No description available.

The focus of this work is the integration of alkali vapor atomic vapor cells into common silicon wafer microfabrication processes. Such integrated platforms enable the study of quantum coherence effects such as electromagnetically induced transparency, which can in turn be used to demonstrate slow light. Slow and stopped light devices have applications in the optical communications and quantum computing fields. This project uses hollow core anti-resonant reflecting optical waveguides (ARROWs) to build such slow light devices. An explanation of light-matter interactions and the physics of slow light is first provided, as well as a detailed overview of the fabrication process. Following the discovery of a vapor transport issue, a custom capillary-based testing platform is developed to quantify the effect of confinement, temperature, and wall coatings on rubidium transport. A mathematical model is derived from the experimental results and predicts long transport times. A new design methodology is presented that addresses the transport problem by increasing the number of rubidium entry points. This design also improves chip durability and decreases environmental susceptibility through the use of a single copper reservoir and buried channel waveguides (BCWs). New chips are successfully fabricated, loaded, and monitored for rubidium spectra. Absorption is observed in several chips and absorption peaks depths in excess of 10% are reported. The chip lifetime remains comparable to previous designs. This new design can be expanded to a multi-core platform suitable for slow and stopped light experimentation.

No description available.

No description available.

All cells maintain essential metal nutrients at optimal levels by metal homeostasis. P-type ATPases, a crucial superfamily of integral membrane proteins, are involved in the active transport of metal ions across biological membranes driven by the motive force of ATP- hydrolysis. The PIB-type ATPase subfamily, also called CPx-ATPases, fulfills a key role in heavy metal homoeostasis among the most widespread species from bacteria to human. In humans, the defect in copper transporters is the direct cause of severe neurological and hepatic disorders such as Wilson and Menkes diseases, therefore, understanding the molecular function of these pumps is of paramount importance in human health. Cu+-ATPases have two transmembrane metal binding sites (TM-MBS) and three cytosolic domains, namely the actuator (A-domain) and phosphorylation and nucleotide-binding domain (PN), and regulatory N-terminal heavy metal binding domain (HMBD). Here, we have studied the Legionella pneumophila CopA (LpCopA) and its isolated cytosolic domains to improve our understanding of the functional interaction of the protein domains during metal transport relate this to the known structure of this ATPase. To elucidate how cytosolic ligands (Cu+ and nucleotide) stimulate the interactions among the cytosolic domains and may transmit conformational changes to the TM-MBS, the interactions among recombinant isolated cytosolic domains were first examined biochemically by co-purification and spectroscopically by circular dichroism, time-resolved fluorescence and site-directed fluorescent labeling assays. The Cu+-dependent interaction between the A-domain and HMBD has been postulated as a mechanism for activating the ATPase cycle. This question was addressed here by studying copper-dependent interactions between the isolated expressed domains. Spectroscopic evidence is provided that an HMBD-A complex is formed in the presence of Cu+ which binds with 100-200 nM affinity to the recombinant HMBD. In contrast, the A-domain interacts with the PN domain in a nucleotide-dependent fashion. This molecular recognition is required for the dephosphorylation step in the catalytic cycle. The interaction was investigated in more detail by the use of a decameric peptide derived from the PN-binding interface of the A-domain and carrying the conserved TGE-motif involved in dephosphorylation. Its binding to the isolated PN domain in a weakly nucleotide-dependent manner, is demonstrated here by stopped-flow fluorescence spectroscopy. Several ATPase assays were modified to assess the functionality of the PN-domain and full length LpCopA. The peptide was found to reduce the catalytic turnover of full length LpCopA. This agrees with the expected slowing down of the reformation of the PN-A-domain interaction since the peptide occupies their binding interface. Thus, the synthetic peptide provides a means to study specifically the influence of PN-A-domain interactions on the structure and function of LpCopA. This was done by time-correlated single photon counting (TCSPC) method. The time-dependent Stokes shift of the environmentally sensitive fluorophore BADAN which was covalently attached to the conserved CPC-motif in the TM-MBS was measured. The data indicate that the interior of the ATPase is hydrated and the mobility of the intra-protein water varies from high to low at C382 at the “luminal side” and C384 at the “cytosolic side” of the TM-MBS, respectively. This finding is consistent with the recent MD simulation of LpCopA, bringing the first experimental evidence on a luminal-open conformation of E2~P state. The A-domain-derived decapeptide, although binding to the cytosolic head piece, induces structural changes also at the TM-MBS. The peptide-stabilized state (with a disrupted PN-A interface) renders the C384 environment more hydrophobic as evidenced by TCSPC. Taken together, the data from cytosolic domain interactions, ATPase assays and of time-dependent Stoke shift analyses of BADAN-labeled LpCopA reveal the presence of hydrated intramembraneous sites whose degree of hydration is regulated by the rearrangement of cytosolic domains, particularly during the association and dissociation of the PN-A domains. Copper affects this arrangement by inducing the linkage of the A-domain to the HMBD. The latter appears to play not only an autoinhibitory but also a chaperone-like role in transferring Cu+ to the TM-MBS during catalytic turnover.

No description available.

All cells maintain essential metal nutrients at optimal levels by metal homeostasis. P-type ATPases, a crucial superfamily of integral membrane proteins, are involved in the active transport of metal ions across biological membranes driven by the motive force of ATP- hydrolysis. The PIB-type ATPase subfamily, also called CPx-ATPases, fulfills a key role in heavy metal homoeostasis among the most widespread species from bacteria to human. In humans, the defect in copper transporters is the direct cause of severe neurological and hepatic disorders such as Wilson and Menkes diseases, therefore, understanding the molecular function of these pumps is of paramount importance in human health. Cu+-ATPases have two transmembrane metal binding sites (TM-MBS) and three cytosolic domains, namely the actuator (A-domain) and phosphorylation and nucleotide-binding domain (PN), and regulatory N-terminal heavy metal binding domain (HMBD). Here, we have studied the Legionella pneumophila CopA (LpCopA) and its isolated cytosolic domains to improve our understanding of the functional interaction of the protein domains during metal transport relate this to the known structure of this ATPase. To elucidate how cytosolic ligands (Cu+ and nucleotide) stimulate the interactions among the cytosolic domains and may transmit conformational changes to the TM-MBS, the interactions among recombinant isolated cytosolic domains were first examined biochemically by co-purification and spectroscopically by circular dichroism, time-resolved fluorescence and site-directed fluorescent labeling assays. The Cu+-dependent interaction between the A-domain and HMBD has been postulated as a mechanism for activating the ATPase cycle. This question was addressed here by studying copper-dependent interactions between the isolated expressed domains. Spectroscopic evidence is provided that an HMBD-A complex is formed in the presence of Cu+ which binds with 100-200 nM affinity to the recombinant HMBD. In contrast, the A-domain interacts with the PN domain in a nucleotide-dependent fashion. This molecular recognition is required for the dephosphorylation step in the catalytic cycle. The interaction was investigated in more detail by the use of a decameric peptide derived from the PN-binding interface of the A-domain and carrying the conserved TGE-motif involved in dephosphorylation. Its binding to the isolated PN domain in a weakly nucleotide-dependent manner, is demonstrated here by stopped-flow fluorescence spectroscopy. Several ATPase assays were modified to assess the functionality of the PN-domain and full length LpCopA. The peptide was found to reduce the catalytic turnover of full length LpCopA. This agrees with the expected slowing down of the reformation of the PN-A-domain interaction since the peptide occupies their binding interface. Thus, the synthetic peptide provides a means to study specifically the influence of PN-A-domain interactions on the structure and function of LpCopA. This was done by time-correlated single photon counting (TCSPC) method. The time-dependent Stokes shift of the environmentally sensitive fluorophore BADAN which was covalently attached to the conserved CPC-motif in the TM-MBS was measured. The data indicate that the interior of the ATPase is hydrated and the mobility of the intra-protein water varies from high to low at C382 at the “luminal side” and C384 at the “cytosolic side” of the TM-MBS, respectively. This finding is consistent with the recent MD simulation of LpCopA, bringing the first experimental evidence on a luminal-open conformation of E2~P state. The A-domain-derived decapeptide, although binding to the cytosolic head piece, induces structural changes also at the TM-MBS. The peptide-stabilized state (with a disrupted PN-A interface) renders the C384 environment more hydrophobic as evidenced by TCSPC. Taken together, the data from cytosolic domain interactions, ATPase assays and of time-dependent Stoke shift analyses of BADAN-labeled LpCopA reveal the presence of hydrated intramembraneous sites whose degree of hydration is regulated by the rearrangement of cytosolic domains, particularly during the association and dissociation of the PN-A domains. Copper affects this arrangement by inducing the linkage of the A-domain to the HMBD. The latter appears to play not only an autoinhibitory but also a chaperone-like role in transferring Cu+ to the TM-MBS during catalytic turnover.

The kinetic and mechanistic features of a new series ofplatinum-thallium cyano compounds containing a direct andunsupported by ligands metal-metal bond have been studied insolution, using standard mix–and–measurespectrophotometric technique and stopped–flow method.These reactions are interpreted as oxidative addition of the cspecies to the square planar Pt(CN)42-complex. Each of these processes was found to befirst-order in Pt(CN)42-, the corresponding TIIIIcomplex and a cyanide ion donating species whichacts as a catalyst. Both di- and trinuclear complexes werestudied, and the kinetically significant thallium complexes intheir formation and the catalytically active cyanide sourcesare as follows: [(CN)5PtTl(CN)3]3-: Tl(CN)4–(alkaline region), Tl(CN)3(slightly acidic region) and CN–; [(CN)5Pt–Tl(CN)]–: Tl(CN)2+and Tl(CN)2+; [(CN)5Pt–Tl–Pt(CN)5]3-: [(CN)5Pt–Tl(CN)]–and HCN. Appropriatemechanisms were postulated for the overall reactions in allcases, which include i) metal–metal bond formation stepand ii) coordination of an axial cyanide ion to the platinumcenter. Two experimentally indistinguishable kinetic modelswere proposed for the formation of the dinuclear complexeswhich are different in the sequence of the two steps. In thecase of the trinuclear complex, experimental evidence isavailable to exclude one of the alternative reaction paths, andit was proven that the metal–metal bond formation precedesthe axial cyanide coordination. The cyanide ligands coordinated to TIIIIin the Pt–Tl complexes could be replacedsuccessfully with aminopolycarboxylates e.g.: mimda2-, nta3-, edta4-. The [(CN)5Pt–Tl(edta)]4-complex, with a direct metal–metal bond hasbeen prepared in solution by two different reactions: a)dissolution of [(CN)5Pt–Tl](s) in an aqueous solution of edta, b)directly from Pt(CN)42-and Tl(edta)(CN)2-. The decomposition reaction is greatlyaccelerated by cyanide and significantly inhibited by edta. Itproceeds through the [(CN)5Pt–Tl(CN)3]3-intermediate. The formation of [(CN)5Pt–Tl(edta)]4-can proceed via two different pathways dependingon the ratio of the cyanide to the edta ligand concentrations.The’direct path’at excess of edta means theformation of intermediate[(CN)4Pt···Tl(CN)(edta)]4-, followed by a release of the cyanide from theTl–centre followed by coordination of a cyanide from thebulk to the Pt–centre of the intermediate. The’indirect path’dominates in the absence of extraedta and the formation of the Pt–Tl bond occours betweenPt(CN)42-and Tl(CN)4–. Homoligand MTl(CN)4(M = TlI, K, Na) and, for the first time, Tl(CN)3species have been synthesized in the solid stateand their structures solved by single crystal X–raydiffraction method. Interesting redox processes have been foundbetween TIIIIand CN–in non–aqueous solution and in Tl2O3-CN–aqueous suspension. In the crystal structureof Tl(CN)3·H2O, the thallium(III) ion has a trigonal bypiramidalcoordination geometry with three cyanides in the trigonalplane, while an oxygen atom of the water molecule and anitrogen atom from a cyanide ligand attached to a neighboringthallium complex, form a linear O–Tl–N fragment.Cyanide ligand bridges thallium units forming an infinitezigzag chain structure. Among the thallium(III) tetracyanocompounds, the isostructural M[Tl(CN)4](M = Tl and K) and Na[Tl(CN)4]·3H2O crystallize in different crystal systems, but thethallium(III) ion has in all cases the same tetrahedralgeometry in the [Tl(CN)4]–unit. Three adducts of mercury(II) (isoelectronic with TIIII) (K2PtHg(CN)6·2H2O, Na2PdHg(CN)6·2H2O and K2NiHg(CN)6·2H2O) have been prepared from Hg(CN)2and square planar transition metal cyanides MII(CN)42-and their structure have been studied by singlecrystal X–ray diffraction, XPS and Raman spectroscopy inthe solid state. The structure of (K2PtHg(CN)6·2H2O consists of strictly linear one dimensional wireswith PtIIand HgIIcenters located alternately, dHg–Pt= 3.460 Å. The structure of Na2PdHg(CN)6·2H2O and K2NiHg(CN)6·2H2O can be considered as double salts, the lack ofhetero–metallophilic interaction between both the HgIIand PdIIatoms, dHg–Pd= 4.92 Å, and HgIIand NiIIatoms, dNi–Pd= 4.60 Å, seems obvious. Electronbinding energy values of the metallic centers measured by XPSshow that there is no electron transfer between the metal ionsin all three adducts. In solution, experimental findingsclearly indicate the lack of metal–metal bond formation inall studied HgII–CN-–MII(CN)42-systems (M = Pt, Pd and Ni). It is in contrary tothe platinum–thallium bonded cyanides. KEYWORDS:metal–metal bond, platinum, thallium,kinetics, mechanism, stopped flow, oxidative addition, cyanocomplexes, edta, redox reaction, metal cyanides, X–raydiffraction, Raman, NMR, mercury, palladium, nickel, onedimensional wire

This thesis consists of a summary and four scientific articles. All four articles consider various aspects of stochastic differential equations and the purpose of the summary is to provide an introduction to this subject and to supply the notions required in order to fully understand the articles. In the first article we conduct a thorough study of the multi-dimensional Skorohod problem in time-dependent domains. In particular we prove the existence of cádlág solutions to the Skorohod problem with oblique reflection in time-independent domains with corners. We use this existence result to construct weak solutions to stochastic differential equations with oblique reflection in time-dependent domains. In the process of obtaining these results we also establish convergence results for sequences of solutions to the Skorohod problem and a number of estimates for solutions, with bounded jumps, to the Skorohod problem. The second article considers the problem of determining the sensitivities of a solution to a second order parabolic partial differential equation with respect to perturbations in the parameters of the equation. We derive an approximate representation of the sensitivities and an estimate of the discretization error arising in the sensitivity approximation. We apply these theoretical results to the problem of determining the sensitivities of the price of European swaptions in a LIBOR market model with respect to perturbations in the volatility structure (the so-called ‘Greeks’). The third article treats stopped diffusions in time-dependent graph domains with low regularity. We compare, numerically, the performance of one adaptive and three non-adaptive numerical methods with respect to order of convergence, efficiency and stability. In particular we investigate if the performance of the algorithms can be improved by a transformation which increases the regularity of the domain but, at the same time, reduces the regularity of the parameters of the diffusion. In the fourth article we use the existence results obtained in Article I to construct a projected Euler scheme for weak approximation of stochastic differential equations with oblique reflection in time-dependent domains. We prove theoretically that the order of convergence of the proposed algorithm is 1/2 and conduct numerical simulations which support this claim.

Tyrosine Hydroxylase (TyrH) is a pterin-dependent mononuclear non-heme iron oxygenase. TyrH catalyzes the hydroxylation reaction of tyrosine to dihydroxyphenylalanine (DOPA). This reaction is the first and the rate-limiting step in the biosynthesis of the catecholamine neurotransmitters. The active site iron in TyrH is coordinated by the common facial triad motif, 2-His-1-Glu. A combination of kinetic and spectroscopic techniques was applied in order to obtain insight into the catalytic mechanism of this physiologically important enzyme. Analysis of the TyrH reaction by rapid freeze-quench Mossbauer spectroscopy allowed the first direct characterization of an Fe(IV) intermediate in a mononuclear nonheme enzyme catalyzing aromatic hydroxylation. Further rapid kinetic studies established the kinetic competency of this intermediate to be the long-postulated hydroxylating species, Fe(IV)O. Spectroscopic investigations of wild-type (WT) and mutant TyrH complexes using magnetic circular dichroism (MCD) and X-ray absorption spectroscopy (XAS) showed that the active site iron is 6-coordinate in the resting form of the enzyme and that binding of either tyrosine or 6MPH4 alone does not change the coordination. However, when both tyrosine and 6MPH4 are bound, the active site becomes 5-coordinate, creating an open site for reaction with O2. Investigation of the kinetics of oxygen reactivity of TyrH complexes in the absence and presence of tyrosine and/or 6MPH4 indicated that there is a significant enhancement in reactivity in the 5-coordinate complex in comparison to the 6-coordinate form. Similar investigations with E332A TyrH showed that Glu332 residue plays a role in directing the protonation of the bridged complex that forms prior to the formation of Fe(IV)O. Rapid chemical quench analyses of DOPA formation showed a burst of product formation, suggesting a slow product release step. Steady-state viscosity experiments established a diffusional step as being significantly rate-limiting. Further studies with stopped-flow spectroscopy indicated that the rate of TyrH reaction is determined by a combination of a number of physical and chemical steps. Investigation of the NO complexes of TyrH by means of optical absorption, electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) techniques revealed the relative positions of the substrate and cofactor with respect to NO, an O2 mimic, and provided further insight into how the active site is tuned for catalytic reactivity upon substrate and cofactor binding.