Virus-Inspired Declarative Geometric Computation

EIA-0218435 Meera Sitharam佛罗里达大学病毒启发的声明性几何计算该项目的目标是开发几何计算模型和工具，用于从其组成蛋白质和病毒晶体包装中组装病毒。此外，上述过程的灵感被用来重新思考计算上易处理的声明性几何（DG），定义为直观的，基于约束的表示和有效实现的简单的交互几何对象的复合材料，从复合材料的属性的声明性规范开始。特别是，一个新的博弈论约束模型正在开发的基本类的代数几何计算和相应的代数品种。PI的几何约束求解器FRONTIER形式的现有软件正在形成实施新的计算框架的基础。新的病毒计算模型被用于研究以下关于精心选择的、具有几何意义的病毒的未回答的问题：（a）在组装过程中关键几何事件的隔离（有助于破坏装配）;（B）分离装配事件-如分子构象变化-其需要病毒基因组物质的参与，（有助于理解DNA-蛋白质相互作用）;以及（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病毒模型正在通过检查与病毒及其组成蛋白在组装过程中的已知行为的一致性进行改进和验证。和结晶。正在进行少数其他高度集中的实验;选择性X射线晶体学和/或冷冻电子显微镜。作为帮助实现上述两个目标的重要参与者，将使用独特的玉米条纹病毒（MSV），其结构和特性特别适合该项目的目标。新的几何病毒模型与其他基于几何的计算病毒模型的比较。

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.