BIC: Large-Scale DNA Associative Memories

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Intellectual Merit:In a DNA memory, information is encoded into DNA sequences and retrieved through template-matching hybridization reactions among DNA oligonucleotides. The template matching, hybridization reaction between DNA oligonucleotides is important in biotechnology and medicine (DNA microarrays),and nanotechnology (DNA directed self-assembly of nanostructures).The project should lead to a better understanding of how information can be encoded into an ensemble of hybridizing DNA oligonucleotides, and to better models andways of characterizing large ensembles.Simple protocols can be used to manipulate the contents of the memory to achieve information processing. In the statistical DNA memory, an ensemble of DNA molecules are trained with test tube protocols to reproduce particular input/output mappings, similar to artificial neural networks. Rather than a one to one mapping, information is encoded probabilistically into the DNA sequences and their hybridization interactions. These two architectures will be experimentally tested and modeled computationally and physically, and finally simulated to better understand how information is stored and manipulated through DNA template-matching hybridization reactions.Broader Impacts:Graduate students will participate in the project, and thus, will be trained in the interdisciplinary knowledge and methods required of computational research using biological systems. They will be mentored to produce research publications, attend professional conferences and write graduate theses. Curricular modules associated with the research will be developed for incorporation into both biological and computer curricula. These modules will provide instruction and demonstrations in the topic that show the interplay between the disciplines, as well as experimental, theoretical, and simulation methods. The goal is to produce students that are better prepared for careers and challenges in the emerging synthesis of biology and computation. The project results will be disseminated through a dedicated web site, and through conference and journals in the relevant disciplines.