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 …

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 …

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 …

In Silico Sequence Optimization For The Reproducible Generation Of Dna Structures, Michael D. Tobiason

Boise State University Theses and Dissertations

Biologically, deoxyribonucleic acid (DNA) molecules have been used for information storage for more than 3 billion years. Today, modern synthesis tools have made it possible to use synthetic DNA molecules as a material for engineering nanoscale structures. These self-assembling structures are capable of both resolutions as fine as 4 angstroms and executing programed dynamic behavior. Numerous approaches for creating structures from DNA have been proposed and validated, however it remains commonplace for engineered systems to exhibit unexpected behaviors such as low formation yields, poor performance, or total failure. It is plausible that at least some of these behaviors arise due …

Kinetic Control Of Nucleic Acid Strand Displacement Reactions, Xiaoping Olson

Boise State University Theses and Dissertations

Nucleic acids are information-dense, programmable polymers that can be engineered into primers, probes, molecular motors, and signal amplification circuits for computation, diagnostic, and therapeutic purposes. Signal amplification circuits increase the signal-to-noise ratio of target nucleic acids in the absence of enzymes and thermal cycling. Amplification is made possible via toehold mediated strand displacement – a process where one nucleic acid strand binds to a nucleation site on a complementary helix, which then displaces one of the two strands in a nucleic acid complex. When compared to polymerase chain reactions (PCR), the sensitivity and stability of toehold-mediated strand displacement reactions suffer …

Coarse-Grained Simulations Of The Self-Assembly Of Dna-Linked Gold Nanoparticle Building Blocks, Charles Wrightsman Armistead

Graduate Theses and Dissertations

The self-assembly of nanoparticles (NPs) of varying shape, size, and composition for the purpose of constructing useful nanoassemblies with tailored properties remains challenging. Although progress has been made to design anisotropic building blocks that exhibit the required control for the precise placement of various NPs within a defined arrangement, there still exists obstacles in the technology to maximize the programmability in the self-assembly of NP building blocks. Currently, the self-assembly of nanostructures involves much experimental trial and error. Computational modeling is a possible approach that could be utilized to facilitate the purposeful design of the self-assembly of NP building blocks …

Design, Synthesis, And Characterization Of Nanoscale Optical Devices Using Dna Directed Self-Assembly, William Peter Klein

Boise State University Theses and Dissertations

Near-field energy transfer has great potential for use in nanoscale communications, biosensing, and light harvesting photonic devices. However, the light collecting and energy transferring efficiency of current devices is poor, resulting in few commercially available applications. Current human-made light harvesting devices lack the benefits of natural selection. Natural systems are typically highly optimized and highly efficient. For example, transfer efficiency in photosynthesis is greater than 90%.

In this work, two classes of optical devices were designed, synthesized, and characterized: Plasmonic waveguides and FRET-based photonic devices. In the case of plasmonic waveguides, a multi-scaffold DNA origami synthesis method was developed to …

Molecular Combing Of Dna Nanofibers And Comparison To Electrospinning, Tanner L. Buresh

UCARE Research Products

The goal of these experiments was to create DNA nanofibers through the method of molecular combing (MC) and then compare the MC fibers to fibers created with electrospinning (ES). The experiment was designed and initial samples were created. After confirming that the method would succeed in creating DNA fibers, several parametric studies were performed in order to optimize the experiment and create the most uniform fibers possible. The parametric studies were done on the following variables: substrate material, pH level of DNA solution, and DNA solution concentration. After completion of all experiments, it was determined that although fibers could be …

Functionalization And Length Fractionation Of Single-Wall Carbon Nanotubes, Nina A. Bragg, Jing Pan, Jong Hyun Choi

The Summer Undergraduate Research Fellowship (SURF) Symposium

Single-wall carbon nanotubes (SWCNTs) are a promising material for future biological applications such as imaging and targeted drug delivery. SWCNTs can be made soluble in water through surface functionalization, a priority for their use in biology. By studying the surface chemistry of SWCNTs, various functionalization methods can be accomplished without perturbing their electronic structure. This study probes the use of pyrene derivatives and phospholipids to non-covalently functionalize SWCNTs, maintaining useful surface properties. Phospholipids cross-linked to polyethylene glycol (PEG) or 1-pyrenebutyric acid conjugated to DNA is anchored onto the sidewalls of SWCNTs by hydrophobic interactions or π-stacking. The PEG/DNA portion is …

Nanoenabled Microelectromechanical Sensor For Volatile Organic Chemical Detection, Chiara Zuniga, Matteo Rinaldi, Samuel M. Khamis, A. T. Johnson, Gianluca Piazza

Matteo Rinaldi

A nanoenabled gravimetric chemical sensor prototype based on the large scale integration of single-stranded DNA (ss-DNA) decorated single-walled carbon nanotubes (SWNTs) as nanofunctionalization layer for aluminum nitride contour-mode resonant microelectromechanical (MEM) gravimetric sensors has been demonstrated. The capability of two distinct single strands of DNA bound to SWNTs to enhance differently the adsorption of volatile organic compounds such as dinitroluene (simulant for explosive vapor) and dymethyl-methylphosphonate (simulant for nerve agent sarin) has been verified experimentally. Different levels of sensitivity (17.3 and 28 KHz µm^2/fg) due to separate frequencies of operation (287 and 450 MHz) on the same die have also …

Artificial And Natural Nucleic Acid Self Assembling Systems, Marcus Wood

Wayne State University Dissertations

Nucleic acids are good candidates for nanomachine construction. They participate in all the processes of life, and so can function as structural building blocks and dynamic catalysts. However, to use nucleic acids as nanomachines, a better understanding of their material properties, how to design structures using them, and their dynamics is needed. We have tried to address these issues, in a small way, with nucleic acid force field development, an attempt at nanostructural design and synthesis using DNA, and a study of the RNA/protein regulatory dynamics of the tryptophan regulatory attenuation protein.

Dna-Decorated Carbon Nanotubes As Sensitive Layer For Aln Contour-Mode Resonant-Mems Gravimetric Sensor, Chiara Zuniga, Matteo Rinaldi, Samuel M. Khamis, Timothy S. Jones, A T. Johnson, Gianluca Piazza

Matteo Rinaldi

In this work a nano-enabled gravimetric chemical sensor prototype based on single-stranded DNA (ss-DNA) decorated single-walled carbon nanotubes (SWNT) as nano-functionalization layer for Aluminun Nitride (AIN) contour-mode resonant-MEMS gravimetric sensors has been demonstrated. Two resonators fabricated on the same silicon chip and operating at different resonance frequencies, 287 and 450 MHz, were functionalized with this novel bio-coating layer to experimentally prove the capability of two distinct single strands of DNA bound to SWNT to enhance differently the adsorption of volatile organic compounds such as dinitroluene (DNT, simulant for explosive vapor) and dymethyl-methylphosphonate (DMMP, a simulant for nerve agent sarin). The …

Nanoenabled Microelectromechanical Sensor For Volatile Organic Chemical Detection, Chiara Zuniga, Matteo Rinaldi, Samuel M. Khamis, A. T. Johnson, Gianluca Piazza

Matteo Rinaldi

A nanoenabled gravimetric chemical sensor prototype based on the large scale integration of single-stranded DNA (ss-DNA) decorated single-walled carbon nanotubes (SWNTs) as nanofunctionalization layer for aluminum nitride contour-mode resonant microelectromechanical (MEM) gravimetric sensors has been demonstrated. The capability of two distinct single strands of DNA bound to SWNTs to enhance differently the adsorption of volatile organic compounds such as dinitroluene (simulant for explosive vapor) and dymethyl-methylphosphonate (simulant for nerve agent sarin) has been verified experimentally. Different levels of sensitivity (17.3 and 28 KHz µm^2/fg) due to separate frequencies of operation (287 and 450 MHz) on the same die have also …

Cationic Surfactant Mediated Hybridization And Hydrophobization Of Dna Molecules At The Liquid/Liquid Interface And Their Phase Transfer, Murali Sastry, Ashavani Kumar, Mrunalini Pattarkine, Vidya Ramakrishnan, Krishna N. Ganesh

Faculty Works

Hybridization of complementary oligonucleotides mediated by a cationic surfactant at the water/hexane interface leads to hydrophobic, double-helical DNA which may be readily phase transferred to the organic phase and cast into thin films on solid substrates.

Study Of The Effect Of Rare Earth Ions On Dna Using Cyclic Voltammetry And Spectroscopy, Heibai Shen, Yuzhuan Kang, Haifeng Yang, Lin Yu, Zongrang Zhang

Journal of Electrochemistry

The interaction between rare earth ions(e.g.Eu 3+ ,Ce 3+ ,Er 3+ ,Sm 3+ ,Tb 3+ ,La 3+ and Nd 3+ ) and DNA had been investigated by using Cyclic Voltammetry, Ultraviolet and Raman Spectroscopy. After the adding of Ce 3+ ion to DNA solution, the cathodic peak current of Ce 3+ ion reduction was found to decrease obviously, and the anodic peak current to decrease even more significantly. Differential UV spectra of Ce 3+ ion depicted hyperchromic effect after the reaction of these two species and a new peak of 272 nm was found. Differential UV spectra of DNA also …