Proton-coupled electron transfer (PCET) is one of the elementary reactions occurring in many chemical and biological systems, such as photosystem II where the oxidation of tyrosine (TyrZ) is coupled to deprotonation of the phenolic proton. This reaction is here modelled by the oxidation of a phenol covalently linked to a Ru(bpy)32+-moitey, which is photo-oxidized by a laser flash-quench method. This model system is unusual as mechanism of PCET is studied in a unimolecular system in water solution. Here we address the question how the nature of the proton accepting base and its hydrogen bond to phenol influence the PCET reaction. In the first part we investigate the effect of an internal hydrogen bond PCET from. Two similar phenols are compared. For both these the proton accepting base is a carboxylate group linked to the phenol on the ortho-position directly or via a methylene group. On the basis of kinetic and thermodynamic arguments it is suggested that the PCET from these occurs via a concerted electron proton transfer (CEP). Moreover, numerical modelling of the kinetic data provides an in-depth analysis of this CEP reaction, including promoting  vibrations  along the O–H–O coordinate that are required to explain the data. The second part describes the study on oxidation of phenol where either water or an external base the proton acceptor. The pH-dependence of the kinetics reveals four mechanistic regions for PCET within the same molecule when water is the base. It is shown that the competition between the mechanisms can be tuned by the strength of the oxidant. Moreover, these studies reveal the conditions that may favour a buffer-assisted PCET over that with deprotonation to water solution.

The scientific progress about the important chemotherapeutic drug substance cisplatin (CDDP) and its function has often been rendered by data difficult to interpret, and still many questions about its mode of action remains to be clarified by the scientific community. However, studies of CDDP possess a high complexity due to; i) low intracellular concentration, ii) many potential biomolecule targets, iii) poor or unknown stability of the intact drug and its biomolecule adducts and iv) complex and varying sample matrices. Metallomic studies, using advanced analytical techniques may contribute to clarify the interactions between CDDP and intracellular biomolecules. For a successful outcome sample preparation conditions as well as separation and detection techniques must be carefully selected and optimized to achieve accurate results and correct interpretation of data.         This thesis describes some new and improved analytical methodologies for characterizing the Pt metallome in CDDP-exposed malignant cells. The developed methods are based on powerful liquid chromatography (LC) methods hyphenated to sensitive detection by inductively coupled plasma- (ICP) and electrospray ionization mass spectrometry (ESIMS). Consideration has also been taken about sample preparation conditions.         By selecting “chemically inert” sample preparation (cell lysis by osmosis) and separation (using only nonreactive or no additatives) conditions we could avoid the formation of platinum artifact compounds previously described in the literature (Paper I and II). Using oxygen containing organic solvents with high boiling points (dimethylformamide; DMF, 1,4-dioxane, n-propanol and ethanol) as alternatives to acetonitrile in the LC separations, significant improvements were achieved in ICPMS sensitivity and robustness. When evaluated in combination with chromatographic performance and ESIMS detection the overall best performance was achieved with n-propanol (Paper II, III and IV). From the studies in Paper II we could show that free intact CDDP can be found in malignant cells, as supporting evidence for passive or endocytotic uptake of the drug and further estimate a half-life for intracellular CDDP to about 15 minutes. Such data has not been shown before. In Paper V, the above improved LC methods were used to demonstrate differences in the platinum and cupper metallome from sensitive and resistant T289 melanoma cells exposed to CDDP at near clinical levels.         In a wider perspective we have shown the potential of using hydrophilic liquid interaction chromatography (HILIC) hyphenated to ICPMS detection as a general approach for analysis of hydrophilic metallo-compounds (Paper II). Taking advantage of the superior ICPMS performance using n-propanol gradients for reversed phase liquid chromatography (RPLC) possess a true alternative and /or complimentary technique to size exclusion chromatography (SEC) commonly applied within metallomic studies of biomolecules (Paper V). Using n-propanol in HILIC as well as in RPLC enables parallel detection by ICP- and ESIMS using only one set of chromatographic parameters (Paper III and IV), something commonly called for by scientists in the field.

In this paper we propose an algorithm for solving systems of coupled monotone inclusions in Hilbert spaces. The operators arising in each of the inclusions of the system are processed in each iteration separately, namely, the single-valued are evaluated explicitly (forward steps), while the set-valued ones via their resolvents (backward steps). In addition, most of the steps in the iterative scheme can be executed simultaneously, this making the method applicable to a variety of convex minimization problems. The numerical performances of the proposed splitting algorithm are emphasized through applications in average consensus on colored networks and image classification via support vector machines.

3BP2 is a pleckstrin homology (PH) domain- and Src homology 2 (SH2) domain-containing adapter protein that has been linked through genetic evidence to a rare human disease called cherubism 146. 3BP2 was originally cloned in a screen to identify c-Abl SH3 binding proteins 23,24. In overexpression studies, 3BP2 has been implicated as a positive regulatory adapter molecule coupled to immunoreceptor on T cells 67,69,70, B cells 68, NK cells 71-73 and mast cells 74,75. It was also evident that 3BP2 forms complexes with a number of signaling molecules, such as Zap-70, LAT, phospholipase C-γ1 (PLC-γ1), Grb2, Cbl, and Fyn in Jurkat cells 67 and Vav1, Vav2, PLC-γ, and Syk in Daudi B cells 68. Despite the growing body of biochemical data to support the importance of 3BP2 in cells of the hematopoietic lineage, a clear picture of the biological function of 3BP2 has yet to emerge. To elucidate the in vivo function of 3BP2, our laboratory has generated 3BP2 gene-deficient mice through homologous recombination 452. The 3BP2-deficient (3BP2-/-) mice were born at the expected Mendelian frequency and were fertile and viable. 3BP2-/- mice accumulate splenic marginal-zone (MZ) B cells, possess a reduced frequency of peritoneal B-1 B cells, and have a diminished thymus-independent type 2 (TI-2) antigen response. 3BP2-/- B cells demonstrate diminished proliferation and cell survival following cross-linking of the B-cell receptor (BCR). Following BCR ligation, 3BP2 might be recruited to BCR complex through its inducible interaction with BCR costimulatory molecule CD19. In the absence of 3BP2, the activation of BCR downstream effectors such as MAPK Erk1/2, JNK, and c-Abl is normal; however, 3BP2 deficiency leads to defects in Syk phosphorylation and calcium flux. In addition to defects in peripheral B cell activities, 3BP2 deficiency contributes to defects in neutrophil activities. In response to the chemotactic peptide, fMLF, 3BP2-/- neutrophils fail to establish directional migration in vitro. There is a defect in the accumulation of filamentous actin at the leading edge of migrating 3BP2-/- neutrophils which might be responsible for the random movement of these cells under shallow gradient of fMLF. In vivo, there is a delay in the recruitment of circulating neutrophils to the site of chemically induced inflammation in 3BP2-/- mice. Compared to wildtype neutrophils, 3BP2-/- neutrophils fail to properly produce superoxide anion (O2-) following fMLF stimulation. Defects in both directional migration and superoxide production of 3BP2-/- neutrophils might contribute to the reduction in bacteria clearance and the increased mortality in 3BP2-/- mice post Listeria Monocytogenes infection. In Chapter 1 of this thesis, I have reviewed basic structures and functions of the domain modules found in adapter proteins. In addition, I have reviewed the findings from numerous reports on the function of 3BP2 in different cell types. A discussion of the physical appearance and some of the initial characterization of 3BP2-deficient mice (3BP2-/-) we have generated in our laboratory are included in Chapter 1. The second part of Chapter 1 consists of an introduction on B cell receptor signaling pathway and B-cell development and activation. A discussion of G protein-coupled receptor-mediated neutrophil functions can also be found in Chapter 1. Chapter 2 contains all the methods and materials used in my study. Chapter 3 includes the characterization of peripheral B cell compartment of 3BP2-/- mice as well as the role of 3BP2 downstream of B-cell antigen receptor and in T-independent immune response. In chapter 4, I present data from experiments designed to examine the role of 3BP2 downstream of a G protein-coupled receptor, fMLF receptor, of neutrophils. I also show the requirement of 3BP2 in the clearance of Listeria Monocytogenes. In chapter 5, I propose two models for 3BP2 action based on the findings in B cells and neutrophils and discuss future areas for investigation.

In modern low pressure plasma discharges, the electron mean free path often exceeds the device dimensions. Under such conditions the electron velocity distribution function may significantly deviate from Maxwellian, which strongly affects the discharge properties. The description of such plasmas has to be kinetic and often requires the use of numerical methods. This thesis presents the study of kinetic effects in inductively coupled plasmas and Hall thrusters carried out by means of particle-in-cell simulations. The important result and the essential part of the research is the development of particle-in-cell codes. <p>An advective electromagnetic 1d3v particle-in-cell code is developed for modelling the inductively coupled plasmas. An electrostatic direct implicit 1d3v particle-in-cell code EDIPIC is developed for plane geometry simulations of Hall thruster plasmas. The EDIPIC code includes several physical effects important for Hall thrusters: collisions with neutral atoms, turbulence, and secondary electron emission. In addition, the narrow sheath regions crucial for plasma-wall interaction are resolved in simulations. The code is parallelized to achieve fast run times. <p>Inductively coupled plasmas sustained by the external RF electromagnetic field are widely used in material processing reactors and electrodeless lighting sources. In a low pressure inductive discharge, the collisionless electron motion strongly affects the absorption of the external electromagnetic waves and, via the ponderomotive force, the density profile. The linear theory of the anomalous skin effect based on the linear electron trajectories predicts a strong decrease of the ponderomotive force for warm plasmas. Particle-in-cell simulations show that the nonlinear modification of electron trajectories by the RF magnetic field partially compensates the effects of electron thermal motion. As a result, the ponderomotive force in warm collisionless plasmas is stronger than predicted by linear kinetic theory. <p>Hall thrusters, where plasma is maintained by the DC electric field crossed with the stationary magnetic field, are efficient low-thrust devices for spacecraft propulsion. The energy exchange between the plasma and the wall in Hall thrusters is enhanced by the secondary electron emission, which strongly affects electron temperature and, subsequently, thruster operation. Particle-in-cell simulations show that the effect of secondary electron emission on electron cooling in Hall thrusters is quite different from predictions of previous fluid studies. Collisionless electron motion results in a strongly anisotropic, nonmonotonic electron velocity distribution function, which is depleted in the loss cone, subsequently reducing the electron wall losses compared to Maxwellian plasmas. Secondary electrons form two beams propagating between the walls of a thruster channel in opposite radial directions. The secondary electron beams acquire additional energy in the crossed external electric and magnetic fields. The energy increment depends on both the field magnitudes and the electron flight time between the walls. <p>A new model of secondary electron emission in a bounded plasma slab, allowing for emission due to the counter-propagating secondary electron beams, is developed. It is shown that in bounded plasmas the average energy of plasma bulk electrons is far less important for the space charge saturation of the sheath than it is in purely Maxwellian plasmas. A new regime with relaxation oscillations of the sheath has been identified in simulations. Recent experimental studies of Hall thrusters indirectly support the simulation results with respect to the electron temperature saturation and the channel width effect on the thruster discharge.

The induction of synaptic plasticity at CA1 synapses requires NMDAR activation. Modulation of NMDAR function by various GPCRs can shift the thresholds for LTP and LTD induction and contribute to metaplasticity. Here we showed that the activity of GluN2A- and GluN2B-containing NMDARs is differentially regulated by Gαi/o-coupled, Gαq- and Gαs-coupled receptors. Furthermore, enhancing the relative function of GluN2A-to-GluNB NMDAR activity by GPCRs can alter the balance of LTP and LTD induction and contribute to metaplasticity. In CA1 neurons, activation of the Gαs-coupled D1/D5R selectively recruited Fyn kinase and enhanced GluN2B-mediated NMDAR currents. Biochemical experiments confirmed that D1/D5R stimulation activates Fyn kinase and enhances the tyrosine phosphorylation of GluN2B subunits. In contrast, activation of the Gαq-coupled PAC1R selectively recruited Src kinase to enhance the function of GluN2A-containing NMDARs. Enhancing the functional ratio of GluN2A-to-GluN2B subunits by PAC1R activation lowered the threshold for LTP induction whereas enhancing the functional ratio of GluN2B-to-GluN2A subunits by D1/D5R activation increased the threshold for LTP induction. Unexpectedly, activation of the Gαi/o-coupled mGluR2/3 enhanced NMDAR-mediated function via a previously unidentified mechanism. Inhibition of the cAMP-PKA pathway via mGluR2/3 activation resulted in activation of Src via decreased phosphorylation of its C-terminal Tyr527 by Csk. Stimulation of mGluR2/3 selectively potentiated the function of GluN2A-containing NMDARs but whether it shifted the modification threshold θm to the left requires further investigation.

The vertical electronic excitation energies for the narrow-bandgap polymers LBPF, EP37 and EP62 have been calculated using Density Functional Theory (DFT). Also the vertical excitation energies for the acceptor unit of LBPF have been calculated using the Hartree-Fock (HF), DFT and Coupled Cluster (CC) methods. The calculations cover the visible and infrared wave length region and two strong transitions are obtained, one corresponding to the pi to pi* transition and one corresponding to the pi to Acceptor transition. The excitation energies obtained from DFT are below the corresponding experimental results and attempts have therefore been made to perform bench-marking calculations using a hierarchy of CC methods.

Obsidian has been a center of interest both for geologists and archaeologists. Geologists have studied on physical and chemical properties of obsidian where archaeologists have worked on this material as a common artifact found in excavations. In this study, obsidian samples from &Ccedil / atalh&ouml / y&uuml / k excavations are examined using their rare earth element (REE) concentrations. Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) have been used for this purpose. A mixture (4:1) of lithium metaborate and lithium tetraborate was used for fusion of samples. Because of the low concentrations of REEs, a preconcentration step is needed. Successful recovery results have been achieved with Amberlite IR-120. The developed method is tested using the standard reference material SARM-1.

3BP2 is a pleckstrin homology (PH) domain- and Src homology 2 (SH2) domain-containing adapter protein that has been linked through genetic evidence to a rare human disease called cherubism 146. 3BP2 was originally cloned in a screen to identify c-Abl SH3 binding proteins 23,24. In overexpression studies, 3BP2 has been implicated as a positive regulatory adapter molecule coupled to immunoreceptor on T cells 67,69,70, B cells 68, NK cells 71-73 and mast cells 74,75. It was also evident that 3BP2 forms complexes with a number of signaling molecules, such as Zap-70, LAT, phospholipase C-γ1 (PLC-γ1), Grb2, Cbl, and Fyn in Jurkat cells 67 and Vav1, Vav2, PLC-γ, and Syk in Daudi B cells 68. Despite the growing body of biochemical data to support the importance of 3BP2 in cells of the hematopoietic lineage, a clear picture of the biological function of 3BP2 has yet to emerge. To elucidate the in vivo function of 3BP2, our laboratory has generated 3BP2 gene-deficient mice through homologous recombination 452. The 3BP2-deficient (3BP2-/-) mice were born at the expected Mendelian frequency and were fertile and viable. 3BP2-/- mice accumulate splenic marginal-zone (MZ) B cells, possess a reduced frequency of peritoneal B-1 B cells, and have a diminished thymus-independent type 2 (TI-2) antigen response. 3BP2-/- B cells demonstrate diminished proliferation and cell survival following cross-linking of the B-cell receptor (BCR). Following BCR ligation, 3BP2 might be recruited to BCR complex through its inducible interaction with BCR costimulatory molecule CD19. In the absence of 3BP2, the activation of BCR downstream effectors such as MAPK Erk1/2, JNK, and c-Abl is normal; however, 3BP2 deficiency leads to defects in Syk phosphorylation and calcium flux. In addition to defects in peripheral B cell activities, 3BP2 deficiency contributes to defects in neutrophil activities. In response to the chemotactic peptide, fMLF, 3BP2-/- neutrophils fail to establish directional migration in vitro. There is a defect in the accumulation of filamentous actin at the leading edge of migrating 3BP2-/- neutrophils which might be responsible for the random movement of these cells under shallow gradient of fMLF. In vivo, there is a delay in the recruitment of circulating neutrophils to the site of chemically induced inflammation in 3BP2-/- mice. Compared to wildtype neutrophils, 3BP2-/- neutrophils fail to properly produce superoxide anion (O2-) following fMLF stimulation. Defects in both directional migration and superoxide production of 3BP2-/- neutrophils might contribute to the reduction in bacteria clearance and the increased mortality in 3BP2-/- mice post Listeria Monocytogenes infection. In Chapter 1 of this thesis, I have reviewed basic structures and functions of the domain modules found in adapter proteins. In addition, I have reviewed the findings from numerous reports on the function of 3BP2 in different cell types. A discussion of the physical appearance and some of the initial characterization of 3BP2-deficient mice (3BP2-/-) we have generated in our laboratory are included in Chapter 1. The second part of Chapter 1 consists of an introduction on B cell receptor signaling pathway and B-cell development and activation. A discussion of G protein-coupled receptor-mediated neutrophil functions can also be found in Chapter 1. Chapter 2 contains all the methods and materials used in my study. Chapter 3 includes the characterization of peripheral B cell compartment of 3BP2-/- mice as well as the role of 3BP2 downstream of B-cell antigen receptor and in T-independent immune response. In chapter 4, I present data from experiments designed to examine the role of 3BP2 downstream of a G protein-coupled receptor, fMLF receptor, of neutrophils. I also show the requirement of 3BP2 in the clearance of Listeria Monocytogenes. In chapter 5, I propose two models for 3BP2 action based on the findings in B cells and neutrophils and discuss future areas for investigation.

THz and mm-wave technology has become increasingly significant in a very diverse range of applications such as spectroscopy, imaging, and communication as a consequence of a plethora of significant advances in this field. However to achieve a mass production of THz systems, all the commercial aspects should be considered. The main concerns are attributed to the robustness, compactness, and a low cost device. In this regard, research efforts should be focused on the elimination of obstacles standing in the way of commercializing the THz technology. To this end, in this study, low cost fabrication technologies for various parts of mm-wave/THz systems are investigated and explored to realize compact, integrated, and rugged components. This task is divided into four phases. In the first phase, a robust fiber-based beam delivery configuration is deployed instead of the free beam optics which is essential to operate the low cost THz photomixers and photoconductive antennas. The compensation of different effects on propagation of the optical pulse along the optical fiber is achieved through all-fiber system to eliminate any bulky and unstable optical components from the system. THz measurements on fiber-coupled systems exhibit the same performance and even better compared to the free beam system. In the next phase, the generated THz wave is coupled to a rectangular dielectric waveguide through design of a novel transition with low insertion loss. The structure dimensions are reported for various range of frequencies up to 650GHz with insertion loss less than 1dB. The structure is fabricated through a standard recipe. In third phase, as consequence of the advent of high performance active device at mm-wave and THz frequency, a transition is proposed for coupling the electromagnetic wave to the active devices with CPW ports. Different approaches are devised for different frequencies as at higher frequencies any kind of metallic structure can introduce a considerable amount of loss to the system. The optimized structures show minimum insertion loss as low as 1dB and operate over 10% bandwidth. The various configurations are fabricated for lower frequencies to verify the transition performance. The last phase focuses on the design, optimization, fabrication and measurements of a new dielectric side-grating antenna for frequency scanning applications. The radiation mechanism is extensively studied using two different commercial full-wave solvers as well as the measured data from the fabricated samples. The optimized antenna achieves a radiation efficiency of 90% and a gain of 18dB. The measured return loss and radiation pattern show a good agreement with the simulation results.