AF: Small: Explorations of Theoretical Models of Self-Assembly

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Project AbstractIn this proposal the PIs present plans to investigate a number of fundamental problems within theoretical models of self-assembly, as well as plans to directly engage a large number of students in research activities. Self-assembly is the process by which simple components autonomously come together by way of local interactions to form complex structures. Self-assembling systems are abundant in nature and are the key mechanisms for the formation of biological organisms. Further, self-assembly technology is emerging as a powerful tool for manipulating matter at the nanoscale. The development of a mature mathematical and computational understanding of self-assembly theory is an important step towards harnessing the power of self-assembly for the large scale fabrication of complex nanoscale devices such as circuits, molecular motors, nanoscale computers, and nano-biomedical devices.The focus of this project is theoretical studies which involve mathematical analyses and also the development of simulation software. Such theoretical work well complements ongoing experimental research and a key portion of this project involves regular visits to top experimental research labs such as Erik Winfree?s DNA and Natural Algorithms Group at Caltech and Russell Deaton?s DNA and Biomolecular Computing group at the University of Arkansas to engage in mutually beneficial discussions regarding the development of self-assembling models and systems. Such involvement can help to guide their long range experimental paths as well as provide the PIs with invaluable insight into the laboratory realities.In this proposal the PIs present a diverse array of projects which they will pursue with heavy student involvement. The following are brief descriptions of a few: the PIs will study the ability of self-assembling systems to self-replicate and evolve. These abilities are the fundamental cornerstones of living systems, and such studies will provide insights into how living systems originated and function. The PIs will extend, along several directions, a powerful model of fault tolerance which they recently introduced, fuzzy temperature fault tolerance. New fault tolerance techniques are of extreme importance if substantial products are to be realized from artificial self-assembling systems. The PIs will pursue studies in the power of randomization techniques for reducing tile complexity while generating close approximations of self-assembled shapes. The PIs will greatly extend the self-assembly software available for both teachers and researchers. The PIs simulator is currently used by several instructors and research groups and has great promise to help draw more students into the field, and research in general.The emphasis on undergraduate research of this project has broader impacts that are of particular interest to the NSF. The University of Texas-Pan American (UTPA), located in the South Texas Rio Grande Valley area, has more than 18,000 students, with an 89% Hispanic and 59% female student population. A primary goal of this proposal is to increase the research activity of UTPA Computer Science students by developing a large portion of the research within the environment of student-centered research seminars. The PIs plan to further develop current research seminars into full courses to involve a larger number of students in original research. Because of the nature of the UTPA student body, this plan will help broaden participation in post graduate Computer Science among under-represented minority groups. The PIs also propose to support the broader research community by providing much needed educational and research software.