Direct-Write Ion Beam Lithography

Patterning with a focused ion beam (FIB) is an extremely versatile fabrication process that can be used to create microscale and nanoscale designs on the surface of practically any solid sample material. Based on the type of ion-sample interaction utilized, FIB-based manufacturing can be both subtractive and additive, even in the same processing step. Indeed, the capability of easily creating three-dimensional patterns and shaping objects by milling and deposition is probably the most recognized feature of ion beam lithography (IBL) and micromachining. However, there exist several other techniques, such as ion implantation- and ion damage-based patterning and surface functionalization types of processes that have emerged as valuable additions to the nanofabrication toolkit and that are less widely known. While fabrication throughput, in general, is arguably low due to the serial nature of the direct-writing process, speed is not necessarily a problem in these IBL applications that work with small ion doses. Here we provide a comprehensive review of ion beam lithography in general and a practical guide to the individual IBL techniques developed to date. Special attention is given to applications in nanofabrication

Demonstration of Automated DNA Assembly on a Digital Microfluidic Device

The rapid manufacturing of highly accurate synthetic DNA is crucial for its use as a molecular tool, the understanding and engineering of regulatory elements, protein engineering, genetic refactoring, engineered genetic networks and metabolic pathways, and whole-genome syntheses [1,2]. Recent efforts in the development of enzyme mediated oligonucleotide synthesis have shown much potential to benefit conventional DNA synthesis [3–5]. With its success in applications as chemical microreactors [6–10], biological assays [8–14], and clinical diagnostic tools [10,15–19], digital microfluidic (DMF) devices are an attractive platform to apply the promising benefits of enzymatic oligonucleotide synthesis to the manufacturing of synthetic DNA. This thesis work aims to demonstrate automated DNA assembly using oligonucleotides on a DMF device through the demonstration and validation of an automated DNA assembly protocol. The prototyping process performed through this work revealed various important design considerations for the reliability of fluid handling performance and the mitigation of failure modes. To prevent dielectric breakdown or electrolysis, a relatively thick SU-8 3005 dielectric is used to remove the sensitivity of the device to variances in dielectric thickness and quality. To enable droplet creation, the gap distance between the DMF chip and top-plate is created and minimized using a thick SU-8 2100 layer. Reliable droplet creation is achieved through the use of electrode geometry that targets predictable fluid delivery and cutting. Reliable droplet transport is achieved through the use of a electrode interdigitation geometry that targets lower total electrode surface area and higher interdigitation contact area. The testing of DNA laden fluids revealed that biofouling can be a large concern for the demonstration of DNA assembly on a DMF device if droplets are moved through an air medium. To mitigate its effects, the final DMF device design featured the use of a permanently bonded top-plate with bored inlet/outlet ports as well as a silicone oil medium. The final DMF device design was used to demonstrate automated DNA assembly. This demonstration involved the creation, transport, and mixing of DNA brick samples. These samples are subsequently incubated on a chemical bench or on the DMF chip to create recombinant DNA containing genetic information. DNA gel imaging of DNA assembly products from on-chip protocols compared to protocols performed on a chemical benchtop revealed comparable results. Through the course of this work, the applicability of automated DNA assembly on a DMF device was validated to provide preliminary results in the ultimate goal of DNA synthesis using enzymatic oligonucleotide synthesis

Solid immersion lens applications for nanophotonic devices

Solid immersion lens (SIL) microscopy combines the advantages of conventional microscopy with those of near-field techniques, and is being increasingly adopted across a diverse range of technologies and applications. A comprehensive overview of the state-of-the-art in this rapidly expanding subject is therefore increasingly relevant. Important benefits are enabled by SIL-focusing, including an improved lateral and axial spatial profiling resolution when a SIL is used in laser-scanning microscopy or excitation, and an improved collection efficiency when a SIL is used in a light-collection mode, for example in fluorescence micro-spectroscopy. These advantages arise from the increase in numerical aperture (NA) that is provided by a SIL. Other SIL-enhanced improvements, for example spherical-aberration-free sub-surface imaging, are a fundamental consequence of the aplanatic imaging condition that results from the spherical geometry of the SIL. Beginning with an introduction to the theory of SIL imaging, the unique properties of SILs are exposed to provide advantages in applications involving the interrogation of photonic and electronic nanostructures. Such applications range from the sub-surface examination of the complex three-dimensional microstructures fabricated in silicon integrated circuits, to quantum photoluminescence and transmission measurements in semiconductor quantum dot nanostructures