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Recent attempts to increase the capacity of the compact disc (CD) and digital versatile disc (DVD) have explored the use of multilevel recording instead of binary recording. Systems that achieve an increase in capacity of about three times that of conventional CD have been proposed for production. Marks in these systems are multilevel and fixed-length as opposed to binary and variable length in CD and DVD. The main objective of this work is to evaluate the performance of multilevel ($M$-ary) runlength-limited (RLL) coded sequences in optical data storage. First, the waterfilling capacity of a multilevel optical recording channel ($M$-ary ORC) is derived and evaluated. This provides insight into the achievable user bit densities, as well as a theoretical limit against which simulated systems can be compared. Then, we evaluate the performance of RLL codes on the $M$-ary ORC. A new channel model that includes the runlength constraint in the transmitted signal is used. We compare the performance of specific RLL codes, namely $M$-ary permutation codes, to that of real systems using multilevel fixed-length marks for recording and the theoretical limits. The Viterbi detector is used to estimate the original recorded symbols from the readout signal. Then, error correction is used to reduce the symbol error probability. We use a combined ECC/RLL code for phrase encoding. We evaluate the use of trellis coded modulation (TCM) for amplitude encoding. The detection of the readout signal is also studied. A post-processing algorithm for the Viterbi detector is introduced, which ensures that the detected word satisfies the code constraints. Specifying the codes and detector for the $M$-ary ORC gives a complete system whose performance can be compared to that of the recently developed systems found in the literature and the theoretical limits calculated in this research.

We have developed a high-throughput system of closed-loop electrical stimulation and optical recording that facilitates the rapid characterization of extracellular stimulus-evoked neural activity. The ability to selectively stimulate a neuron is a defining characteristic of next-generation neural prostheses. Greater stimulus control and differential activation of specific neuronal populations allows for prostheses that better mimic their biological counterparts. In our system, we deliver square current pulses using a microelectrode array; automated real-time image processing of high-speed digital video identifies the neuronal response; and a feedback controller alters the applied stimulus to achieve a targeted response. The system controller performs directed searches within the strength-duration (SD) stimulus parameter space to build probabilistic neuronal activation curves. An important feature of this closed-loop system is a reduction in the number of stimuli needed to derive the activation curves when compared to the more commonly used open-loop system: this allows the closed-loop system to spend more time probing stimulus regions of interest in the multi-parameter waveform space, facilitating high resolution analysis. The stimulus-evoked activation data were well-fit to a sigmoid model in both the stimulus strength (current) and duration (pulse width) slices through the waveform space. The 2-D analysis produced a set of probability isoclines corresponding to each neuron-electrode pairing, which were fit to the SD threshold model described by Lapique (1907). We show that stimulus selectivity within a given neuron pair is possible in the one-parameter search space by using multiple stimulation electrodes. Additionally, by applying simultaneous stimuli to adjacent electrodes, the interaction between stimuli alters the neuronal activation threshold. The interaction between simultaneous multi-electrode multi-parameter stimulus waveforms creates an opportunity for increased stimulus selectivity within a population. We demonstrated that closed-loop imaging and micro-stimulation technology enable the study of neuronal excitation across a large parameter space, which is requisite for controlling neuronal activation in next generation clinical solutions.

Analog and digital structures can be written into thin surface layers of semiconductors by using focused ion beams of submicron dimensions. By inducing the phase transition from the crystalline (c) to the amorphous state (a) optical contrast is generated between areas of different exposure. The aim of this study was to investigate the properties of diamond as a high-density optical recording medium and to determine the corresponding irradiation parameters. To this end, single crystals of diamond were irradiated with self-ions of 75 key energy with fluences between F=0.3-l0xlO15 C/cm2 at about 100 K. The radiation damage, persisting after annealing treatments between 300-1700 K, was studied by Raman measurements, monitoring changes in the atomic bonding arrangements. Since the scattering cross-section of C sp2 bonds is 50x that of C sp3 bonds, this is an extremely sensitive technique in detecting changes in the initially purely sp3 state. The position and linewidth of the characteristic first-order phonon of crystalline diamond at 1332 cm-l reflect crystallinity and stress level, while bands between 1350-1700 cm-l indicate disorder. In utilizing the microscopic resolution of a Raman facility additional information was obtained on the spatial variation of the damage level. The optimum annealing temperature was found to be 1500 K. For F > 3xlO15C/cm2, the damage was irreversible, for F = 3xlO15C/cm2 the damage was only partly repaired after annealing at 1500 K and, for F < 3xlO15C/ cm2, the crystalline/amorphous contrast was reversible. For F < lxl015C/ cm2 Raman spectroscopy was not sensitive enough to detect the incurred damage. Infrared spectroscopy was used to classify the diamond samples according to type. / Dissertation (MSc (Chemistry))--University of Pretoria, 2006. / Chemistry / unrestricted

Les canaux ioniques sont des protéines membranaires permettant le transport ionique au travers des membranes biologiques. Du fait de leur omniprésence dans l'organisme, ils représentent une classe de cibles thérapeutiques encore actuellement peu exploitée du fait de limitations expérimentales dans leur étude. La mesure électrique de l'activité des canaux ioniques au sein de bicouches biomimétiques reconstituées in vitro permettrait de répondre à ces limitations. Cependant, il n'existe actuellement pas de système satisfaisant au cahier des charges complet pour de telles analyses : stabilité et pureté de la bicouche, faible niveau de bruit, insertion rapide des canaux ioniques, intégration dans un dispositif fluidique, possibilité de mener une caractérisation optique simultanée. L'objectif de ces travaux de thèse était d'évaluer dans quelle mesure l'utilisation d'un substrat SOI (Silicon On Insulator) comprenant des nanopores pourrait permettre de répondre à tous ces critères. Des nanopores de diamètre compris entre 10 nm et 160 nm ont été réalisés à partir d'un substrat SOI. Une cellule fluidique transparente est utilisée pour l'adressage fluidique. Cette cellule permet d'autre part la double caractérisation électrique et optique. Les propriétés électriques en milieu liquide du dispositif ont été étudiées et permettent de dégager des perspectives d'amélioration. La double caractérisation électrique et optique est démontrée au moyen d'expériences de capture de nanoparticules fluorescentes sur les nanopores. Enfin, des premiers résultats prometteurs d'obtention d'une bicouche lipidique suspendue sont présentés. / Ion channels are membrane proteins responsible for ion transport across biological membranes. Due to their ubiquity, they are promising drug targets but are not yet fully exploited as such due to experimental restrictions in their study. Electrical measurement of ion channels activity within in vitro artificial lipid bilayers would enable to overcome these restrictions. However, there is not yet a system satisfying all the requirements for ion channels studies: stability and purity of the lipid bilayer, low noise level, fast insertion of ion channels, fluidic integration, ability to perform simultaneous optical characterization. The aim of this phD was to assess in which extent the use of an SOI (Silicon On Insulator) substrate bearing nanopores could satisfy all these requirements. 10 nm to 160 nm diameter nanopores were fabricated in an SOI substrate and characterized. A transparent fluidic cell was used for fluidic addressing. This transparent cell allows combined electrical and optical characterization. Electrical properties of the device in aqueous environment were studied, allowing to bring out improvement prospects. The combined electrical and optical characterization was demonstrated with fluorescent nanoparticle trapping experiments on the nanopores. Finally, promising results about the formation of a free-standing lipid bilayer are presented.