Nanoscience and Nanotechnology Commons^™

Control Mechanisms For Adaptive Nanoscale Devices, David Arredondo

Nanoscience and Microsystems ETDs

Nanotechnology promises to revolutionize many areas of applied science including materials, synthetic biology, and medicine. Devices may consist of solution-phase information processing systems or molecular robots. Of particular interest are DNA-based systems due to their composability and relatively simple interactions that are suited to bottom-up design. This work introduces high-level designs of robust control mechanisms for nanoscale devices with immediate applications in molecular computing, synthetic biology, and DNA robotics.

Nanoscale systems are dominated by probabilistic chemical behavior, so engineers must take careful consideration to produce predictable systems. Probabilistic behavior in chemical reaction networks (CRNs) yields deterministic evolution of species concentrations …

Atomic Force Microscopy Based Dna Sensing And Manipulation, Matthew Shubert

Mechanical Engineering Undergraduate Honors Theses

Sequencing DNA provides a positive impact for the biomedical community by understanding a wide variety of applications such as human genetics, disease, and pathogens. The reason the Arkansas Micro & Nano Systems lab is involved with research in DNA sequencing is due to the current, leading industry method. Nanopore sequencing was developed by Oxford Nanopore Technology in which its sequencing method separates double stranded DNA to electrically characterize individual nucleotides traveling through a charged nanopore. Unfortunately, nanopore sequencing uses biological materials that require a shelf life and drives high cost. Therefore, the Arkansas Micro & Nano Systems lab has developed …

A Versatile Python Package For Simulating Dna Nanostructures With Oxdna, Kira Threlfall

Computer Science and Computer Engineering Undergraduate Honors Theses

The ability to synthesize custom DNA molecules has led to the feasibility of DNA nanotechnology. Synthesis is time-consuming and expensive, so simulations of proposed DNA designs are necessary. Open-source simulators, such as oxDNA, are available but often difficult to configure and interface with. Packages such as oxdna-tile-binding pro- vide an interface for oxDNA which allows for the ability to create scripts that automate the configuration process. This project works to improve the scripts in oxdna-tile-binding to improve integration with job scheduling systems commonly used in high-performance computing environments, improve ease-of-use and consistency within the scripts compos- ing oxdna-tile-binding, and move …