The Bioinformatics Center at Rensselaer and Wadsworth. Research -- Molecular Simulations


	*The Bioinformatics Center at Rensselaer and Wadsworth*

Gene Expression

Nucleic Acids Folding

Protein Structure
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Molecular Simulations

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Mitochondrial Structure

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Molecular Thermodynamics and Simulations of Biological Systems

Involved Researcher: Professor Garde

Introduction: Prof. Garde is interested in exploring molecular thermodynamics and simulations of biological systems, statistical mechanics of liquids and polymers, and solvation phenomena -- especially in aqueous solutions (water structure, hydrophobic interactions). We focus on understanding and modeling the role of water structure in inducing interactions between various hydrophobic, polar, and ionic molecules which ultimately leads to many important self-assembly processes in water.

Researcher
Introduction
Main publications in Molecular Simulations
Online Resources
Courses
Prof. Garde's publications

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Main publications in Molecular Simulations:
    • Hansson T, Oostenbrink C, van Gunsteren W. Molecular dynamics simulations. Current Opinion in Structural Biology. 2002 Apr;12(2):190-6

    • Bystroff C, Garde S. Related Articles, Links Helix propensities of short peptides: Molecular dynamics versus bioinformatics. Proteins. 2003 Mar 1;50(4):552-62

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Online resources in Molecular Simulations:
    • View great animations of molecular simulations on Prof. Garde's fun page

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Courses: Prof. Garde teaches the following courses:
     • Mathematical Methods in Chemical Engineering CHME-6610 (view agenda from the Fall 2002 semester ).
     • Energy, Entropy, and Equilibrium CHME-2220 (view agenda from the Spring 2003 semester)
     • View more courses from Prof. Garde's Teaching page

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Prof. Garde's publications in Molecular Simulations:
    Journal articles:
    • S. Garde, L. Yang, J. S. Dordick, and M. E. Paulaitis, "Molecular Dynamics Simulation of C_8E_5 Micelle in Explicit Water: Structure and Hydrophobic Solvation Thermodynamics", Molecular Physics, 100, 2299-2306 (2002).

    • T. Ghosh, Angel E. Garcia, and S. Garde, "Molecular Dynamics Simulations of Pressure Effects on Hydrophobic Interactions", J. Am. Chem. Soc., 123, 10997-11003 (2001).

    • G. Hummer, A. E. García, and S. Garde, "Helix nucleation kinetics using molecular simulations in explicit solvent", Proteins: Struct. Funct. Genet., 42, 77-84 (2001).

    • M. A. Gomez, L. R. Pratt, G. Hummer, and S. Garde, "Molecular realism in default models for information theories of hydrophobic effects", J. Phys. Chem., 103, 3520 (1999).

    • H. S. Ashbaugh, S. Garde, G. Hummer, E. W. Kaler, and M. E. Paulaitis, "Conformational equilibria of hydrophobic solutes in aqueous solution: relationship to inhomogeneous water structure", Biophys. J., 77, 645-654 (1999).

     Book Chapter:
    • S. Garde, G. Hummer, and M. E. Paulaitis, "Hydration of tetramethylammonium ion: from water structure to the free energy of hydration", Proceedings of AIP Conference: Simulation and Theory of Electrostatic Interactions in Solutio, L. R. Pratt and G. Hummer (eds.), Santa Fe, New Mexico, 202-224 (1999).
     >>more publications

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