Virus-Inspired Declarative Geometric Computation

受病毒启发的声明式几何计算

• 批准号: 0218435
• 负责人: Meera Sitharam
• 金额: $ 30万
• 依托单位: University of Florida
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-01 至 2006-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0218435&HistoricalAwards=false
• 关键词: Virus; Inspired; Declarative; Geometric; Computation

EIA-0218435Meera SitharamUniversity of Florida Virus-Inspired Declarative Geometric ComputationThe goal of the project is to develop geometric computational models and tools for virus assembly from their constituent proteins, and virus crystal packing. Furthermore, inspiration of the above processes is being used to rethink computationally tractable declarative geometry (DG), defined as the intuitive, constraint-based representation and efficient realization of composites of simple interacting geometric objects, starting from a declarative specification of the composite's properties. In particular, a new game-theoretic constraint model is being developed for the underlying class of algebraic-geometric computations and corresponding algebraic varieties. Existing software in the form of the PI's geometric constraint solver FRONTIER is forming the base for implementing the new computational framework. The new virus computational models is used for the studying the following unanswered questions on carefully chosen, geometrically significant viruses: (a) the isolation of crucial geometric events during assembly (helpful for disrupting assembly); (b) the isolation of assembly events - such as molecular conformational changes - that require the involvement of viral genomic material, (helpful for understanding DNA-protein interactions); and (c) the isolation of key geometric events during virus crystallization (as an idealized version of molecular crystallization).The new DG virus models is being refined and validated by checking consistency with known behavior of viruses and their constituent proteins during assembly and crystallization. A small number of other highly focused experiments; selective X-ray crystallography and/or cryoelectron microscopy is being performed. As a significant player to help with both of the above goals, use the distinctive Maize-streak virus (MSV) will be used, whose structure and properties are particularly suited to goals of the project. A comparison of the new geometric virus models with other geometry-based computational virus models is being made.

EIA-0218435Meera sitharamuniversity佛罗里达病毒启发的声明的几何计算该项目的目标是从其成本蛋白和病毒晶体包装开发用于病毒组装的几何计算模型和工具。此外，上述过程的灵感被用来重新考虑计算上可触犯的声明几何（DG），该几何（DG）定义为基于直观的，基于约束的表示，并有效地实现了简单交互几何对象的复合材料，从复合材料的声明规范开始。特别是，为基础代数几何计算和相应的代数品种开发了一种新的游戏理论约束模型。 PI几何约束求解器边境形式的现有软件正在构成实施新计算框架的基础。新的病毒计算模型用于研究有关精心选择的，几何意义的病毒的以下未解决的问题：（a）在组装过程中隔离至关重要的几何事件（有助于干扰组装）； （b）需要隔离病毒基因组材料的组装事件（例如分子构象变化）（有助于理解DNA-蛋白质相互作用）； （c）病毒结晶过程中关键几何事件的分离（作为分子结晶的理想化版本）。新的DG病毒模型正在通过与已知的病毒行为及其组成蛋白的一致性进行完善和验证，并在组装和结晶过程中。少数其他高度专注的实验；选择性X射线晶体学和/或冷冻电子显微镜正在进行。作为帮助实现这两个目标的重要参与者，将使用独特的玉米污染病毒（MSV），其结构和属性特别适合该项目的目标。正在对新几何病毒模型与其他基于几何的计算病毒模型进行比较。