Publications

1.         Beveridge, D. L., Maye, P. V., Jayaram, B., Ravishanker, G. & Mezei, M. (1980). Journal of Biomolecular Structure and Dynamics 2, 85.

2.         Beveridge, D. L., Mezei, M., Mehrotra, P. K., Marchese, F. T., Vasu, T. R. & Ravishanker, G. (1981). Liquid State Computer Simulation Studies of Biomolecualr Solvaton Problems. Ann. N.Y. Acad. Sci. 367, 108.

3.         Ravishanker, G., Mezei, M. & Beveridge, D. L. (1982). Monte Carlo Computer Simulation Studies of the Hydrophobic Effect:  Potential of Mean Force for [(CH4)2] at 25o and 50o C. Symp. Faraday Soc.

4.         Beveridge, D. L., Mezei, M., Mehrotra, P. K., Marchese, F. T., Ravishanker, G., Vasu, T. R. & Swaminathan, S. (1983). Monte Carlo Computer Simulation Studies of the Equilibrium Properties and Structure of Liquid Water. In Molecular-Based Study of Fluids (Haile, J. M. & Mansoori, G. A., eds.), Vol. 204, pp. 297-351. American Chemical Society, Washington, D.C.

5.         Beveridge, D. L., Maye, P. V., Jayaram, B., Ravishanker, G. & Mezei, M. (1984). Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies. J. Biomol. Struct. Dyn. 2, 261-270.

6.         Beveridge, D. L., Ravishanker, G. & Mezei, M. (1984). Solvent Separated Hydrophobic Interactions. In Structure and Dynamics of Proteins and Nucleic Acids(Clementi, E., ed.). Adenine Press, New York.

7.         Ravishanker, G., Mehrotra, P. K., Mezei, M. & Beveridge, D. L. (1984). Aqueous Hydration of Benzene. J. Am. Chem. Soc. 106, 4102.

8.         Ravishanker, G. & Beveridge, D. L. (1985). Potential of Mean Force for the Stacking of Phenyl Rings in Aqueous Solution. J. Am. Chem. Soc. 107, 2565.

9.         Beveridge, D. L., Mezei, M., Ravishanker, G. & Jayaram, B. (1985). Free Energy Simulations:  Applications to the Study of Liquid Water, Hydrophobic Interactions and Solvent Effects on Conformational Stability. Proc. Int. Symp. Biomol. Struct. Interactions, Suppl. J. Biosci. 8, 167.

10.       Mezei, M., Harrison, S. W., Ravishanker, G. & Beveridge, D. L. (1986). Monte Carlo Studies of the Aqueous Hydration of cis- and trans-N-Methyl Acetamide:  Sensitivity of Results to Convergence and to Choice of Intermolecular Potential Functions. Isr. J. Chem. 27, 163-172.

11.       Ravishanker, G. & Beveridge, D. L. (1986). Theoretical Studies of the Hydrophobic Effect. In Theoretical Chemistry of Biological Systems (Naray-Szabo, G., ed.). Elsevier Publishers, Amsterdam.

12.       Beveridge, D. L., Mezei, M., Ravishanker, G. & Gedulin, B. (1986). Solvent Effects on Conformational Stability of the Ala Dipeptide:  Full Free Energy Simulations. In Proc. 4th Conversation in Biomolecular Stereodynamics (Sarma, R. H., ed.). Adenine Press, New York.

13.       Ravishanker, G., Mezei, M. & Beveridge, D. L. (1986). Conformational Stability and Flexibility of the Ala Dipeptide in Free Space and In Water:  Monte Carlo Computer Simulation Studies. J. Comput. Chem. 7, 345.

14.       Subramanian, P. S., Ravishanker, G. & Beveridge, D. L. (1988). Theoretical Considerations on the “Spine of Hydration” in the Minor Groove of d(CGCGAATTCGCG) Duplex: Monte Carlo Computer Simulation. Proc. Natl. Acad. Sci. (USA) 85, 1836-1840.

15.       Ravishanker, G., Swaminathan, S., Beveridge, D. L., Lavery, R. & Sklenar, H. (1989). Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: “curves”, dials and windows. J. Biomol. Struct. Dyn. 6, 669-699.

16.       Swaminathan, S., Ravishanker, G., Beveridge, D. L., Lavery, R., Etchebest, C. & Sklenar, H. (1990). Conformational and Helicoidal Analysis of the Molecular Dynamics of Proteins: “curves,” dials and windows for a 50 psec dynamic trajectory of BPTI. Proteins 8, 179-193.

17.       Beveridge, D. L., Subramanian, P., Jayaram, B., Swaminathan, S. & Ravishanker, G. (1990). Molecular Simulation Studies on the d(CGCGAATTCGCG) Duplex: Hydration, Ion Atmosphere, Structure and Dynamics. In Structure and Methods III. DNA AND RNA (Sarma, R. H. & Sarma, M. H., eds.), Vol. III, pp. 79-112. Adenine Press, New York.

18.       Beveridge, D. L., Swaminathan, S., Ravishanker, G., Whitka, J., Srinivasan, J., Prevost, C., Louise-May, S., DiCapua, F. M. & Bolton, P. H. (1991). Methodological Considerations in Molecular Dynamics Simulations of DNA Oligonucleotides. InAdvances in Biomolecular Simulations (Lavery, R., Rivail, J.-L. & Smith, J., eds.). American Institute of Physics, New York.

19.       Swaminathan, S., Ravishanker, G. & Beveridge, D. L. (1991). Molecular Dynamics of B-DNA Including Water and Counterions: A 140 ps Trajectory for d(CGCGAATTCGCG) Based on the GROMOS Force Field. J. Am. Chem. Soc. 113, 5027-5040.

20.       Ravishanker, G. (1991). Molecular Dynamics Toolchest:  Analysis and Graphical  Display of Computer Simulation Results on Proteins and Nucleic Acids. Wesleyan University, Middletown, CT.

21.       Ravishanker, G. (1992). WesDyn 20: Molecular Dynamics and Monte Carlo Simulation for Proteins and DNA. Wesleyan University, MIddletown, CT.

22.       Vijayakumar, S., Vishveshwara, S., Ravishanker, G. & Beveridge, D. L. (1993). Differential stability of b-sheets and a-helices in b-lactamase: a high temperature molecular dynamics study of unfolding intermediates. Biophys. J. 65, 2304-2312.

23.       Prevost, C., Louise May, S., Ravishanker, G., Lavery, R. & Beveridge, D. L. (1993). Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers 33, 335-350.

24.       Beveridge, D. L., Swaminathan, S., Ravishanker, G., Withka, J. M., Srinivasan, J., Prevost, C., Louise-May, S., Langley, D. R., DiCapua, F. M. & Bolton, P. H. (1993). Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers. In Water and Biological Molecules (Westhof, E., ed.), pp. 165-225. The Macmillan Press, Ltd., London.

25.       Fritsch, V., Ravishanker, G., Beveridge, D. L. & Westhof, E. (1993). Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations. Biopolymers 33, 1537-1552.

26.       Prevost, C., Louise-May, S., Ravishanker, G., Lavery, R. & Beveridge, D. L. (1993). Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers 33, 335-50.

27.       Vijayakumar, S., Vishveshwara, S., Ravishanker, G. & Beveridge, D. L. (1993). Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates. Biophys J65, 2304-12.

28.       Young, M. A., Nirmala, R., Srinivasan, J., McConnell, K. J., Ravishanker, G., Beveridge, D. L. & Berman, H. M. (1994). Analysis of Helix Bending in Crystal Structures and Molecular Dynamics Simulations of DNA Oligonucleotides. InStructural Biology: The State of the Art. Proceedings of the 8th Conversation.(Sarma, R. H. & Sarma, R. H., eds.), Vol. 2, pp. 197-214. 2 vols. Adenine Press, Albany, New York.

29.       McConnell, K. M., Nirmala, R., Young, M. A., Ravishanker, G. & Beveridge, D. L. (1994). A Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix: Evidence for Substates. J. Am. Chem. Soc. 116, 4461-4462.

30.       Beveridge, D. L. & Ravishanker, G. (1994). Molecular Dynamics Studies of DNA. Curr. Opin. Struct. Bio. 4, 246-255.

31.       Ptaszek, L. M., Vijayakumar, S., Ravishanker, G. & Beveridge, D. L. (1994). Molecular dynamics studies of the human CD4 protein. Biopolymers 34, 1145-1153.

32.       Ravishanker, G., Vijayakumar, S. & Beveridge, D. L. (1994). STRIPS:  An Algorithm for Generating Two-Dimensional Hydrogen-Bond Topology Diagram for Proteins. In Modeling the Hydrogen Bond (Smith, D. A., ed.), Vol. 569, pp. 209-219.

33.       Vijayakumar, S., Vishuveshwara, S., Ravishanker, G. & Beveridge, D. L. (1994). Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulations. In Modeling the Hydrogen Bond (Smith, D. A., ed.), Vol. 569, pp. 175-193.

34.       Beveridge, D. L., McConnell, K. J., Nirmala, R., Young, M. A., Vijayakumar, S. & Ravishanker, G. (1994). Molecular Dynamics Simulations of DNA and Protein-DNA Complexes Including Solvent: Recent Progress. ACS symposium series 568, 381-394.

35.       Vijayakumar, S., Ravishanker, G., Pratt, R. F. & Beveridge, D. L. (1995). Molecular Dynamics Simulation of a Class A -Lactamase: Structural and Mechanistic Implications. J. Am. Chem. Soc. 117, 1722-1730.

36.       Young, M. A., Ravishanker, G., Beveridge, D. L. & Berman, H. M. (1995). Analysis of Local Helix Bending in Crystal Structures of DNA Oligonucleotides and DNA-Protein Complexes. Biophysical Journal 68, 2454-2468.

37.       Beveridge, D. L., McConnell, K. J., Young, M. A., Vijayakumar, S. & Ravishanker, G. (1995). Molecular Dynamics Simulations on DNA and a Protein-DNA Complex Including Solvent. In Modeling of Biomolecular Structures and Mechanisms(Pullman, A. & Pullman, B., eds.), pp. 409-423. Kluew Academic Publishers.

38.       Ravishanker, G., Auffinger, P., Langley, D. R., Jayaram, B., Young, M. A. & Beveridge, D. L. (1997). Treatment of Counterions in Computer Simulations of DNA.Rev. of Comp. Chem. 11, 317-372.

39.       Young, M. A., Ravishanker, G. & Beveridge, D. L. (1997). A 5-Nanosecond Molecular Dynamics Trajectory for B-DNA: Analysis of Structure, Motions and Solvation. Biophys. J. 73, 2313-2336.

40.       Sprous, D., Wang, W., Ravishanker, G., Young, M. A. & Beveridge, D. L. (1998). Molecular Dynamics Information Extraction. In Rational Drug Design (D.G. Truhlar, W. J. H., A.J. Hopfinger, J. Blaney, R.A. Dammkoehler, ed.), Vol. 108, pp. 127-148. Springer-Verlag, New York.

41.       Ravishanker, G. (1998). Molecular Dynamics Tool Chest 2.0.

42.       Kombo, D. C., Ravishanker, G., Rackovsky, S. & Beveridge, D. L. (1999). Computational analysis of variants of the operator binding domain of the bacteriophage lambda repressor. International Journal of Quantum Chemistry 75, 313-325.

43.       Wang, W., Liu, Y., Ravishanker, G. & Beveridge, D. L. (2003). Molecular Dynamics Tool Chest: An Integrated Software Package for the Analysis of Molecular Dynamics Simulation Results of  Biological Macromolecules.

44.       Alberto Isgut & Ganesan Ravishanker & Tanya Rosenblat, 2005. “The Basics of International Trade: A Classroom Experiment, Wesleyan Economics Working Papers 2005-013, Wesleyan University, Department of Economics.

45.       Ravishanker, Ganesan (Ravi). “Doing Academic Analytics Right: Intelligent Answers to Simple Questions”, (Research Bulletin 2, 2011). Boulder, CO: EDUCAUSE Center for Applied Research, 2011, available from http://www.educause.edu/ecar. – To be published in Feb, 2011.

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