DEVELOPMENT OF THEORETICAL METHODS FOR STUDYING BIOLOGICAL MACROMOLECULES

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New theoretical techniques under development are often coupled with software and hardware development. These involve the generation of new simulation techniques and the systematic testing and evaluation of methods. Specific projects include: - Development of Quantum Mechanical Potentials and Appropriate Algorithms for Use in Molecular Dynamics Simulations - Determination of Protein Structure by NMR and Molecular Modelling - Slow Growth Homology Modeling (SGHM) for the Determination of Protein Structures - Development of an Optimized Protocol for the Preparation Of Low Temperature States - Development of Flexible MD Techniques That Remove High- Frequency Degrees of Freedom - Free Energy Perturbation Simulations in Solution, Examining the Effect of Restraints - Conversion of Physical Models into Three-dimensional Coordinates for Computer Analysis and Simulation. - Development of Ray-Traced Molecular Graphics Software for HP Workstations, High-Resolution Color Printers and for Movies Using NTSC Video Equipment. - Adaptation of a Truncated Newton minimizer for CHARMM and biomolecular applications Parameters sets and models are generally available for most macromolecular systems, but there is considerable room for improvement and alternate models that improve realism, or reduce computational costs, need to be examined. This effort involves the refinement of parameter and the exploration of alternate energetic models for molecules and environmental conditions. Ongoing projects include: - Development of Parameters for Alkane Systems - Approximation of Long-Range Interactions in Macromolecular Simulation Variants of the Cell Multiple Method - New Methods for Long Range Truncation of the Energy Potential: Evaluation and Comparison of Implicit and Explicit Water Models for Simulations Examining the Hydration of Proteins - Molecular Dynamics Simulation Studies of DNA: Analysis of the Parameter Sets Using an Infinite DNA Helix - Analysis of Conformation of Changes in Solvent Ab Initio Studies