Formation and dissociation of protonated pyridine-methanol cluster ions at 355 and 266 nm

The multi-photon ionization process of the hydrogen-bond cluster of pyridine-methanol has been investigated using a conventional and reflectron time-of-flight mass spectrometer (RTOF-MS) at 355 and 266 nm laser wavelengths, respectively. The sequences of the protonated cluster ions (CH3OH)(n)H+ and (C5H5Nn)(CH3OH)(m)H+ (n = 1,2) were observed at both laser wavelengths, while the sequence of the cluster ions (CH3)OHn (H2O)H+ was observed only at 355 nm laser wavelength. The difference between the relative signal intensities of the protonated methanol cluster ions at different laser wavelengths is attributed to different photoionization mechanisms. Some nascent cluster ions in metastable states dissociated during free flight to the detector. The dissociation kinetics is also discussed. (C) 2000 Elsevier Science B.V.

Photoelectron spectroscopy of ammonia via a fast predissociative state

We report a study on resonance enhanced multiphoton ionization photoelectron spectroscopy (REMPI-PES) involving the fast predissociative (A) over tilde state of ammonia, using nano- and femtosecond lasers. The multiphoton scheme involves (1 + 1), (2 + 2), (2 + 2) + 1 and (2 + 2) + 2 photon processes. We have found a progression of stretching vibrations nu(1) in the PE spectrum when pumping NH3 (A) over tilde upsilon(2) = 0, 1 and 3 as intermediate states. The stretching vibration intensity distributions in the photoelectron spectrum are calculated by using the Chebychev method of the wavepacket propagation. The femtosecond spectrum shows a similar feature to the nanosecond spectrum. However, high laser power also causes band broadening and shifting effect as well as above threshold multiphoton ionization.

X-ray simulations for imaging applications in the agricultural and food industry

R. Zwiggelaar, C.R. Bull, and M.J. Mooney, 'X-ray simulations for imaging applications in the agricultural and food industry', Journal of Agricultural Engineering Research 63(2), 161-170 (1996)

Spatial and energetic mode dynamics of cold atomic systems

In this thesis we relate the formal description of various cold atomic systems in the energy eigenbasis, to the observable spatial mode dynamics. Herein the `spatial mode dynamics' refers to the direction of photon emission following the spontaneous emission of an excited fermion in the presence of a same species and spin ideal anisotropic Fermi sea in its internal ground state. Due to the Pauli principle, the presence of the ground state Fermi sea renders the phase space, anisotropic and only partially accessible, thereby a ecting the direction of photon emission following spontaneous emission. The spatial and energetic mode dynamics also refers to the quantum `tunneling' interaction between localised spatial modes, synonymous with double well type potentials. Here we relate the dynamics of the wavefunction in both the energetic and spatial representations. Using this approach we approximate the relationship between the spatial and energetic representations of a wavefunction spanning three spatial and energetic modes. This is extended to a process known as Spatial Adiabatic Passage, which is a technique to transport matter waves between localised spatial modes. This approach allows us to interpret the transport of matter waves as a signature of a geometric phase acquired by the one of the internal energy eigenstates of the system during the cyclical evolution. We further show that this geometric phase may be used to create spatial mode qubit and qutrit states.

Reactivity of sub 1 nm supported clusters: (TiO2)(n) clusters supported on rutile TiO2 (110)

Metal oxide clusters of sub-nm dimensions dispersed on a metal oxide support are an important class of catalytic materials for a number of key chemical reactions, showing enhanced reactivity over the corresponding bulk oxide. In this paper we present the results of a density functional theory study of small sub-nm TiO2 clusters, Ti2O4, Ti3O6 and Ti4O8 supported on the rutile (110) surface. We find that all three clusters adsorb strongly with adsorption energies ranging from -3 eV to -4.5 eV. The more stable adsorption structures show a larger number of new Ti-O bonds formed between the cluster and the surface. These new bonds increase the coordination of cluster Ti and O as well as surface oxygen, so that each has more neighbours. The electronic structure shows that the top of the valence band is made up of cluster derived states, while the conduction band is made up of Ti 3d states from the surface, resulting in a reduction of the effective band gap and spatial separation of electrons and holes after photon absorption, which shows their potential utility in photocatalysis. To examine reactivity, we study the formation of oxygen vacancies in the cluster-support system. The most stable oxygen vacancy sites on the cluster show formation energies that are significantly lower than in bulk TiO2, demonstrating the usefulness of this composite system for redox catalysis.

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.

Voltage properties of optically injected long wavelength VCSELs: Theory and experiment

Future high speed communications networks will transmit data predominantly over optical fibres. As consumer and enterprise computing will remain the domain of electronics, the electro-optical conversion will get pushed further downstream towards the end user. Consequently, efficient tools are needed for this conversion and due to many potential advantages, including low cost and high output powers, long wavelength Vertical Cavity Surface Emitting Lasers (VCSELs) are a viable option. Drawbacks, such as broader linewidths than competing options, can be mitigated through the use of additional techniques such as Optical Injection Locking (OIL) which can require significant expertise and expensive equipment. This thesis addresses these issues by removing some of the experimental barriers to achieving performance increases via remote OIL. Firstly, numerical simulations of the phase and the photon and carrier numbers of an OIL semiconductor laser allowed the classification of the stable locking phase limits into three distinct groups. The frequency detuning of constant phase values (ø) was considered, in particular ø = 0 where the modulation response parameters were shown to be independent of the linewidth enhancement factor, α. A new method to estimate α and the coupling rate in a single experiment was formulated. Secondly, a novel technique to remotely determine the locked state of a VCSEL based on voltage variations of 2mV−30mV during detuned injection has been developed which can identify oscillatory and locked states. 2D & 3D maps of voltage, optical and electrical spectra illustrate corresponding behaviours. Finally, the use of directly modulated VCSELs as light sources for passive optical networks was investigated by successful transmission of data at 10 Gbit/s over 40km of single mode fibre (SMF) using cost effective electronic dispersion compensation to mitigate errors due to wavelength chirp. A widely tuneable MEMS-VCSEL was established as a good candidate for an externally modulated colourless source after a record error free transmission at 10 Gbit/s over 50km of SMF across a 30nm single mode tuning range. The ability to remotely set the emission wavelength using the novel methods developed in this thesis was demonstrated.

New phosphorescence based probes and techniques for the analysis of cellular oxygen and respiration

Real time monitoring of oxygenation and respiration is on the cutting edge of bioanalysis, including studies of cell metabolism, bioenergetics, mitochondrial function and drug toxicity. This thesis presents the development and evaluation of new luminescent probes and techniques for intracellular O2 sensing and imaging. A new oxygen consumption rate (OCR) platform based on the commercial microfluidic perfusion channel μ-slides compatible with extra- and intracellular O2 sensitive probes, different cell lines and measurement conditions was developed. The design of semi-closed channels allowed cell treatments, multiplexing with other assays and two-fold higher sensitivity to compare with microtiter plate. We compared three common OCR platforms: hermetically sealed quartz cuvettes for absolute OCRs, partially sealed with mineral oil 96-WPs for relative OCRs, and open 96-WPs for local cell oxygenation. Both 96-WP platforms were calibrated against absolute OCR platform with MEF cell line, phosphorescent O2 probe MitoXpress-Intra and time-resolved fluorescence reader. Found correlations allow tracing of cell respiration over time in a high throughput format with the possibility of cell stimulation and of changing measurement conditions. A new multimodal intracellular O2 probe, based on the phosphorescent reporter dye PtTFPP, fluorescent FRET donor and two-photon antennae PFO and cationic nanoparticles RL-100 was described. This probe, called MM2, possesses high brightness, photo- and chemical stability, low toxicity, efficient cell staining and high-resolution intracellular O2 imaging with 2D and 3D cell cultures in intensity, ratiometric and lifetime-based modalities with luminescence readers and FLIM microscopes. Extended range of O2 sensitive probes was designed and studied in order to optimize their spectral characteristics and intracellular targeting, using different NPs materials, delivery vectors, ratiometric pairs and IR dyes. The presented improvements provide useful tool for high sensitive monitoring and imaging of intracellular O2 in different measurement formats with wide range of physiological applications.

Measurement of the differential cross section for the reaction gamman-->pi- p from deuterium.

We report a measurement of the differential cross section for the gamman-->pi- p process from the CLAS detector at Jefferson Laboratory in Hall B for photon energies between 1.0 and 3.5 GeV and pion center-of-mass (c.m.) angles (thetac.m.) between 50 degrees and 115 degrees. We confirm a previous indication of a broad enhancement around a c.m. energy ([sqrt]s) of 2.1 GeV at thetac.m.=90 degrees in the scaled differential cross section s7dsigma/dt and a rapid falloff in a center-of-mass energy region of about 400 MeV following the enhancement. Our data show an angular dependence of this enhancement as the suggested scaling region is approached for thetac.m. from 70 degrees to 105 degrees.

Photoelectrocatalysis: Principles, nanoemitter applications and routes to bio-inspired systems

An overview on processes that are relevant in light-induced fuel generation, such as water photoelectrolysis or carbon dioxide reduction, is given. Considered processes encompass the photophysics of light absorption, excitation energy transfer to catalytically active sites and interfacial reactions at the catalyst/solution phase boundary. The two major routes envisaged for realization of photoelectrocatalytic systems, e.g. bio-inspired single photon catalysis and multiple photon inorganic or hybrid tandem cells, are outlined. For development of efficient tandem cell structures that are based on non-oxidic semiconductors, stabilization strategies are presented. Physical surface passivation is described using the recently introduced nanoemitter concept which is also applicable in photovoltaic (solid state or electrochemical) solar cells and first results with p-Si and p-InP thin films are presented. Solar-to-hydrogen efficiencies reach 12.1% for homoepitaxial InP thin films covered with Rh nanoislands. In the pursuit to develop biologically inspired systems, enzyme adsorption onto electrochemically nanostructured silicon surfaces is presented and tapping mode atomic force microscopy images of heterodimeric enzymes are shown. An outlook towards future envisaged systems is given. © 2010 The Royal Society of Chemistry.

Spectral structure of the pygmy dipole resonance.

High-sensitivity studies of E1 and M1 transitions observed in the reaction 138Ba(gamma,gamma{'}) at energies below the one-neutron separation energy have been performed using the nearly monoenergetic and 100% linearly polarized photon beams of the HIgammaS facility. The electric dipole character of the so-called "pygmy" dipole resonance was experimentally verified for excitations from 4.0 to 8.6 MeV. The fine structure of the M1 "spin-flip" mode was observed for the first time in N=82 nuclei.

Waveguide QED: Many-body bound-state effects in coherent and Fock-state scattering from a two-level system

Strong coupling between a two-level system (TLS) and bosonic modes produces dramatic quantum optics effects. We consider a one-dimensional continuum of bosons coupled to a single localized TLS, a system which may be realized in a variety of plasmonic, photonic, or electronic contexts. We present the exact many-body scattering eigenstate obtained by imposing open boundary conditions. Multiphoton bound states appear in the scattering of two or more photons due to the coupling between the photons and the TLS. Such bound states are shown to have a large effect on scattering of both Fock- and coherent-state wave packets, especially in the intermediate coupling-strength regime. We compare the statistics of the transmitted light with a coherent state having the same mean photon number: as the interaction strength increases, the one-photon probability is suppressed rapidly, and the two- and three-photon probabilities are greatly enhanced due to the many-body bound states. This results in non-Poissonian light. © 2010 The American Physical Society.

On-board Robotic Multi-pinhole SPECT System for Region-of-interest (ROI) Imaging

On-board image guidance, such as cone-beam CT (CBCT) and kV/MV 2D imaging, is essential in many radiation therapy procedures, such as intensity modulated radiotherapy (IMRT) and stereotactic body radiation therapy (SBRT). These imaging techniques provide predominantly anatomical information for treatment planning and target localization. Recently, studies have shown that treatment planning based on functional and molecular information about the tumor and surrounding tissue could potentially improve the effectiveness of radiation therapy. However, current on-board imaging systems are limited in their functional and molecular imaging capability. Single Photon Emission Computed Tomography (SPECT) is a candidate to achieve on-board functional and molecular imaging. Traditional SPECT systems typically take 20 minutes or more for a scan, which is too long for on-board imaging. A robotic multi-pinhole SPECT system was proposed in this dissertation to provide shorter imaging time by using a robotic arm to maneuver the multi-pinhole SPECT system around the patient in position for radiation therapy.

A 49-pinhole collimated SPECT detector and its shielding were designed and simulated in this work using the computer-aided design (CAD) software. The trajectories of robotic arm about the patient, treatment table and gantry in the radiation therapy room and several detector assemblies such as parallel holes, single pinhole and 49 pinholes collimated detector were investigated. The rail mounted system was designed to enable a full range of detector positions and orientations to various crucial treatment sites including head and torso, while avoiding collision with linear accelerator (LINAC), patient table and patient.

An alignment method was developed in this work to calibrate the on-board robotic SPECT to the LINAC coordinate frame and to the coordinate frames of other on-board imaging systems such as CBCT. This alignment method utilizes line sources and one pinhole projection of these line sources. The model consists of multiple alignment parameters which maps line sources in 3-dimensional (3D) space to their 2-dimensional (2D) projections on the SPECT detector. Computer-simulation studies and experimental evaluations were performed as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise and acquisition geometry. In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, the six alignment parameters (3 translational and 3 rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by Radon transform, the estimation accuracy was reduced. The estimation error was associated with rounding errors of Radon transform, finite line-source width, Poisson noise, number of line sources, intrinsic camera resolution and detector acquisition geometry. The estimation accuracy was significantly improved by using 4 line sources rather than 3 and also by using thinner line-source projections (obtained by better intrinsic detector resolution). With 5 line sources, median errors were 0.2 mm for the detector translations, 0.7 mm for the detector radius of rotation, and less than 0.5° for detector rotation, tilt and twist. In experimental evaluations, average errors relative to a different, independent registration technique were about 1.8 mm for detector translations, 1.1 mm for the detector radius of rotation (ROR), 0.5° and 0.4° for detector rotation and tilt, respectively, and 1.2° for detector twist.

Simulation studies were performed to investigate the improvement of imaging sensitivity and accuracy of hot sphere localization for breast imaging of patients in prone position. A 3D XCAT phantom was simulated in the prone position with nine hot spheres of 10 mm diameter added in the left breast. A no-treatment-table case and two commercial prone breast boards, 7 and 24 cm thick, were simulated. Different pinhole focal lengths were assessed for root-mean-square-error (RMSE). The pinhole focal lengths resulting in the lowest RMSE values were 12 cm, 18 cm and 21 cm for no table, thin board, and thick board, respectively. In both no table and thin board cases, all 9 hot spheres were easily visualized above background with 4-minute scans utilizing the 49-pinhole SPECT system while seven of nine hot spheres were visible with the thick board. In comparison with parallel-hole system, our 49-pinhole system shows reduction in noise and bias under these simulation cases. These results correspond to smaller radii of rotation for no-table case and thinner prone board. Similarly, localization accuracy with the 49-pinhole system was significantly better than with the parallel-hole system for both the thin and thick prone boards. Median localization errors for the 49-pinhole system with the thin board were less than 3 mm for 5 of 9 hot spheres, and less than 6 mm for the other 4 hot spheres. Median localization errors of 49-pinhole system with the thick board were less than 4 mm for 5 of 9 hot spheres, and less than 8 mm for the other 4 hot spheres.

Besides prone breast imaging, respiratory-gated region-of-interest (ROI) imaging of lung tumor was also investigated. A simulation study was conducted on the potential of multi-pinhole, region-of-interest (ROI) SPECT to alleviate noise effects associated with respiratory-gated SPECT imaging of the thorax. Two 4D XCAT digital phantoms were constructed, with either a 10 mm or 20 mm diameter tumor added in the right lung. The maximum diaphragm motion was 2 cm (for 10 mm tumor) or 4 cm (for 20 mm tumor) in superior-inferior direction and 1.2 cm in anterior-posterior direction. Projections were simulated with a 4-minute acquisition time (40 seconds per each of 6 gates) using either the ROI SPECT system (49-pinhole) or reference single and dual conventional broad cross-section, parallel-hole collimated SPECT. The SPECT images were reconstructed using OSEM with up to 6 iterations. Images were evaluated as a function of gate by profiles, noise versus bias curves, and a numerical observer performing a forced-choice localization task. Even for the 20 mm tumor, the 49-pinhole imaging ROI was found sufficient to encompass fully usual clinical ranges of diaphragm motion. Averaged over the 6 gates, noise at iteration 6 of 49-pinhole ROI imaging (10.9 µCi/ml) was approximately comparable to noise at iteration 2 of the two dual and single parallel-hole, broad cross-section systems (12.4 µCi/ml and 13.8 µCi/ml, respectively). Corresponding biases were much lower for the 49-pinhole ROI system (3.8 µCi/ml), versus 6.2 µCi/ml and 6.5 µCi/ml for the dual and single parallel-hole systems, respectively. Median localization errors averaged over 6 gates, for the 10 mm and 20 mm tumors respectively, were 1.6 mm and 0.5 mm using the ROI imaging system and 6.6 mm and 2.3 mm using the dual parallel-hole, broad cross-section system. The results demonstrate substantially improved imaging via ROI methods. One important application may be gated imaging of patients in position for radiation therapy.

A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150-L110 robot). An imaging study was performed with a phantom (PET CT PhantomTM), which includes 5 spheres of 10, 13, 17, 22 and 28 mm in diameter. The phantom was placed on a flat-top couch. SPECT projections were acquired with a parallel-hole collimator and a single-pinhole collimator both without background in the phantom, and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180 degrees and 228 degrees respectively. The pinhole detector viewed a 14.7 cm-diameter common volume which encompassed the 28 mm and 22 mm spheres. The common volume for parallel-hole was a 20.8-cm-diameter cylinder which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the flat-top table while avoiding collision with the table and maintaining the closest possible proximity to the common volume. For image reconstruction, detector trajectories were described by radius-of-rotation and detector rotation angle θ. These reconstruction parameters were obtained from the robot base and tool coordinates. The robotic SPECT system was able to maneuver the parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector to center-of-rotation (COR) distance. In no background case, all five spheres were visible in the reconstructed parallel-hole and pinhole images. In with background case, three spheres of 17, 22 and 28 mm diameter were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameter) were readily observed in the pinhole ROI imaging.

In conclusion, the proposed on-board robotic SPECT can be aligned to LINAC/CBCT with a single pinhole projection of the line-source phantom. Alignment parameters can be estimated using one pinhole projection of line sources. This alignment method may be important for multi-pinhole SPECT, where relative pinhole alignment may vary during rotation. For single pinhole and multi-pinhole SPECT imaging onboard radiation therapy machines, the method could provide alignment of SPECT coordinates with those of CBCT and the LINAC. In simulation studies of prone breast imaging and respiratory-gated lung imaging, the 49-pinhole detector showed better tumor contrast recovery and localization in a 4-minute scan compared to parallel-hole detector. On-board SPECT could be achieved by a robot maneuvering a SPECT detector about patients in position for radiation therapy on a flat-top couch. The robot inherent coordinate frames could be an effective means to estimate detector pose for use in SPECT image reconstruction.

Imaging Learned Song Representations in Populations of Sensorimotor Neurons Essential to Vocal Communication

Perceiving or producing complex vocalizations such as speech and birdsongs require the coordinated activity of neuronal populations, and these activity patterns can vary over space and time. How learned communication signals are represented by populations of sensorimotor neurons essential to vocal perception and production remains poorly understood. Using a combination of two-photon calcium imaging, intracellular electrophysiological recording and retrograde tracing methods in anesthetized adult male zebra finches (Taeniopygia guttata), I addressed how the bird's own song and its component syllables are represented by the spatiotemporal patterns of activity of two spatially intermingled populations of projection neurons (PNs) in HVC, a sensorimotor area required for song perception and production. These experiments revealed that neighboring PNs can respond at markedly different times to song playback and that different syllables activate spatially intermingled HVC PNs within a small region. Moreover, noise correlation analysis reveals enhanced functional connectivity between PNs that respond most strongly to the same syllable and also provides evidence of a spatial gradient of functional connectivity specific to PNs that project to song motor nucleus (i.e. HVC_RA cells). These findings support a model in which syllabic and temporal features of song are represented by spatially intermingled PNs functionally organized into cell- and syllable-type networks.

Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy.

Time-lapse fluorescence microscopy is an important tool for measuring in vivo gene dynamics in single cells. However, fluorescent proteins are limited by slow chromophore maturation times and the cellular autofluorescence or phototoxicity that arises from light excitation. An alternative is luciferase, an enzyme that emits photons and is active upon folding. The photon flux per luciferase is significantly lower than that for fluorescent proteins. Thus time-lapse luminescence microscopy has been successfully used to track gene dynamics only in larger organisms and for slower processes, for which more total photons can be collected in one exposure. Here we tested green, yellow, and red beetle luciferases and optimized substrate conditions for in vivo luminescence. By combining time-lapse luminescence microscopy with a microfluidic device, we tracked the dynamics of cell cycle genes in single yeast with subminute exposure times over many generations. Our method was faster and in cells with much smaller volumes than previous work. Fluorescence of an optimized reporter (Venus) lagged luminescence by 15-20 min, which is consistent with its known rate of chromophore maturation in yeast. Our work demonstrates that luciferases are better than fluorescent proteins at faithfully tracking the underlying gene expression.