Integrated genetic analysis systems

The overall objective of this thesis is to integrate a number of micro/nanotechnologies into integrated cartridge type systems to implement such biochemical protocols. Instrumentation and systems were developed to interface such cartridge systems: (i) implementing microfluidic handling, (ii) executing thermal control during biochemical protocols and (iii) detection of biomolecules associated with inherited or infectious disease. This system implements biochemical protocols for DNA extraction, amplification and detection. A digital microfluidic chip (ElectroWetting on Dielectric) manipulated droplets of sample and reagent implementing sample preparation protocols. The cartridge system also integrated a planar magnetic microcoil device to generate local magnetic field gradients, manipulating magnetic beads. For hybridisation detection a fluorescence microarray, screening for mutations associated with CFTR gene is printed on a waveguide surface and integrated within the cartridge. A second cartridge system was developed to implement amplification and detection screening for DNA associated with disease-causing pathogens e.g. Escherichia coli. This system incorporates (i) elastomeric pinch valves isolating liquids during biochemical protocols and (ii) a silver nanoparticle microarray for fluorescent signal enhancement, using localized surface plasmon resonance. The microfluidic structures facilitated the sample and reagent to be loaded and moved between chambers with external heaters implementing thermal steps for nucleic acid amplification and detection. In a technique allowing probe DNA to be immobilised within a microfluidic system using (3D) hydrogel structures a prepolymer solution containing probe DNA was formulated and introduced into the microfluidic channel. Photo-polymerisation was undertaken forming 3D hydrogel structures attached to the microfluidic channel surface. The prepolymer material, poly-ethyleneglycol (PEG), was used to form hydrogel structures containing probe DNA. This hydrogel formulation process was fast compared to conventional biomolecule immobilization techniques and was also biocompatible with the immobilised biomolecules, as verified by on-chip hybridisation assays. This process allowed control over hydrogel height growth at the micron scale.

Techniques for engineering quantum states

In this thesis I theoretically study quantum states of ultracold atoms. The majority of the Chapters focus on engineering specific quantum states of single atoms with high fidelity in experimentally realistic systems. In the sixth Chapter, I investigate the stability and dynamics of new multidimensional solitonic states that can be created in inhomogeneous atomic Bose-Einstein condensates. In Chapter three I present two papers in which I demonstrate how the coherent tunnelling by adiabatic passage (CTAP) process can be implemented in an experimentally realistic atom chip system, to coherently transfer the centre-of-mass of a single atom between two spatially distinct magnetic waveguides. In these works I also utilise GPU (Graphics Processing Unit) computing which offers a significant performance increase in the numerical simulation of the Schrödinger equation. In Chapter four I investigate the CTAP process for a linear arrangement of radio frequency traps where the centre-of-mass of both, single atoms and clouds of interacting atoms, can be coherently controlled. In Chapter five I present a theoretical study of adiabatic radio frequency potentials where I use Floquet theory to more accurately model situations where frequencies are close and/or field amplitudes are large. I also show how one can create highly versatile 2D adiabatic radio frequency potentials using multiple radio frequency fields with arbitrary field orientation and demonstrate their utility by simulating the creation of ring vortex solitons. In the sixth Chapter I discuss the stability and dynamics of a family of multidimensional solitonic states created in harmonically confined Bose-Einstein condensates. I demonstrate that these solitonic states have interesting dynamical instabilities, where a continuous collapse and revival of the initial state occurs. Through Bogoliubov analysis, I determine the modes responsible for the observed instabilities of each solitonic state and also extract information related to the time at which instability can be observed.

A simulation-based design method to transfer surface mount RF system to flip-chip die implementation

The flip-chip technology is a high chip density solution to meet the demand for very large scale integration design. For wireless sensor node or some similar RF applications, due to the growing requirements for the wearable and implantable implementations, flip-chip appears to be a leading technology to realize the integration and miniaturization. In this paper, flip-chip is considered as part of the whole system to affect the RF performance. A simulation based design is presented to transfer the surface mount PCB board to the flip-chip die package for the RF applications. Models are built by Q3D Extractor to extract the equivalent circuit based on the parasitic parameters of the interconnections, for both bare die and wire-bonding technologies. All the parameters and the PCB layout and stack-up are then modeled in the essential parts' design of the flip-chip RF circuit. By implementing simulation and optimization, a flip-chip package is re-designed by the parameters given by simulation sweep. Experimental results fit the simulation well for the comparison between pre-optimization and post-optimization of the bare die package's return loss performance. This design method could generally be used to transfer any surface mount PCB to flip-chip package for the RF systems or to predict the RF specifications of a RF system using the flip-chip technology.

Developing wireless measurement system for building deployed capacitive sensors with optimized RF front end circuit

In this paper, a prototype of miniaturized, low power, bi-directional wireless sensor node for wireless sensor networks (WSN) was designed for doors and windows building monitoring. The capacitive pressure sensors have been developed particularly for such application, where packaging size and minimization of the power requirements of the sensors are the major drivers. The capacitive pressure sensors have been fabricated using a 2.4 mum thick strain compensated heavily boron doped SiGeB diaphragm is presented. In order to integrate the sensors with the wireless module, the sensor dice was wire bonded onto TO package using chip on board (COB) technology. The telemetric link and its capabilities to send information for longer range have been significantly improved using a new design and optimization process. The simulation tool employed for this work was the Designerreg tool from Ansoft Corporation.

System packaging & integration for a swallowable capsule using a direct access sensor

Technological developments in biomedical microsystems are opening up new opportunities to improve healthcare procedures. Swallowable diagnostic capsules are an example of this. In this paper, a diagnostic capsule technology is described based on direct-access sensing of the Gastro Intestinal (GI) fluids throughout the GI tract. The objective of this paper is two-fold: i) develop a packaging method for a direct access sensor, ii) develop an encapsulation method to protect the system electronics. The integrity of the interconnection after sensor packaging and encapsulation is correlated to its reliability and thus of importance. The zero level packaging of the sensor was achieved by using a so called Flip Chip Over Hole (FCOH) method. This allowed the fluidic sensing media to interface with the sensor, while the rest of the chip including the electrical connections can be insulated effectively. Initial tests using Anisotropic Conductive Adhesive (ACA) interconnect for the FCOH demonstrated good electrical connections and functionality of the sensor chip. Also a preliminary encapsulation trial of the flip chipped sensor on a flexible test substrate has been carried out and showed that silicone encapsulation of the system is a viable option.

Development and reliability of a direct access sensor using flip chip on flex technology with anisotropic conductive adhesive

Technological developments in biomedical microsystems are opening up new opportunities to improve healthcare procedures. Swallowable diagnostic sensing capsules are an example of these. In none of the diagnostic sensing capsules, is the sensor’s first level packaging achieved via Flip Chip Over Hole (FCOH) method using Anisotropic Conductive Adhesive (ACA). In a capsule application with direct access sensor (DAS), ACA not only provides the electrical interconnection but simultaneously seals the interconnect area and the underlying electronics. The development showed that the ACA FCOH was a viable option for the DAS interconnection. Adequate adhesive formed a strong joint that withstood a shear stress of 120N/mm2 and a compressive stress of 6N required to secure the final sensor assembly in place before encapsulation. Electrical characterization of the ACA joint in a fluid environment showed that the ACA was saturated with moisture and that the ions in the solution actively contributed to the leakage current, characterized by the varying rate of change of conductance. Long term hygrothermal aging of the ACA joint showed that a thermal strain of 0.004 and a hygroscopic strain of 0.0052 were present and resulted in a fatigue like process. In-vitro tests showed that high temperature and acidity had a deleterious effect of the ACA and its joint. It also showed that the ACA contact joints positioned at around or over 1mm would survive the gastrointestinal (GI) fluids and would be able to provide a reliable contact during the entire 72hr of the GI transit time. A final capsule demonstrator was achieved by successfully integrating the DAS, the battery and the final foldable circuitry into a glycerine capsule. Final capsule soak tests suggested that the silicone encapsulated system could survive the 72hr gut transition.