DEVELOPMENT OF THEORETICAL METHODS FOR STUDYING BIOLOGICAL MACROMOLECULES

正在开发的新理论技术经常与 软件和硬件开发。这些都涉及到新的 仿真技术及其系统测试与评估 方法：研究方法。具体项目包括： -量子力学势的发展和适当的 用于分子动力学模拟的算法 -通过核磁共振和分子模拟确定蛋白质结构 -用于蛋白质测定的慢增长同源模型(SGHM) 构筑物 -制定一项最佳方案，以编制最低工资标准 温度状态 -开发灵活的MD技术，消除高频 自由度 --解中的自由能微扰模拟，检验效果 《禁闭》 -将物理模型转换为三维坐标 计算机分析与仿真。 -HP光线追踪分子图形软件的开发 工作站、高分辨率彩色打印机和使用NTSC的电影 视频设备。 -截断牛顿极小化算法对CHARMM和生物分子的适应性 应用 参数集和模型通常适用于大多数 大分子体系，但仍有相当大的改进空间 以及提高真实感或降低计算成本的替代模型， 需要检查一下。这项工作涉及到参数的改进 以及探索分子和分子的替代能量模型 环境条件。正在进行的项目包括： -开发烷烃体系的参数 --大分子模拟中的长程相互作用近似 细胞倍增法的变种 -能量势长期截断的新方法： 隐式和显式水模型的评价和比较 蛋白质水合反应的模拟研究 -DNA的分子动力学模拟研究：分析 使用无限DNA螺旋的参数集 -溶剂构象变化的分析从头算研究

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