Collaborative Research: Constrained and Error-Control Coding for DNA Computers

项目摘要在过去的几十年里，信息处理和存储领域的理论进步导致了现代通信技术领域的杰出发展。在数学和计算机科学方面积累的大量有关这一主题的知识，预计将在包括分子生物学和生物医学工程在内的其他不同科学和工程分支的未来进展中发挥重要作用。生物系统是已知的最完美的信息处理和存储设备，但人们对其功能和操作的数学原理知之甚少。如果不能更深入地了解这些特征，许多旨在复制自然交流途径的新兴技术将无法充分发挥其潜力。这个问题对基于DNA和RNA的计算机具有特别重要的意义，这些计算机被提议用于涉及计算困难问题的解算器的应用，以及用于能够调节和正常化癌细胞中基因表达水平的“智能药物”系统。研究人员解决了基于DNA的计算机和DNA存储设备的差错控制和约束编码的各个方面，这有助于提高正在考虑的系统的性能和可靠性。该研究从信息论和统计物理的角度分析了RNA和单链DNA折叠和杂交模式的数学性质，并开发了用于算法DNA自组装的构建DNA瓦集的新的纠错方法。本研究基于代数信道编码、组合优化和设计理论的经典思想和一些新思想。此外，研究人员根据与编码理论迭代系统密切相关的图形结构来研究基因调控网络的建模问题。

Project AbstractIn the past decades, theoretical advances in the area of information processing and storage have lead to outstanding developments in the field of modern communication technology. The vast accumulated knowledge in mathematics and computer science pertaining to this subject matter is expected to play a major role in the future progress of other diverse scientific and engineering branches, including molecular biology and biomedical engineering. Biological systems are the most perfect known information processing and storage devices, but very little is known about the mathematical principles of their functions and operations. Without a deeper understanding of these characteristics, many emerging technologies aimed at replicating nature's communication pathways will not achieve their full potential. This issue is of special importance for DNA and RNA-based computers, proposed for applications involving solvers of computationally hard problems and for use in "smart drug" systems, capable of regulating and normalizing gene expressions levels in cancerous cells. The investigators address various aspects of error-control and constrained coding for DNA based computers and DNA storage devices, which can aid in improving the performance and reliability of the systems under consideration. The research involves analyzing mathematical properties of RNA and single-stranded DNA folding and hybridization patterns from the perspective of information theory and statistical physics, and developing novel error-correction methods for constructing DNA tile sets used in algorithmic DNA self-assembly. The study is based on classical and some novel ideas from algebraic channel coding, combinatorial optimization and design theory. Furthermore, the investigators study the problem of modeling gene regulatory networks in terms of graphical structures closely related to coding-theoretic iterative systems.