Virus-Inspired Declarative Geometric Computation

meera sitharamflorida大学病毒启发的声明式几何计算该项目的目标是为病毒的组成蛋白组装和病毒晶体包装开发几何计算模型和工具。此外，上述过程的灵感被用于重新思考计算上可处理的声明性几何（DG），定义为直观的、基于约束的表示和简单交互几何对象的组合的有效实现，从组合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础类代数几何计算和相应的代数变种。以PI的几何约束求解器FRONTIER形式存在的软件正在形成实现新的计算框架的基础。新的病毒计算模型用于研究以下未解决的问题，这些问题涉及精心挑选的具有几何意义的病毒：(a)在组装过程中分离出关键的几何事件（有助于破坏组装）；(b)分离需要病毒基因组物质参与的组装事件，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版本）。通过检查病毒及其组成蛋白在组装和结晶过程中的已知行为的一致性，正在对新的DG病毒模型进行改进和验证。少量其他高度集中的实验；选择性x射线晶体学和/或低温电子显微镜正在进行。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），其结构和性质特别适合项目的目标。正在将新的几何病毒模型与其他基于几何的计算病毒模型进行比较。

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.