BIC: Cellular Inspired Garbage Collection: Ubiquitin System and Memory Management

BIC：细胞启发的垃圾收集：泛素系统和内存管理

• 批准号: 0432025
• 负责人: Daniel Lee
• 金额: $ 12.5万
• 依托单位: University of Pennsylvania
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-08-15 至 2006-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0432025&HistoricalAwards=false
• 关键词: BIC; Cellular; Inspired; Garbage; Collection

Garbage collection is a crucial component of many modern computer programming languages. Garbage collection frees programmers from the burden of explicit memory management, and is necessary for the independence of functional data objects in object-oriented programming paradigms. Unfortunately, traditional garbage collection algorithms are not ideally suited for concurrent operation in real-time embedded systems. On the other hand, cellular systems must also be able to identify and reclaim proteins that are no longer being used or are damaged or incomplete. The selective destruction and recycling of proteins is accomplished by the ubiquitin system in the cell. Proteins to be selectively destroyed are first identified and tagged with ubiquitin through a series of enzymatic reactions. These proteins are then degraded in the proteosome, and their constituent amino acids are recycled for the construction of new proteins.We propose using hybrid systems to model the enzymatic pathways in the ubiquitin system to gain insight into their computational properties. Our modeling and simulation efforts will describe how the ubiquitin conjugation ligases and the proteosome interact to selectively recognize the appropriate protein substrates. Our results on the ubiquitin system will help motivate new garbage recognition algorithms for memory management in computer systems. These algorithms will be based upon the hierarchical composition of classifiers that recognize characteristic features of the objects in memory.The educational goals of this proposal are closely tied to our research agenda. We hope to introduce students as well as other researchers to the importance of viewing biomolecular sytems as computational systems. The ubiquitin system will serve as a teaching illustration for students in seminars and future workshops, as well as for the public community through our collaboration with the Franklin Institute, the university's AMP summer program, and our annual Robotics for Girls workshop. Other educational activities will serve to inform and open dialogue between researchers in the engineering, biological sciences, and medical communities.

垃圾收集是许多现代计算机编程语言的关键组成部分。垃圾收集使程序员从明确的内存管理负担中释放出来，对于在面向对象的编程范式中的功能数据对象的独立性是必要的。不幸的是，传统的垃圾收集算法不适合在实时嵌入式系统中同时操作。另一方面，蜂窝系统还必须能够识别和回收不再使用或损坏或不完整的蛋白质。蛋白质的选择性破坏和回收通过细胞中的泛素系统完成。首先通过一系列酶促反应将要选择性破坏的蛋白质用泛素标记并标记为蛋白质。然后将这些蛋白质降解在蛋白质体中，其组成氨基酸被回收以构建新蛋白质。我们建议使用杂化系统对泛素系统中的酶促途径进行建模，以洞悉其计算特性。我们的建模和模拟工作将描述泛素结合连接酶和蛋白质体如何相互作用，以选择性地识别适当的蛋白质底物。我们在泛素系统上的结果将有助于激发计算机系统内存管理的新垃圾识别算法。这些算法将基于分类器的层次结构组成，这些分类器识别记忆中对象的特征特征。该提案的教育目标与我们的研究议程密切相关。我们希望向学生和其他研究人员介绍将生物分子系统视为计算系统的重要性。泛素系统将通过我们与富兰克林学院（Franklin Institute），大学的AMP夏季计划和我们的年度Girls Wormotics For Girls Workshop的合作，为研讨会和未来研讨会的学生以及公共社区的学生提供教学插图。其他教育活动将有助于为工程，生物科学和医学界研究人员之间的对话提供和公开对话。