FAST INTEGRAL METHOD FOR THE POISSON-BOLTZMANN EQUATION

泊松-玻尔兹曼方程的快速积分方法

• 批准号: 6015317
• 负责人: ALEXANDER H BOSCHITSCH
• 金额: $ 36.94万
• 依托单位: CONTINUUM DYNAMICS, INC.
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-04-01 至 2001-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6015317
• 关键词: computer program /software; computer system design /evaluation; ionic bond; mathematics; method development; molecular dynamics; physical chemical interaction; technology /technique development

The Phase I effort successfully developed a fast boundary element method (BEM) to solve the linear Poisson-Boltzmann equation (PBE) for biomolecules immersed in ionic solution. Unlike previous fast BEMs which were limited to the Poisson equation (corresponding to zero ionic strength), the new BEM accommodates ionic strength effects and thus represents a major advance in biomolecular modeling. Problems involving up to 80,000 boundary elements were successfully carried out upon readily accessibly workstations. In Phase II, this new capability will be extended to solve the nonlinear PBE, efficiently couple the PBE solutions to molecular dynamics (MD) codes and model multiple molecules in relative motion. Modeling enhancements designed to further improve accuracy and reduce computational requirements will also be incorporated, including a novel local correction method for close surface-charge interactions. The fast parallel BEM analysis developed in Phase II will be extended to accommodate these new capabilities. To promote strong commercialization prospects, the input/output will be configured to interface with existing MD and molecular surface generation codes. The fast BEM PBE solver will be applied to large-scale biomolecular systems that have been previous inaccessible with emphasis upon advancing basic biological research and demonstrating the modeling capabilities of the fast nonlinear PBE analysis. PROPOSED COMMERCIAL APPLICATIONS: Successful completion of the Phase II effort will result in new powerful computational tools to address an enormous range of applications governed by the linear/nonlinear Poisson/Poisson/Boltzmann PDEs. The resulting software tools will allow researchers in government, academia and industry to carry out accurate electrostatic modeling studies of the large-scale biological systems on workstations or PCs. The knowledge gained from such studies will be valuable to the pharmaceutical and biomedical community.

第一阶段的努力成功开发了一种快速边界元素方法（BEM），以求解浸入离子溶液中的生物分子的线性泊松托架方程（PBE）。与以前仅限于泊松方程（对应于零离子强度）的快速BEM不同，新的BEM可容纳离子强度效应，因此代表了生物分子建模的重大进展。在容易访问的工作站上，成功实现了涉及多达80,000个边界要素的问题。在第二阶段，将扩展该新功能以求解非线性PBE，有效地将PBE溶液与分子动力学（MD）代码相结合，并在相对运动中模拟多个分子。旨在进一步提高准确性并降低计算需求的建模增强功能也将合并，包括一种新型的局部校正方法，用于近距离表面充电相互作用。在第二阶段开发的快速平行BEM分析将扩展以适应这些新功能。为了促进强大的商业化前景，输入/输出将配置为与现有的MD和分子表面生成代码的接口。快速BEM PBE求解器将应用于以前无法访问的大型生物分子系统，重点是推进基本的生物学研究并证明快速非线性PBE分析的建模能力。拟议的商业应用程序：成功完成II期的工作将导致新的强大计算工具，以解决由线性/非线性泊松/泊松/泊松/玻尔兹曼PDES控制的大量应用程序。最终的软件工具将使政府，学术界和行业的研究人员能够对工作站或PC上的大型生物系统进行准确的静电建模研究。从此类研究中获得的知识将对制药和生物医学界有价值。