Kinetic and structural evidence for the importance of Tyr236 for the integrity of the Mo active site in a bacterial sulfite dehydrogenase

The sulfite dehydrogenase from Starkeya novella is the only known sulfite-oxidizing enzyme that forms a permanent heterodimeric complex between a molybdenum and a heme c-containing subunit and can be crystallized in an electron transfer competent conformation. Tyr236 is a highly conserved active site residue in sulfite oxidoreductases and has been shown to interact with a nearby arginine and a molybdenum-oxo ligand that is involved in catalysis. We have created a Tyr236 to Phe substitution in the SorAB sulfite dehydrogenase. The purified SDHY236F protein has been characterized in terms of activity, structure, intramolecular electron transfer, and EPR properties. The substituted protein exhibited reduced turnover rates and substrate affinity as well as an altered reactivity toward molecular oxygen as an electron acceptor. Following reduction by sulfite and unlike SDHWT, the substituted enzyme was reoxidized quickly in the presence of molecular oxygen, a process reminiscent of the reactions of the sulfite oxidases. SDHY236F also exhibited the pH-dependent CW-EPR signals that are typically observed in vertebrate sulfite oxidases, allowing a direct link of CW-EPR properties to changes caused by a single-amino acid substitution. No quantifiable electron transfer was seen in laser flash photolysis experiments with SDHY236F. The crystal structure of SDHY236F clearly shows that as a result of the substitution the hydrogen bonding network surrounding the active site is disturbed, resulting in an increased mobility of the nearby arginine. These disruptions underline the importance of Tyr236 for the integrity of the substrate binding site and the optimal alignment of Arg55, which appears to be necessary for efficient electron transfer.

T-Q relation and exact solution for the XYZ chain with general non-diagonal boundary terms

We propose that the Baxter's Q-operator for the quantum XYZ spin chain with open boundary conditions is given by the j -> infinity limit of the corresponding transfer matrix with spin-j (i.e., (2j + I)-dimensional) auxiliary space. The associated T-Q relation is derived from the fusion hierarchy of the model. We use this relation to determine the Bethe Ansatz solution of the eigenvalues of the fundamental transfer matrix. The solution yields the complete spectrum of the Hamiltonian. (c) 2006 Elsevier B.V. All rights reserved.

Generalized Perk-Schultz models: solutions of the Yang-Baxter equation associated with quantized orthosymplectic superalgebras

The Perk-Schultz model may be expressed in terms of the solution of the Yang-Baxter equation associated with the fundamental representation of the untwisted affine extension of the general linear quantum superalgebra U-q (gl(m/n)], with a multiparametric coproduct action as given by Reshetikhin. Here, we present analogous explicit expressions for solutions of the Yang-Baxter equation associated with the fundamental representations of the twisted and untwisted affine extensions of the orthosymplectic quantum superalgebras U-q[osp(m/n)]. In this manner, we obtain generalizations of the Perk-Schultz model.

Factors associated with degeneration of the thallus centre in foliose lichens

Degeneration of the older parts of foliose lichen thalli often lead to the formation of a space or 'window' in the centre of the colonies. The percentage of thalli of different size which exhibited 'windows' was studied in twenty saxicolous lichen populations in south Gwynedd, Wales. The proportion of thalli with 'windows' increased with thallus size. The size class at which 50% and 100% of thalli exhibited 'windows' varied between populations. Differences between populations were not correlated with distance from the sea, aspect, slope or porosity of the substrate or the total number of lichen species present. However, a higher percentage of smaller thalli had 'windows' on rock surfaces with a greater lichen cover. There were no significant differences in the levels of Ca, Mg, Cu or Zn in large (>4 cm) and small (<2 cm) Parmelia conspersa (Ehrh. ex Ach.) Ach. thalli or in the centres and marginal lobes of these thalli. The concentration of ribitol, arabitol and mannitol was significantly reduced in the centre of large thalli compared with the margin of large thalli and the centre of small thalli. However, carbohydrate levels were similar in the centre of large thalli and the margin of small thalli. The data suggest that loss of the thallus centre is a degenerative process related to thallus size. In the field, the formation of 'windows' may be related to the intensity of competition on a substrate. Central degeneration was not associated with a deficiency or an accumulation of Ca, Mg, Cu and Zn in the thallus centre. However, degeneration may be associated with a reduction in carbohydrates in the centre compared with the marginal lobes.

3D reconstruction of complex dielectric function of the glass during the femtosecond micro-fabrication

We measure complex amplitude of scattered wave in the far field, and justify theoretically and numerically solution of the inverse scattering problem. This allows single-shot reconstructing of dielectric function distribution during direct femtosecond laser micro-fabrication.

Theoretical studies of the mid-latitude ionosphere

Following a brief description of the atmosphere and ionosphere in Chapter I we describe how the equations of continuity and momentum for 0+, H+, He+, 0++ are derived from the formulations of St-Maurice and Schunk(1977) and Quegan et al.(1981) in Chapter II. In Chapter III we investigate the nature of the downward flow of protons in a collapsing post-sunset ionosphere. We derive an analytical form for the limiting temperature, we also note the importance of the polarization field term and concluded that the flow will remain subsonic for realistic conditions. The time-dependent behaviour of He+ under sunspot minimum conditions is investigated in Chapter IV. This is achieved by numerical solution of the 0+, H+ and,He+ continuity and momentum equations, treating He+ as a minor ion with 0+ , H+ as major ions. We found that He+ flows upwards during the day-time and downwards during the nighttime. He+ flux tube content reached a maximum on the 8th day of the integration period and started to decreasing. This is due to the large amount of H+ present at the late stages of the integration period which makes He+ unable to diffuse through the H+ layer away from the loss region. In Chapter V we investigate the behaviour of 0++ using sunspot maximum parameters. Although our results support the findings of Geis and Young (1981) that the large amounts of 0++ at the equator are caused mainly by thermal diffusion, the model used by Geis and Young overemphesizes the effect of thermal diffusion. The importance of 0++ - 0+ collision frequency is also noted. In Chapter VI we extend the work of Chapter IV, presenting a comparative study of H and He at sunspot minimum and sunspot maximum.In this last Chapter all three ions, O+ ,H+ and He+ , are treated theoretically as major ions and we concentrate mainly on light ion contents and fluxes. The results of this Chapter indicate that by assuming He+ as a minor ion we under-estimate He+ and over-estimate. H+. Some interesting features concerning the day to day behaviour of the light ion fluxes arise. In particular the day-time H+ fluxes decrease from day to day in contrast to the work of Murphy et al.(1976). In appendix.A we derive some analytical forms for the optical depth so that the models can include a realistic description of photoionization.

Parabolic optical pulses under the action of the third-order dispersion

Recent developments in nonlinear optics reveal an interesting class of pulses with a parabolic intensity profile in the energy-containing core and a linear frequency chirp that can propagate in a fiber with normal group-velocity dispersion. Parabolic pulses propagate in a stable selfsimilar manner, holding certain relations (scaling) between pulse power, width, and chirp parameter. In the additional presence of linear amplification, they enjoy the remarkable property of representing a common asymptotic state (or attractor) for arbitrary initial conditions. Analytically, self-similar (SS) parabolic pulses can be found as asymptotic, approximate solutions of the nonlinear Schr¨odinger equation (NLSE) with gain in the semi-classical (largeamplitude/small-dispersion) limit. By analogy with the well-known stable dynamics of solitary waves - solitons, these SS parabolic pulses have come to be known as similaritons. In practical fiber systems, inherent third-order dispersion (TOD) in the fiber always introduces a certain degree of asymmetry in the structure of the propagating pulse, eventually leading to pulse break-up. To date, there is no analytic theory of parabolic pulses under the action of TOD. Here, we develop aWKB perturbation analysis that describes the effect of weak TOD on the parabolic pulse solution of the NLSE in a fiber gain medium. The induced perturbation in phase and amplitude can be found to any order. The theoretical model predicts with sufficient accuracy the pulse structural changes induced by TOD, which are observed through direct numerical NLSE simulations.

Parabolic optical pulses under the action of the third-order dispersion

Recent developments in nonlinear optics reveal an interesting class of pulses with a parabolic intensity profile in the energy-containing core and a linear frequency chirp that can propagate in a fiber with normal group-velocity dispersion. Parabolic pulses propagate in a stable selfsimilar manner, holding certain relations (scaling) between pulse power, width, and chirp parameter. In the additional presence of linear amplification, they enjoy the remarkable property of representing a common asymptotic state (or attractor) for arbitrary initial conditions. Analytically, self-similar (SS) parabolic pulses can be found as asymptotic, approximate solutions of the nonlinear Schr¨odinger equation (NLSE) with gain in the semi-classical (largeamplitude/small-dispersion) limit. By analogy with the well-known stable dynamics of solitary waves - solitons, these SS parabolic pulses have come to be known as similaritons. In practical fiber systems, inherent third-order dispersion (TOD) in the fiber always introduces a certain degree of asymmetry in the structure of the propagating pulse, eventually leading to pulse break-up. To date, there is no analytic theory of parabolic pulses under the action of TOD. Here, we develop aWKB perturbation analysis that describes the effect of weak TOD on the parabolic pulse solution of the NLSE in a fiber gain medium. The induced perturbation in phase and amplitude can be found to any order. The theoretical model predicts with sufficient accuracy the pulse structural changes induced by TOD, which are observed through direct numerical NLSE simulations.

3D reconstruction of complex dielectric function of the glass during the femtosecond micro-fabrication

We measure complex amplitude of scattered wave in the far field, and justify theoretically and numerically solution of the inverse scattering problem. This allows single-shot reconstructing of dielectric function distribution during direct femtosecond laser micro-fabrication.

Breakup of a multisoliton state of the linearly damped nonlinear Schrödinger equation

We address the breakup (splitting) of multisoliton solutions of the nonlinear Schrödinger equation (NLSE), occurring due to linear loss. Two different approaches are used for the study of the splitting process. The first one is based on the direct numerical solution of the linearly damped NLSE and the subsequent analysis of the eigenvalue drift for the associated Zakharov-Shabat spectral problem. The second one involves the multisoliton adiabatic perturbation theory applied for studying the evolution of the solution parameters, with the linear loss taken as a small perturbation. We demonstrate that in the case of strong nonadiabatic loss the evolution of the Zakharov-Shabat eigenvalues can be quite nontrivial. We also demonstrate that the multisoliton breakup can be correctly described within the framework of the adiabatic perturbation theory and can take place even due to small linear loss. Eventually we elucidate the occurrence of the splitting and its dependence on the phase mismatch between the solitons forming a two-soliton bound state. © 2007 The American Physical Society.

3D reconstruction of complex dielectric function of the glass during the femtosecond micro-fabrication

We measure complex amplitude of scattered wave in the far field, and justify theoretically and numerically solution of the inverse scattering problem. This allows single-shot reconstructing of dielectric function distribution during direct femtosecond laser micro-fabrication.

One Application of the Informatics in the Descriptive Geometry

This work acquaints with a program for interactive computer training to students on the subject "Mutual intersecting of pyramids in axonometry ”. Our software is a set of three modules, which we call "student", "teacher" and "autopilot". It gives the final solution of the problem, the traceability of various significant moments in its solution and 3D-image of the finished composition of the two intersecting polyhedra, stripped of the working lines and subjected to rotation and translation.

An Analog of the Tricomi Problem for a Mixed Type Equation with a Partial Fractional Derivative

Mathematics Subject Classification 2010: 35M10, 35R11, 26A33, 33C05, 33E12, 33C20.

Solution of Space-Time Fractional Schrödinger Equation Occurring in Quantum Mechanics

Dedicated to Professor A.M. Mathai on the occasion of his 75-th birthday. Mathematics Subject Classi¯cation 2010: 26A33, 44A10, 33C60, 35J10.

Binomial Skew Polynomial Rings, Artin-Schelter Regularity, and Binomial Solutions of the Yang-Baxter Equation

2000 Mathematics Subject Classification: Primary 81R50, 16W50, 16S36, 16S37.