Publications

(*denotes undergraduate co-author)

1. O'Grady, C.E.*, P. Talpey*, T. E. Elgren, and A. W. Van Wynsberghe, 2014. The development and implementation of a bio-molecular docking exercise for the general chemistry laboratory. In Annual Reports in Computational Chemistry, Vol. 10. Ralph Wheeler, editor. Elsevier, United Kingdom, pp. 167-187.
2. Kinnel, R. B., A. W. Van Wynsberghe, I. J. Rosenstein, K. S. Brewer, M. Cotten, G. C. Shields, C. J. Borton, S. Z. Senior, G. S. Rahn, and T. E. Elgren, 2013. A Departmental Focus on High Impact Undergraduate Research Experiences. In Developing and Maintaining a Successful Undergraduate Research Program. T. W. Chapp and M. A. Benvenuto, editors. ACS Symposium Series; American Chemical Society: Washington, D.C., vol. 1156:5-22.
3. 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 scattering combined with computational modeling reveals multiple conformations of covalently-bound ubiquitin on PCNA. Proc. Natl. Acad. Sci. 108(43):17672-17677.
4. Sinko, W., C. de Oliveira, S. Williams, A. Van Wynsberghe, J. Durrant, R. Cao, E. Oldfield, and J. A. McCammon, 2011. Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target. Chem. Biol. Drug Des. 77(6):412-420.
5. Van Wynsberghe, A. W. and Q. Cui, 2010. Conservation and Variation of Structural Flexibility in Protein Families. Structure. 18:281-283.
6. 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.
7. Van Wynsberghe, A. W., L. Ma, X. Chen, and Q. Cui, 2008. Functional Motions in Biomolecules: Insights from Computational Studies at Multiple Scales. In Computational Structural Biology. T. Schwede and M. Peitsch, editors. World Scientic Publishing.
8. 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.
9. Van Wynsberghe, A., and Q. Cui, 2006. Interpreting correlated motions using normal mode analysis. Structure. 14:1647-1653.
10. 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.
11. Li, G., A. Van Wynsberghe, O. N. A. Demerdash, and Q. Cui. 2005. Normal Mode Analysis of Macromolecules: From Enzyme Active Sites to Molecular Machines. In Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Q. Cui and I. Bahar, editors. CRC Press, Boca Raton.
12. 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 anionic biopolymer surface: Why glycine betaine is an eective osmoprotectant but also a compatible solute. Biochem. 43:14732-14743.
13. 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.
14. 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, diraction, and ab initio results. J. Phys. Chem. A 104:8702-8708.

Presentations

(*denotes undergraduate co-author)

1. Dacres, D. F.*, J. F. Graziadei*, P. F. Marris*, and A. W. Van Wynsberghe, 2015. Investigation of Sialic Acid Association Kinetics to H274Y Neuraminidase Using Molecular Dynamics Simulations. Poster- 14th MERCURY Conference on Computational Chemistry, Lewisburg, PA.
2. Lewis, E. M.*, R. W. Wenner*, P. F. Marris*, and A. W. Van Wynsberghe, 2015. Examining the Binding Pathways of Oseltamivir to H274Y Neuraminidase. Poster- 14th MERCURY Conference on Computational Chemistry, Lewisburg, PA.
3. Marris, P. F.*, L. M. Krause*, J. Sørensen, and A. W. Van Wynsberghe, 2015. Investigating binding pathways to neuraminidase using MM/GBSA free energy analysis. Poster- 14th MERCURY Conference on Computational Chemistry, Lewisburg, PA.
4. Kang, G. M.*, D. J. Mermelstein*, R. B. Clayton*, and A. W. Van Wynsberghe, 2015. Investigation of different binding kinetics among the neuraminidase inhibitors. Poster- 249th ACS National Meeting, Denver, CO.
5. Wenner, R. W.*, L. M. Krause*, J. F. Graziadei*, P. F. Marris*, and A. W. Van Wynsberghe, 2015. Calculation of the association trajectories of oseltamivir and sialic acid to wild type and H274Y viral neuraminidase. Poster- 249th ACS National Meeting, Denver, CO.
6. Kang, G. M.*, D. J. Mermelstein*, R. B. Clayton*, and A. W. Van Wynsberghe, 2014. Investigation of Different Binding Kinetics Among the Neuraminidase Inhibitors. Poster- 13th MERCURY Conference on Computational Chemistry, Lewisburg, PA.
7. Marris, P. F*, R. W. Wenner*, L. M. Krause*, J. Sørensen, A. R. Wu*, R. E. Amaro, and A. W. Van Wynsberghe, 2014. Investigating oseltamivir binding pathways to H274Y neuraminidase using molecular dynamics simulations and MM/GBSA analysis. Poster- 13th MERCURY Conference on Computational Chemistry, Lewisburg, PA.
8. Wenner, R. W.*, P. F. Marris*, J. E. Adelman*, and A. W. Van Wynsberghe, 2014. Observing the Diffusion of Oseltamivir into the Active and Secondary Sites of Neuraminidase Wild Type and the H274Y Variant. Poster- 13th MERCURY Conference on Computational Chemistry, Lewisburg, PA.
9. Van Wynsberghe, A.W., 2014. Multi-Scale Simulations of ligand-binding pathways to influenza neuraminidase. Siena College, Chemistry and Biochemistry Departmental Seminar
10. Alvarado, S. M.*, L. Krause*, A. R. Wu*, and A. W. Van Wynsberghe, 2013. Close-Range Behavior of Oseltamivir with Viral Neueraminidase. Poster- 12th MERCURY Conferencd on Computational Chemistry, Lewisburg, PA.
11. Banman B. J.*, J. E. Adelman*, A. R. Wu*, and A. W. Van Wynsberghe, 2013. Observing the inter- and intramolecular Evants of Sialic Acid Binding to the Active Site of Neuraminidase. Poster- 12th MERCURY Conferencd on Computational Chemistry, Lewisburg, PA.
12. Ho, J. H.*, C. M. Montangon*, R. B. Clayton*, and A. W. Van Wynsberghe, 2013. Investigation of the effects of molecular charges and water desolvation on the complex formation of Neuraminidase and its inhibitors. Poster- 12th MERCURY Conferencd on Computational Chemistry, Lewisburg, PA.
13. O'Grady, C. E.*, P. Talpey*, and A. W. Van Wynsberghe, 2013. Development of a molecular docking exercise to elucidate principles of biophysical chemistry in the general chemistry lab. Poster- 12th MERCURY Conferencd on Computational Chemistry, Lewisburg, PA.
14. Montagnon, 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
15. 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
16. Van Wynsberghe, A. W., 2013. Simulations of ligand binding pathways: directed diffusion with Hamilton College undergraduates: Molecular Dynamics and Markov State Models. University of California-San Diego, Amaro Laboratory Group Meeting
17. A. W. Van Wynsberghe, 2012. Simulations of ligand binding pathways: directed diffusion with Hamilton College undergraduates. Seminar- University of California-San Diego, Modeling Diffusional Encounter and Subsequent Events Mini-Symposium.
18. A. W. Van Wynsberghe, 2012. Hitting the Target: Simulations of the ligand binding pathways of influenza neuraminidase. Seminar- Colgate University, Chemistry Department Seminar Series
19. 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 as Applied to the Influenza Neuraminidase-Sialic Acid System. Poster- 7th National Biomedical Computation Resource Summer Institute, San Diego, CA
20. Clayton, R. B.*, C. M. Montagnon*, E. L. Losito*, and A. W. Van Wynsberghe, 2012. Investigation of Dierences in Desolvation Energy Between Ligands. Poster- 11th MERCURY conference on Computational Chemistry, Lewisburg, PA
21. 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 as Applied to the Influenza Neuraminidase-Sialic Acid System. Poster- 11th MERCURY conference on Computational Chemistry, Lewisburg, PA
22. 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
23. 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 Dynamics in Sialic Acid Binding to Neuraminidase. Poster- 243rd ACS National Meeting, San Diego, CA
24. 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
25. Wu, A. R.*, R. S. Green*, and A. W. Van Wynsberghe, 2012. Characterization of the Association between Neuraminidase and Sialic Acid Using Molecular Dynamics Simulations. Poster- 243rd ACS National Meeting, San Diego, CA
26. 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 Dynamics in Sialic Acid Binding to Neuraminidase. Poster- 10th MERCURY conference on Computational Chemistry, Lewisburg, PA
27. 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
28. Wu, A. R.*, R. S. Green*, and A. W. Van Wynsberghe, 2011. Characterization of the Association between Neuraminidase and Sialic Acid Using Molecular Dynamics Simulations. Poster- 10th MERCURY conference on Computational Chemistry, Lewisburg, PA
29. Adelman, J. E.*, J. C. Sung*, and A. W. Van Wynsberghe, 2010. A novel paradigm for finding the kinetics of the the influenza neuraminidase-sialic acid system. Poster- 9th MERCURY conference on Computational Chemistry, Clinton, NY
30. 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 and secondary sites. Poster- 9th MERCURY conference on Computational Chemistry, Clinton, NY
31. Hagstrom, A. L.*, Sam Ha Eun Cho*, and A. W. Van Wynsberghe, 2010. Analysis of conformational changes in thrombin mutants and their effects on thrombomodulin binding. Poster- 9th MERCURY conference on Computational Chemistry
32. 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
33. 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
34. 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
35. Van Wynsberghe, A. W., and J. A. McCammon, 2008. Investigation of ThrombinThrombomodulin Association Kinetics Using Brownian Dynamics Simulations. Poster- 52nd Biophysical Society National Meeting, Long Beach, CA
36. 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 crystallographic data and coarse-grained normal mode analysis. Poster- 234th ACS National Meeting, Boston, MA
37. Van Wynsberghe, A. and Q. Cui, 2006. Identifying important residues through computational "Alanine Scanning" and the Kullback-Leibler divergence and a discussion on interpreting correlated motion using normal modes. Poster-32nd Steenbock Symposium, Madison, WI.
38. 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.
39. 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 using normal modes. Poster- 32nd Steenbock Symposium, Madison, WI.
40. Van Wynsberghe, A. and Q. Cui, 2004. Nucleic acid conformational flexibility and function: Molecular dynamics and normal mode analyses of the hammerhead ribozyme. Platform- 228th ACS National Meeting, Philadelphia, PA
41. 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, Saxtons River, VT
42. 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
43. Van Wynsberghe, A.*, S. A. Peebles, R. A. Peebles, and R. L. Kuczkowski, 2000. Determining molecular structure with FT-microwave spectroscopy: expectations and surprises. Platform- 44th Meeting of the Cleveland Section of the Society for Applied Spectroscopy, Cleveland, OH
44. 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
45. 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-microwave spectroscopy. Poster- Central Ohio Undergraduate Research Symposium, Columbus, OH