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

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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.