Control circuits for avalanche photodiodes

Avalanche Photodiodes (APDs) have been used in a wide range of low light sensing applications such as DNA sequencing, quantum key distribution, LIDAR and medical imaging. To operate the APDs, control circuits are required to achieve the desired performance characteristics. This thesis presents the work on development of three control circuits including a bias circuit, an active quench and reset circuit and a gain control circuit all of which are used for control and performance enhancement of the APDs. The bias circuit designed is used to bias planar APDs for operation in both linear and Geiger modes. The circuit is based on a dual charge pumps configuration and operates from a 5 V supply. It is capable of providing milliamp load currents for shallow-junction planar APDs that operate up to 40 V. With novel voltage regulators, the bias voltage provided by the circuit can be accurately controlled and easily adjusted by the end user. The circuit is highly integrable and provides an attractive solution for applications requiring a compact integrated APD device. The active quench and reset circuit is designed for APDs that operate in Geiger-mode and are required for photon counting. The circuit enables linear changes in the hold-off time of the Geiger-mode APD (GM-APD) from several nanoseconds to microseconds with a stable setting step of 6.5 ns. This facilitates setting the optimal `afterpulse-free' hold-off time for any GM-APD via user-controlled digital inputs. In addition this circuit doesn’t require an additional monostable or pulse generator to reset the detector, thus simplifying the circuit. Compared to existing solutions, this circuit provides more accurate and simpler control of the hold-off time while maintaining a comparable maximum count-rate of 35.2 Mcounts/s. The third circuit designed is a gain control circuit. This circuit is based on the idea of using two matched APDs to set and stabilize the gain. The circuit can provide high bias voltage for operating the planar APD, precisely set the APD’s gain (with the errors of less than 3%) and compensate for the changes in the temperature to maintain a more stable gain. The circuit operates without the need for external temperature sensing and control electronics thus lowering the system cost and complexity. It also provides a simpler and more compact solution compared to previous designs. The three circuits designed in this project were developed independently of each other and are used for improving different performance characteristics of the APD. Further research on the combination of the three circuits will produce a more compact APD-based solution for a wide range of applications.

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.

Nanofiber control of ultracold quantum gases

While a great amount of attention is being given to the development of nanodevices, both through academic research and private industry, the field is still on the verge. Progress hinges upon the development of tools and components that can precisely control the interaction between light and matter, and that can be efficiently integrated into nano-devices. Nanofibers are one of the most promising candidates for such purposes. However, in order to fully exploit their potential, a more intimate knowledge of how nanofibers interact with single neutral atoms must be gained. As we learn more about the properties of nanofiber modes, and the way they interface with atoms, and as the technology develops that allows them to be prepared with more precisely known properties, they become more and more adaptable and effective. The work presented in this thesis touches on many topics, which is testament to the broad range of applications and high degree of promise that nanofibers hold. For immediate use, we need to fully grasp how they can be best implemented as sensors, filters, detectors, and switches in existing nano-technologies. Areas of interest also include how they might be best exploited for probing atom-surface interactions, single-atom detection and single photon generation. Nanofiber research is also motivated by their potential integration into fundamental cold atom quantum experiments, and the role they can play there. Combining nanofibers with existing optical and quantum technologies is a powerful strategy for advancing areas like quantum computation, quantum information processing, and quantum communication. In this thesis I present a variety of theoretical work, which explores a range of the applications listed above. The first work presented concerns the use of the evanescent fields around a nanofiber to manipulate an existing trapping geometry and therefore influence the centre-of-mass dynamics of the atom. The second work presented explores interesting trapping geometries that can be achieved in the vicinity of a fiber in which just four modes are allowed to propagate. In a third study I explore the use of a nanofiber as a detector of small numbers of photons by calculating the rate of emission into the fiber modes when the fiber is moved along next to a regularly separated array of atoms. Also included are some results from a work in progress, where I consider the scattered field that appears along the nanofiber axis when a small number of atoms trapped along that axis are illuminated orthogonally; some interesting preliminary results are outlined. Finally, in contrast with the rest of the thesis, I consider some interesting physics that can be done in one of the trapping geometries that can be created around the fiber, here I explore the ground states of a phase separated two-component superfluid Bose-Einstein condensate trapped in a toroidal potential.

The exploration of potato-associated bacteria in the Central Andean Highlands and their application in integrated crop management systems

Potato is the most important food crop after wheat and rice. A changing climate, coupled with a heightened consumer awareness of how food is produced and legislative changes governing the usage of agrochemicals, means that alternative more integrated and sustainable approaches are needed for crop management practices. Bioprospecting in the Central Andean Highlands resulted in the isolation and in vitro screening of 600 bacterial isolates. The best performing isolates, under in vitro conditions, were field trialled in their home countries. Six of the isolates, Pseudomonas sp. R41805 (Bolivia), Pseudomonas palleroniana R43631 (Peru), Bacillus sp. R47065, R47131, Paenibacillus sp. B3a R49541, and Bacillus simplex M3-4 R49538 (Ecuador), showed significant increase in the yield of potato. Using – omic technologies (i.e. volatilomic, transcriptomic, proteomic and metabolomic), the influence of microbial isolates on plant defence responses was determined. Volatile organic compounds of bacterial isolates were identified using GC/MS. RT-qPCR analysis revealed the significant expression of Ethylene Response Factor 3 (ERF3) and the results of this study suggest that the dual inoculation of potato with Pseudomonas sp. R41805 and Rhizophagus irregularis MUCL 41833 may play a part in the activation of plant defence system via ERF3. The proteomic analysis by 2-DE study has shown that priming by Pseudomonas sp. R41805 can induce the expression of proteins related to photosynthesis and protein folding in in vitro potato plantlets. The metabolomics study has shown that the total glycoalkaloid (TGA) content of greenhouse-grown potato tubers following inoculation with Pseudomonas sp. R41805 did not exceed the acceptable safety limit (200 mg kg-1 FW). As a result of this study, a number of bacteria have been identified with commercial potential that may offer sustainable alternatives in both Andean and European agricultural settings.

Photonic packaging: transforming silicon photonic integrated circuits into photonic devices

Dedicated multi-project wafer (MPW) runs for photonic integrated circuits (PICs) from Si foundries mean that researchers and small-to-medium enterprises (SMEs) can now afford to design and fabricate Si photonic chips. While these bare Si-PICs are adequate for testing new device and circuit designs on a probe-station, they cannot be developed into prototype devices, or tested outside of the laboratory, without first packaging them into a durable module. Photonic packaging of PICs is significantly more challenging, and currently orders of magnitude more expensive, than electronic packaging, because it calls for robust micron-level alignment of optical components, precise real-time temperature control, and often a high degree of vertical and horizontal electrical integration. Photonic packaging is perhaps the most significant bottleneck in the development of commercially relevant integrated photonic devices. This article describes how the key optical, electrical, and thermal requirements of Si-PIC packaging can be met, and what further progress is needed before industrial scale-up can be achieved.