CDI-Type II: Collaborative Research: Computing with Biomolecules: From Network Motifs to Complex and Adaptive Systems

分子可以被组织，甚至是自组织来执行复杂的任务吗？这个问题似乎应该有一个肯定的答案，因为我们周围的世界，尤其是其中的生物，是由大量的分子组成的。然而，与电子学和计算机相比，化学迄今所取得的分子系统或网络的复杂性相形见绌。一个由化学家、工程师和计算机科学家组成的团队联手探索如何利用分子来实现复杂的行为，包括简单形式的计算、适应和学习。他们将致力于发现制造大而有用的分子电路所需的工程原理。他们将从构建DNA酶网络开始，其中一种酶的作用会刺激另一种酶，就像活细胞中的蛋白质酶会相互刺激一样。他们将建立能够探测环境变化模式的网络；例如，周期性刺激的强度和频率。最终，他们将建立一个大型网络，该网络具有学习（记忆和概括）过去刺激模式的能力，并相应地对环境中的新条件做出反应。智力优势：该项目将开发生物相容性的DNA分子传感器和执行器，将立即用于病原体检测、非侵入性诊断和智能治疗。随着项目的进展，这些将与我们将开发的更强大的生物分子学习机器相结合，但它们也可以被其他研究人员或医生独立使用。更广泛的影响：该项目将延伸到俄勒冈州、新墨西哥州和纽约市中心服务不足的社区，为高中生和本科生提供参与跨学科科学研究的机会。

Can molecules be organized, or even self-organize, to perform complex tasks? This question seemingly should have an answer in the affirmative, because all the world around us, and especially the living things in it, is a mass of molecules. Yet the complexity of molecular systems, or networks, that chemistry has achieved to date pales in comparison with electronics and computers. A team of chemists, engineers, and computer scientists join forces to explore how molecules can be harnessed to achieve complex behaviors, including simple forms of computation, adaptation, and learning. They will work to discover the engineering principles needed to make large and useful molecular circuits. They will start by building networks of DNA enzymes, where actions of one enzyme stimulate another, just as protein enzymes stimulate one another in a living cell. They will build networks that can detect patterns of change in the environment; for example, the strength and the frequency of a periodic stimulation. Ultimately, they will build large networks that embody the ability to learn (memorize and generalize) patterns of past stimulation, and respond to new conditions in the environment accordingly.Intellectual Merit: The project will develop biocompatible, DNA molecular sensors and actuators that will be of immediate use in pathogen detection, non-invasive diagnostics, and intelligent therapeutics. As the project progresses, these will be combined with ever more capable biomolecular learning machines we will develop, but they can also be used independently by other researchers or medical doctors.Broader Impacts: The project will reach out to underserved communities in Oregon, New Mexico, and inner-city New York, providing high-school students and undergraduates an opportunity to engage in interdisciplinary scientific research.