CAREER: Deoxyribozyme-Deoxyribozyme Logic, a New Computational Substrate

脱氧核酶-脱氧核酶逻辑，一种新的计算底物脱氧核酶（核酸酶）是一系列分子级基本逻辑门的基础，这些逻辑门具有相同类型的输入和输出信号，如寡核苷酸浓度，并在溶液中工作。 这些门的化学动力学特性正在通过协作实验，分析建模和计算机模拟进行研究。 正在研究由基本门组成的能够自主执行复杂布尔函数（决策）以及其他计算任务的大型电路的动态特性，包括门之间通信的可靠性，以表征此类电路的功能行为和性能。 通过这项工作，有关大规模化学动力学建模、寡核苷酸库设计和其他组合问题的知识水平正在提高，计算机科学与生物化学和纳米技术之间的跨学科合作正在建立。通过参与研究和编制课程，正在对本科生和研究生进行生物信息学新兴领域的培训。最后，正在为诊断和治疗应用奠定基础，在这些应用中，可以根据布尔标准分析单个细胞，从而可以可靠地将患病细胞与健康细胞区分开来，并进行特定治疗。

EIA-0243796Darko StefanovicUniversity of New MexicoDeoxyribozyme-deoxyribozyme Logic, a new computational substrateDeoxyribozymes (nucleic acid enzymes) are the basis for a family of molecular-scale elementary logic gates which have input and output signals of the same kind, as concentrations of oligonucleotides, and which operate in solution. Chemical-kinetic properties of these gates are being studied through collaborative experiments, analytical modelling, and computer simulation. Dynamic properties of larger circuits composed of elementary gates and capable of autonomously carrying out complex Boolean functions (decision-making) as well as other computational tasks are being studied, including the reliability of communication between gates, in order to characterize the functional behavior and performance of such circuits. Analysis and synthesis tools tailored to deoxyribozyme-based logic are being developed.Through this work, the state of knowledge about large-scale chemical kinetics modelling, oligonucleotide library design and other combinatorial problems is being advanced, and interdisciplinary collaborations between computer science and biochemistry and nanotechnology are being established. Through involvement in research and through curriculum development, undergraduate and graduate students are being trained in the emerging area of bioinformatics. Finally, foundations are being laid for diagnostic and therapeutic applications in which individual cells can be analyzed according to Boolean criteria, so that diseased cells can be reliably distinguished from healthy ones and specifically treated.