On the opto-electrical properties of ion-implanted single-crystal diamond in the visible and near-visible regime

Diamond is potentially the ultimate material for a vast range of optical and quantum-computing applications. The fabrication of diamond-based optical and photonic devices by ion implantation requires knowledge of the diamond’s modified optical properties. The purpose of this thesis is to determine how the optical properties of ion-implanted diamond depend on the ion implantation fluence. Ion-implanted diamond has been studied structurally, electrically and optically in the range 200 – 1700 nm.   Optical micro-waveguides are of fundamental importance to integrated optics for the transport of light into, out from and around diamond-based quantum devices and other photonic devices. A number of micro-waveguides have been modelled; the dimensions are designed to maintain single-mode propagation in the unimplanted core of the waveguide.   Disagreement in previous studies suggests qualitatively different mechanisms for ion-beam modification, at least at low fluences, between light-ion and heavy-ion implantation. This thesis supports the observation of the lowering of refractive index by low-fluence heavy-ion bombardment. There exists a region of implantation fluences in which the refractive index is lower than that of pristine diamond, while the absorption coefficient is still low enough to enable fabrication of efficient waveguides.   The achieved reduction in the refractive index, n , at 1.95 eV (637 nm vacuum wavelength) was ∆ n   ≈ -0.06; typically waveguides have  ∆ n   ≈ -0.003. The measured extinction coefficient, k , was 0.037 (α  ≈ 7x10 3 cm -1 ). The physical size of photonic components is largely influenced by the refractive index contrast between the two materials; a large contrast allows for smaller structures. However, diamond/air structures need to be very small to maintain single-mode propagation; they are inherently fragile. The smaller refractive index contrast achieved in this work permits the structures to be larger, and hence mechanically sound. Furthermore, the attenuation in the cladding region is inconsequential, due to the short operational lengths of the waveguides.   Refractive index determinations have been performed by spectral ellipsometry, white light reflectance and spectral transmittance, and compared with measurements of the electrical conductivity and the ion-induced surface swelling. The optical measurements all show quantitative agreement with each other. Furthermore, a consistent qualitative relation is shown between the optical measurements and the electrical conductivity measurements, which are comparable with previous measurements in diamond implanted with heavy ions.   It is a further claim of this thesis that the influence of the implanted atoms is negligible compared to the structural modifications that occur upon ion implantation. Furthermore, it is proposed that the lattice-induced pressure is the responsible mechanism that inhibits the decrease of the refractive index under high-energy light-ion implantation.   The conclusion reached is that the behaviour of the refractive index can be completely understood in terms of physical properties; namely material density, dangling-bond density, electric polarisability and electrical conductivity. The magnitude of these effects is highly dependent on the ion fluence; their individual contributions vary depending on the amount of lattice damage. The information contained within this thesis provides a feasible foundation for the production of waveguides and cavities; critical components in the realisation of a room-temperature scalable quantum computer

Investigating Neuroanatomical Features in Top Athletes at the Single Subject Level.

In sport events like Olympic Games or World Championships competitive athletes keep pushing the boundaries of human performance. Compared to team sports, high achievements in many athletic disciplines depend solely on the individual's performance. Contrasting previous research looking for expertise-related differences in brain anatomy at the group level, we aim to demonstrate changes in individual top athlete's brain, which would be averaged out in a group analysis. We compared structural magnetic resonance images (MRI) of three professional track-and-field athletes to age-, gender- and education-matched control subjects. To determine brain features specific to these top athletes, we tested for significant deviations in structural grey matter density between each of the three top athletes and a carefully matched control sample. While total brain volumes were comparable between athletes and controls, we show regional grey matter differences in striatum and thalamus. The demonstrated brain anatomy patterns remained stable and were detected after 2 years with Olympic Games in between. We also found differences in the fusiform gyrus in two top long jumpers. We interpret our findings in reward-related areas as correlates of top athletes' persistency to reach top-level skill performance over years

CYP2C19 expression modulates affective functioning and hippocampal subiculum volume-a large single-center community-dwelling cohort study.

Given controversial findings of reduced depressive symptom severity and increased hippocampus volume in CYP2C19 poor metabolizers, we sought to provide empirical evidence from a large-scale single-center longitudinal cohort in the community-dwelling adult population-Colaus|PsyCoLaus in Lausanne, Switzerland (n = 4152). We looked for CYP2C19 genotype-related behavioral and brain anatomy patterns using a comprehensive set of psychometry, water diffusion- and relaxometry-based magnetic resonance imaging (MRI) data (BrainLaus, n = 1187). Our statistical models tested for differential associations between poor metabolizer and other metabolizer status with imaging-derived indices of brain volume and tissue properties that explain individuals' current and lifetime mood characteristics. The observed association between CYP2C19 genotype and lifetime affective status showing higher functioning scores in poor metabolizers, was mainly driven by female participants (ß = 3.9, p = 0.010). There was no difference in total hippocampus volume between poor metabolizer and other metabolizer, though there was higher subiculum volume in the right hippocampus of poor metabolizers (ß = 0.03, p <sub>FDRcorrected</sub> = 0.036). Our study supports the notion of association between mood phenotype and CYP2C19 genotype, however, finds no evidence for concomitant hippocampus volume differences, with the exception of the right subiculum

Mapping grip force to motor networks.

There is ongoing debate about the role of cortical and subcortical brain areas in force modulation. In a whole-brain approach, we sought to investigate the anatomical basis of grip force whilst acknowledging interindividual differences in connectivity patterns. We tested if brain lesion mapping in patients with unilateral motor deficits can inform whole-brain structural connectivity analysis in healthy controls to uncover the networks underlying grip force. Using magnetic resonance imaging (MRI) and whole-brain voxel-based morphometry in chronic stroke patients (n=55) and healthy controls (n=67), we identified the brain regions in both grey and white matter significantly associated with grip force strength. The resulting statistical parametric maps (SPMs) provided seed areas for whole-brain structural covariance analysis in a large-scale community dwelling cohort (n=977) that included beyond volume estimates, parameter maps sensitive to myelin, iron and tissue water content. The SPMs showed symmetrical bilateral clusters of correlation between upper limb motor performance, basal ganglia, posterior insula and cortico-spinal tract. The covariance analysis with the seed areas derived from the SPMs demonstrated a widespread anatomical pattern of brain volume and tissue properties, including both cortical, subcortical nodes of motor networks and sensorimotor areas projections. We interpret our covariance findings as a biological signature of brain networks implicated in grip force. The data-driven definition of seed areas obtained from chronic stroke patients showed overlapping structural covariance patterns within cortico-subcortical motor networks across different tissue property estimates. This cumulative evidence lends face validity of our findings and their biological plausibility

Altered brain mechanisms of emotion processing in pre-manifest Huntington's disease

Huntington's disease is an inherited neurodegenerative disease that causes motor, cognitive and psychiatric impairment, including an early decline in ability to recognize emotional states in others. The pathophysiology underlying the earliest manifestations of the disease is not fully understood; the objective of our study was to clarify this. We used functional magnetic resonance imaging to investigate changes in brain mechanisms of emotion recognition in pre-manifest carriers of the abnormal Huntington's disease gene (subjects with pre-manifest Huntington's disease): 16 subjects with pre-manifest Huntington's disease and 14 control subjects underwent 1.5 tesla magnetic resonance scanning while viewing pictures of facial expressions from the Ekman and Friesen series. Disgust, anger and happiness were chosen as emotions of interest. Disgust is the emotion in which recognition deficits have most commonly been detected in Huntington's disease; anger is the emotion in which impaired recognition was detected in the largest behavioural study of emotion recognition in pre-manifest Huntington's disease to date; and happiness is a positive emotion to contrast with disgust and anger. Ekman facial expressions were also used to quantify emotion recognition accuracy outside the scanner and structural magnetic resonance imaging with voxel-based morphometry was used to assess the relationship between emotion recognition accuracy and regional grey matter volume. Emotion processing in pre-manifest Huntington's disease was associated with reduced neural activity for all three emotions in partially separable functional networks. Furthermore, the Huntington's disease-associated modulation of disgust and happiness processing was negatively correlated with genetic markers of pre-manifest disease progression in distributed, largely extrastriatal networks. The modulated disgust network included insulae, cingulate cortices, pre- and postcentral gyri, precunei, cunei, bilateral putamena, right pallidum, right thalamus, cerebellum, middle frontal, middle occipital, right superior and left inferior temporal gyri, and left superior parietal lobule. The modulated happiness network included postcentral gyri, left caudate, right cingulate cortex, right superior and inferior parietal lobules, and right superior frontal, middle temporal, middle occipital and precentral gyri. These effects were not driven merely by striatal dysfunction. We did not find equivalent associations between brain structure and emotion recognition, and the pre-manifest Huntington's disease cohort did not have a behavioural deficit in out-of-scanner emotion recognition relative to controls. In addition, we found increased neural activity in the pre-manifest subjects in response to all three emotions in frontal regions, predominantly in the middle frontal gyri. Overall, these findings suggest that pathophysiological effects of Huntington's disease may precede the development of overt clinical symptoms and detectable cerebral atroph

Networks of myelin covariance.

Networks of anatomical covariance have been widely used to study connectivity patterns in both normal and pathological brains based on the concurrent changes of morphometric measures (i.e., cortical thickness) between brain structures across subjects (Evans, ). However, the existence of networks of microstructural changes within brain tissue has been largely unexplored so far. In this article, we studied in vivo the concurrent myelination processes among brain anatomical structures that gathered together emerge to form nonrandom networks. We name these "networks of myelin covariance" (Myelin-Nets). The Myelin-Nets were built from quantitative Magnetization Transfer data-an in-vivo magnetic resonance imaging (MRI) marker of myelin content. The synchronicity of the variations in myelin content between anatomical regions was measured by computing the Pearson's correlation coefficient. We were especially interested in elucidating the effect of age on the topological organization of the Myelin-Nets. We therefore selected two age groups: Young-Age (20-31 years old) and Old-Age (60-71 years old) and a pool of participants from 48 to 87 years old for a Myelin-Nets aging trajectory study. We found that the topological organization of the Myelin-Nets is strongly shaped by aging processes. The global myelin correlation strength, between homologous regions and locally in different brain lobes, showed a significant dependence on age. Interestingly, we also showed that the aging process modulates the resilience of the Myelin-Nets to damage of principal network structures. In summary, this work sheds light on the organizational principles driving myelination and myelin degeneration in brain gray matter and how such patterns are modulated by aging

Multispectral brain morphometry in Tourette syndrome persisting into adulthood

Tourette syndrome is a childhood-onset neuropsychiatric disorder with a high prevalence of attention deficit hyperactivity and obsessive-compulsive disorder co-morbidities. Structural changes have been found in frontal cortex and striatum in children and adolescents. A limited number of morphometric studies in Tourette syndrome persisting into adulthood suggest ongoing structural alterations affecting frontostriatal circuits. Using cortical thickness estimation and voxel-based analysis of T1- and diffusion-weighted structural magnetic resonance images, we examined 40 adults with Tourette syndrome in comparison with 40 age- and gender-matched healthy controls. Patients with Tourette syndrome showed relative grey matter volume reduction in orbitofrontal, anterior cingulate and ventrolateral prefrontal cortices bilaterally. Cortical thinning extended into the limbic mesial temporal lobe. The grey matter changes were modulated additionally by the presence of co-morbidities and symptom severity. Prefrontal cortical thickness reduction correlated negatively with tic severity, while volume increase in primary somatosensory cortex depended on the intensity of premonitory sensations. Orbitofrontal cortex volume changes were further associated with abnormal water diffusivity within grey matter. White matter analysis revealed changes in fibre coherence in patients with Tourette syndrome within anterior parts of the corpus callosum. The severity of motor tics and premonitory urges had an impact on the integrity of tracts corresponding to cortico-cortical and cortico-subcortical connections. Our results provide empirical support for a patho-aetiological model of Tourette syndrome based on developmental abnormalities, with perturbation of compensatory systems marking persistence of symptoms into adulthood. We interpret the symptom severity related grey matter volume increase in distinct functional brain areas as evidence of ongoing structural plasticity. The convergence of evidence from volume and water diffusivity imaging strengthens the validity of our findings and attests to the value of a novel multimodal combination of volume and cortical thickness estimations that provides unique and complementary information by exploiting their differential sensitivity to structural chang

Abnormal brain iron accumulation in obstructive sleep apnea: A quantitative MRI study in the HypnoLaus cohort

Obstructive sleep apnea syndrome (OSA) may be a risk factor for Alzheimer's disease. One of the hallmarks of Alzheimer's disease is disturbed iron homeostasis leading to abnormal iron deposition in brain tissue. To date, there is no empirical evidence to support the hypothesis of altered brain iron homeostasis in patients with obstructive sleep apnea as well. Data were analysed from 773 participants in the HypnoLaus study (mean age 55.9 ± 10.3 years) who underwent polysomnography and brain MRI. Cross-sectional associations were tested between OSA parameters and the MRI effective transverse relaxation rate (R2*) - indicative of iron content - in 68 grey matter regions, after adjustment for confounders. The group with severe OSA (apnea-hypopnea index ≥30/h) had higher iron levels in the left superior frontal gyrus (F3,760 = 4.79, p = 0.003), left orbital gyri (F3,760 = 5.13, p = 0.002), right and left middle temporal gyrus (F3,760 = 4.41, p = 0.004 and F3,760 = 13.08, p < 0.001, respectively), left angular gyrus (F3,760 = 6.29, p = 0.001), left supramarginal gyrus (F3,760 = 4.98, p = 0.003), and right cuneus (F3,760 = 7.09, p < 0.001). The parameters of nocturnal hypoxaemia were all consistently associated with higher iron levels. Measures of sleep fragmentation had less consistent associations with iron content. This study provides the first evidence of increased brain iron levels in obstructive sleep apnea. The observed iron changes could reflect underlying neuropathological processes that appear to be driven primarily by hypoxaemic mechanisms

Creating diamond color centers for quantum optical applications

Nitrogen vacancy (NV) centers in diamond have distinct promise as solid-state qubits. This is because of their large dipole moment, convenient level structure and very long room-temperature coherence times. In general, a combination of ion irradiation and subsequent annealing is used to create the centers, however for the rigorous demands of quantum computing all processes need to be optimized, and decoherence due to the residual damage caused by the implantation process itself must be mitigated. To that end we have studied photoluminescence (PL) from NV$^-$, NV$^0$ and GR1 centers formed by ion implantation of 2MeV He ions over a wide range of fluences. The sample was annealed at $600^{\circ}$C to minimize residual vacancy diffusion, allowing for the concurrent analysis of PL from NV centers and irradiation induced vacancies (GR1). We find non-monotic PL intensities with increasing ion fluence, monotonic increasing PL in NV$^0$/NV$^-$ and GR1/(NV$^0$ + NV$^1$) ratios, and increasing inhomogeneous broadening of the zero-phonon lines with increasing ion fluence. All these results shed important light on the optimal formation conditions for NV qubits. We apply our findings to an off-resonant photonic quantum memory scheme using vibronic sidebands