SHF: Large: Collaborative Research: Molecular computing for the real world

Portland State University, Portland OR

Investigators

Abstract

Molecular computing is a promising computational paradigm in which computational functions are evaluated at the nanoscale, with potential applications in smart molecular diagnostics and therapeutics. A molecular computing system comprises biomolecules, such as DNA strands, which have been designed to detect certain input molecules by binding to them and subsequently to undergo programmed sequences of chemical reactions that serve to compute a logical function based on the observed pattern of input molecules. For example, a molecular system that requires both of its two inputs to be present simultaneously in order to generate an output signal would be referred to as computing a logical "AND" function on the two inputs. However, despite recent advances in the field, prospects for direct application of these techniques to solve real-world problems are limited by the lack of robust interfaces between molecular computers and biological and chemical systems. This project will address this limitation by targeting two specific application domains: wide-spectrum chemical sensing and cell surface analysis using molecular logic cascades. The state of the art in molecular computer design, modeling, and implementation will be advanced by an interdisciplinary combination of research by computer scientists, bioengineers, chemists, and computer engineers, and successful completion of the proposed activity will be a significant step towards routine deployment of molecular computers to address real-world problems in chemical and biological sensing. In this project, molecular circuit architectures that process sensor inputs from chemical sensors and cell-surface analysis reactions will be designed, modeled, and implemented in the laboratory. This will require specific advances in the isolation of aptamers (DNA sequences that exhibit particular binding affinity to one or more target non-nucleic acid molecules) and in their integration into molecular computing systems. In this context, the aptamer will serve as an interface that allows a rationally-designed DNA-based molecular computing system to use small molecules as input signals. Furthermore, computational modeling and simulation will be used to predict and optimize interactions between DNA aptamers and a range of binding targets, and to choose optimal aptamer combinations to produce cross-reactive multi-sensor arrays capable of discriminating between target ligands by effectively projecting the signal into a multi-dimensional aptamer response space. Furthermore, advanced molecular circuit architectures capable of adaptive, bio-inspired behavior, such as dynamic learning and adaptation, will be designed, with a view to future experimental implementations of these features in large-scale molecular computers. This will include research on highly recurrent, bio-inspired information processing networks to extract meaningful responses from potentially non-specific aptamer-based sensors.