Foundational Aspects of Biomolecular Information and Computation

就像我们用字母表的字母来写文本，用0和1位来写计算机机器代码一样，大自然用四个基本的DNA单位(腺嘌呤、鸟嘌呤、胞嘧啶、胸腺嘧啶)以DNA链的形式写入遗传信息。DNA上编码符号信息的可能性，以及DNA链的剪切和粘贴等生化过程已被证明能够进行算术和逻辑运算的事实，导致了DNA计算领域的发展。我研究的主要目标是分析这种在DNA链上存储和操作数据的新方式，因为生物信息和生物计算在几个方面与电子信息和生物计算根本不同。最重要的是，DNA编码的信息与记忆位置无关，而是由无限小的自由漂浮的DNA链组成，由于它们的沃森-克里克互补而相互作用。 这项提议旨在通过定义和研究基于DNA的信息和生物操作的形式语言理论模型，考虑到其生物底物的内在特征，为“生物信息和生物计算理论”奠定基础。除了扩展传统的信息和计算概念以解释自然界中发生的计算之外，本研究的结果还可以提供对生物分子信息的计算特性的见解，从而对其在实际应用中具有潜在的影响，例如，用于医疗诊断的多输入基于RNA的逻辑电路，或为纳米电子和纳米光学器件构建DNA纳米结构。这项研究的另一个方面是通过研究带有DNA瓦片的计算自组装系统模型的能力和局限性来探索通过自组装实现纳米计算的范例。这项研究的结果可能会对生物纳米技术的DNA结构的设计、评估和分析产生潜在的影响。

In the same way we use the letters of the alphabet to write text, and the bits 0 and 1 to write computer machine code, the four basic DNA units (Adenine, Guanine, Cytosine, Thymine) are used by Nature to write genetic information as DNA strands. The possibility of encoding symbolic information on DNA, and the fact that biochemical processes such as cut-and-paste of DNA strands have been proved to be able to perform arithmetic and logic operations, led to the development of the field of DNA computing. The primary goal of my research is to analyze this new way of storing and manipulating data on DNA strands, as bioinformation and biocomputation are fundamentally different from their electronic counterparts in several aspects. Most importantly, DNA-encoded information is not associated with a memory location but consists of infinitesimal free-floating DNA strands that interact with each other due to their Watson-Crick complementarity. This proposal aims to develop the foundations for a "theory of bioinformation and biocomputation", by defining and investigating formal-language-theoretic models of DNA-based information and bio-operations, that take into account the intrinsic characteristics of their biological substrates. Besides expanding the traditional notions of information and computation to account for computation taking place in nature, the results of this research could provide insights into the computational properties of biomolecular information and consequently have potential implications for their practical applications in, e.g., multi-input RNA-based logic circuits for medical diagnosis, or building DNA nanostructures for nanoelectronic and nano-optical devices. Another aspect of the proposed research is an exploration of the paradigm of nanocomputation by self-assembly by investigating the power and limitations of models of computational self-assembly systems with DNA tiles. The results of this research could have potential implications for the design, evaluation, and analysis of DNA architectures for bionanotechnology.