Investigation of micro-devices for neurobiological applications

The aim of this project is to integrate neuronal cell culture with commercial or in-house built micro-electrode arrays and MEMS devices. The resulting device is intended to support neuronal cell culture on its surface, expose specific portions of a neuronal population to different environments using microfluidic gradients and stimulate/record neuronal electrical activity using micro-electrode arrays. Additionally, through integration of chemical surface patterning, such device can be used to build neuronal cell networks of specific size, conformation and composition. The design of this device takes inspiration from the nervous system because its development and regeneration are heavily influenced by surface chemistry and fluidic gradients. Hence, this device is intended to be a step forward in neuroscience research because it utilizes similar concepts to those found in nature. The large part of this research revolved around solving technical issues associated with integration of biology, surface chemistry, electrophysiology and microfluidics. Commercially available microelectrode arrays (MEAs) are mechanically and chemically brittle making them unsuitable for certain surface modification and micro-fluidic integration techniques described in the literature. In order to successfully integrate all the aspects into one device, some techniques were heavily modified to ensure that their effects on MEA were minimal. In terms of experimental work, this thesis consists of 3 parts. The first part dealt with characterization and optimization of surface patterning and micro-fluidic perfusion. Through extensive image analysis, the optimal conditions required for micro-contact printing and micro-fluidic perfusion were determined. The second part used a number of optimized techniques and successfully applied these to culturing patterned neural cells on a range of substrates including: Pyrex, cyclo-olefin and SiN coated Pyrex. The second part also described culturing neurons on MEAs and recording electrophysiological activity. The third part of the thesis described integration of MEAs with patterned neuronal culture and microfluidic devices. Although integration of all methodologies proved difficult, a large amount of data relating to biocompatibility, neuronal patterning, electrophysiology and integration was collected. Original solutions were successfully applied to solve a number of issues relating to consistency of micro printing and microfluidic integration leading to successful integration of techniques and device components.

Integration of micro- and macroscopic models for pedestrian evacuation simulation

Simulation of pedestrian evacuations of smart buildings in emergency is a powerful tool for building analysis, dynamic evacuation planning and real-time response to the evolving state of evacuations. Macroscopic pedestrian models are low-complexity models that are and well suited to algorithmic analysis and planning, but are quite abstract. Microscopic simulation models allow for a high level of simulation detail but can be computationally intensive. By combining micro- and macro- models we can use each to overcome the shortcomings of the other and enable new capability and applications for pedestrian evacuation simulation that would not be possible with either alone. We develop the EvacSim multi-agent pedestrian simulator and procedurally generate macroscopic flow graph models of building space, integrating micro- and macroscopic approaches to simulation of the same emergency space. By “coupling” flow graph parameters to microscopic simulation results, the graph model captures some of the higher detail and fidelity of the complex microscopic simulation model. The coupled flow graph is used for analysis and prediction of the movement of pedestrians in the microscopic simulation, and investigate the performance of dynamic evacuation planning in simulated emergencies using a variety of strategies for allocation of macroscopic evacuation routes to microscopic pedestrian agents. The predictive capability of the coupled flow graph is exploited for the decomposition of microscopic simulation space into multiple future states in a scalable manner. By simulating multiple future states of the emergency in short time frames, this enables sensing strategy based on simulation scenario pattern matching which we show to achieve fast scenario matching, enabling rich, real-time feedback in emergencies in buildings with meagre sensing capabilities.

Optical micro- and nanofibres: Higher mode generation and particle manipulation studies

This thesis is centred on two experimental fields of optical micro- and nanofibre research; higher mode generation/excitation and evanescent field optical manipulation. Standard, commercial, single-mode silica fibre is used throughout most of the experiments; this generally produces high-quality, single-mode, micro- or nanofibres when tapered in a flame-heated, pulling rig in the laboratory. Single mode fibre can also support higher transverse modes, when transmitting wavelengths below that of their defined single-mode regime cut-off. To investigate this, a first-order Laguerre-Gaussian beam, LG01 of 1064 nm wavelength and doughnut-shaped intensity profile is generated free space via spatial light modulation. This technique facilitates coupling to the LP11 fibre mode in two-mode fibre, and convenient, fast switching to the fundamental mode via computer-generated hologram modulation. Following LP11 mode loss when exponentially tapering 125μm diameter fibre, two mode fibre with a cladding diameter of 80μm is selected fir testing since it is more suitable for satisfying the adiabatic criteria for fibre tapering. Proving a fruitful endeavour, experiments show a transmission of 55% of the original LP11 mode set (comprising TE01, TM01, HE21e,o true modes) in submicron fibres. Furthermore, by observing pulling dynamics and progressive mode-lass behaviour, it is possible to produce a nanofibre which supports only the TE01 and TM01 modes, while suppressing the HE21e,o elements of the LP11 group. This result provides a basis for experimental studies of atom trapping via mode-interference, and offers a new set of evanescent field geometries for sensing and particle manipulation applications. The thesis highlights the experimental results of the research unit’s Cold Atom subgroup, who successfully integrated one such higher-mode nanofibre into a cloud of cold Rubidium atoms. This led to the detection of stronger signals of resonance fluorescence coupling into the nanofibre and for light absorption by the atoms due to the presence of higher guided modes within the fibre. Theoretical work on the impact of the curved nanofibre surface on the atomic-surface van der Waals interaction is also presented, showing a clear deviation of the potential from the commonly-used flat-surface approximation. Optical micro- and nanofibres are also useful tools for evanescent-field mediated optical manipulation – this includes propulsion, defect-induced trapping, mass migration and size-sorting of micron-scale particles in dispersion. Similar early trapping experiments are described in this thesis, and resulting motivations for developing a targeted, site-specific particle induction method are given. The integration of optical nanofibres into an optical tweezers is presented, facilitating individual and group isolation of selected particles, and their controlled positioning and conveyance in the evanescent field. The effects of particle size and nanofibre diameter on pronounced scattering is experimentally investigated in this systems, as are optical binding effects between adjacent particles in the evanescent field. Such inter-particle interactions lead to regulated self-positioning and particle-chain speed enhancements.

Development of low-cost sensing and separation devices based on macro, micro and nano technology for health applications

The work presented in this thesis described the development of low-cost sensing and separation devices with electrochemical detections for health applications. This research employs macro, micro and nano technology. The first sensing device developed was a tonerbased micro-device. The initial development of microfluidic devices was based on glass or quartz devices that are often expensive to fabricate; however, the introduction of new types of materials, such as plastics, offered a new way for fast prototyping and the development of disposable devices. One such microfluidic device is based on the lamination of laser-printed polyester films using a computer, printer and laminator. The resulting toner-based microchips demonstrated a potential viability for chemical assays, coupled with several detection methods, particularly Chip-Electrophoresis-Chemiluminescence (CE-CL) detection which has never been reported in the literature. Following on from the toner-based microchip, a three-electrode micro-configuration was developed on acetate substrate. This is the first time that a micro-electrode configuration made from gold; silver and platinum have been fabricated onto acetate by means of patterning and deposition techniques using the central fabrication facilities in Tyndall National Institute. These electrodes have been designed to facilitate the integration of a 3- electrode configuration as part of the fabrication process. Since the electrodes are on acetate the dicing step can automatically be eliminated. The stability of these sensors has been investigated using electrochemical techniques with excellent outcomes. Following on from the generalised testing of the electrodes these sensors were then coupled with capillary electrophoresis. The final sensing devices were on a macro scale and involved the modifications of screenprinted electrodes. Screen-printed electrodes (SPE) are generally seen to be far less sensitive than the more expensive electrodes including the gold, boron-doped diamond and glassy carbon electrodes. To enhance the sensitivity of these electrodes they were treated with metal nano-particles, gold and palladium. Following on from this, another modification was introduced. The carbonaceous material carbon monolith was drop-cast onto the SPE and then the metal nano-particles were electrodeposited onto the monolith material

Micro and nanostructured impedance sensors for biological and biomedical applications

This thesis work covered the fabrication and characterisation of impedance sensors for biological applications aiming in particular to the cytotoxicity monitoring of cultured cells exposed to different kind of chemical compounds and drugs and to the identification of different types of biological tissue (fat, muscles, nerves) using a sensor fabricated on the tip of a commercially available needle during peripheral nerve block procedures. Gold impedance electrodes have been successfully fabricated for impedance measurement on cells cultured on the electrode surface which was modified with the fabrication of gold nanopillars. These nanostructures have a height of 60nm or 100nm and they have highly ordered layout as they are fabricated through the e-beam technique. The fabrication of the threedimensional structures on the interdigitated electrodes was supposed to improve the sensitivity of the ECIS (electric cell-substrate impedance sensing) measurement while monitoring the cytotoxicity effects of two different drugs (Antrodia Camphorata extract and Nicotine) on three different cell lines (HeLa, A549 and BALBc 3T3) cultured on the impedance devices and change the morphology of the cells growing on the nanostructured electrodes. The fabrication of the nanostructures was achieved combining techniques like UV lithography, metal lift-off, evaporation and e-beam lithography techniques. The electrodes were packaged using a pressure sensitive, medical grade adhesive double-sided tape. The electrodes were then characterised with the aid of AFM and SEM imaging which confirmed the success of the fabrication processes showing the nanopillars fabricated with the right layout and dimensions figures. The introduction of nanopillars on the impedance electrodes, however, did not improve much the sensitivity of the assay with the exception of tests carried out with Nicotine. HeLa and A549 cells appeared to grow in a different way on the two surfaces, while no differences where noticed on the BALBc 3T3 cells. Impedance measurements obtained with the dead cells on the negative control electrodes or the test electrodes with the drugs can be compared to those done on the electrodes containing just media in the tested volume (as no cells are attached and cover the electrode surface). The impedance figures recorded using these electrodes were between 1.5kΩ and 2.5 kΩ, while the figures recorded on confluent cell layers range between 4kΩ and 5.5kΩ with peaks of almost 7 kΩ if there was more than one layer of cells growing on each other. There was then a very clear separation between the values of living cell compared to the dead ones which was almost 2.5 - 3kΩ. In this way it was very easy to determine whether the drugs affected the cells normal life cycle on not. However, little or no differences were noticed in the impedance analysis carried out on the two different kinds of electrodes using cultured cells. An increase of sensitivity was noticed only in a couple of experiments carried out on A549 cells growing on the nanostructured electrodes and exposed to different concentration of a solution containing Nicotine. More experiments to achieve a higher number of statistical evidences will be needed to prove these findings with an absolute confidence. The smart needle project aimed to reduce the limitations of the Electrical Nerve Stimulation (ENS) and the Ultra Sound Guided peripheral nerve block techniques giving the clinicians an additional tool for performing correctly the peripheral nerve block. Bioimpedance, as measured at the needle tip, provides additional information on needle tip location, thereby facilitating detection of intraneural needle placement. Using the needle as a precision instrument and guidance tool may provide additional information as to needle tip location and enhance safety in regional anaesthesia. In the time analysis, with the frequency fixed at 10kHz and the samples kept at 12°C, the approximate range for muscle bioimpedance was 203 – 616 Ω, the approximate bioimpedance range for fat was 5.02 - 17.8 kΩ and the approximate range for connective tissue was 790 Ω – 1.55 kΩ. While when the samples were heated at 37°C and measured again at 10kHz, the approximate bioimpedance range for muscle was 100-175Ω. The approximate bioimpedance range of fat was 627 Ω - 3.2 kΩ and the range for connective tissue was 221-540Ω. In the experiments done on the fresh slaughtered lamb carcass, replicating a scenario close to the real application, the impedance values recorded for fat were around 17 kΩ, for muscle and lean tissue around 1.3 kΩ while the nervous structures had an impedance value of 2.9 kΩ. With the data collected during this research, it was possible to conclude that measurements of bioimpedance at the needle tip location can give valuable information to the clinicians performing a peripheral nerve block procedure as the separation (in terms of impedance figures) was very marked between the different type of tissues. It is then feasible to use an impedance electrode fabricated on the needle tip to differentiate several tissues from the nerve tissue. Currently, several different methods are being studied to fabricate an impedance electrode on the surface of a commercially available needle used for the peripheral nerve block procedure.

Uncle Tom's Cabin and the Irish National Tale

Accepted Version