-Doctoral Fellow, Chemistry, Princeton University) Carlos Rico, Chemical Physics ’10 (NSF Pre-Doctoral Fellow, Chemical Biology, Rockefeller University) Jeffrey Sung, Chemistry and Physics ’10 (graduate student, Chemistry, University of Minnesota) Kate Engel, Biochemistry and Genetics ’07 (graduate student, Molecular and Cell Biology, UC-Berkeley) Mischa Wolfson, Chemistry and Computer Science ’06 (graduate student, Chemistry, MIT) Vanderlene Kung, ’04 (M.D.-Ph.D. Student and NIH NRSA Fellow, Northwestern University Lawrence Klein, Chemistry ’04 (NSF Pre-Doctoral Fellow, Biophysics, Stanford University) Dr. Qiang CuiAssociate Professor, Department of Chemistry and Theoretical Chemistry InstituteUniversity of Wisconsin-Madison1101 University Ave.
Madison, WI 53706(608) 262-9801cui@chem.wisc.edu Investigator, Howard Hughes Medical Institute Past Editor, Journal of Chemical Education Joseph E. Mayer Chair of Theoretical Chemistry Director, Institute for Chemical Education

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