Esta Tesis esta motivada por el interés en aplicar procedimientos de optimización global a problemas del mundo real. Para ello, nos hemos centrado en el problema de Coordinación Hidrotérmica de la Generación Eléctrica a Corto Plazo (llamado Problema de Generación en esta Tesis) donde la función objetivo y las restricciones no lineales son polinomios de grado como máximo cuatro. En el Problema de Generación no tenemos disponible una representación en diferencia convexa de las funciones involucradas ni tampoco es posible utilizar la estructura del problema para simplificarlo. No obstante, cuando disponemos de una función continua f(x) definida en un conjunto cerrado y no vacío S el problema puede transformarse en otro equivalente expresado mediante minimize l(z) subject to z 2 D n int. (programa d.c. canónico), donde l(z) es una función convexa (en general suele ser una función lineal) con D y C conjuntos convexos y cerrados. Una estructura matemática tal como Dnint C no resulta siempre aparente y aunque lo fuera siempre queda por realizar una gran cantidad de cálculos para expresarla de manera que se pueda resolver el problema de una manera eficiente desde un punto de vista computacional.La característica más importante de esta estructura es que aparecen conjuntos convexos y complementarios de conjuntos convexos. Por este motivo en tales problemas se pueden usar herramientas analíticas tales como subdifernciales y hiperplanos soporte. Por otro lado, como aparecen conjuntos complementarios de conjuntos convexos, estas herramientas analíticas se deben usar de una manera determinada y combinándolas con herramientas combinatorias tales como cortes por planos, Branco and bound y aproximación interior.En esta tesis se pone de manifiesto la estructura matemática subyacente en el Problema de Generación utilizando el hecho de que los polinomios son expresables como diferencia de funciones convexas. Utilizando esta propiedad describimos el problema como un programa d.c. canónico equivalente. Pero aun mas, partiendo de la estructura de las funciones del Problema de Generación es posible rescribirlo de una manera mas conveniente y obtener de este modo ventajas numéricas desde elpunto de vista de la implementación.Basándonos en la propiedad de que los polinomios homogéneos de grado 1 son un conjunto de generadores del espacio vectorial de los polinomios homogéneos de grado m hemos desarrollamos los conceptos y propiedades necesarios que nos permiten expresar un polinomio cualquiera como diferencia de polinomios convexos, También, se ha desarrollado y demostrado la convergencia de un nuevo algoritmo de optimización global (llamado Algoritmo Adaptado) que permite resolver el Problema de Generación. Como el programa equivalente no esta acotado se ha introducido una técnica de subdivisión mediante prismas en lugar de la habitual subdivisión mediante conos.Para obtener una descomposición óptima de un polinomio en diferencia de polinomios convexos, se ha enunciado el Problema de Norma Mínima mediante la introducción del concepto de Descomposición con Mínima Desviación, con lo cual obtenemos implementaciones m´as eficientes, al reducir el n´umero de iteraciones del Algoritmo Adaptado. Para resolver el problema de Norma Mínima hemos implementado un algoritmo de programación cuadrática semi-infinita utilizando una estrategia de build-up and build-down, introducida por Den Hertog (1997) para resolver programas lineales semi-infinitos, la cual usa un procedimiento de barrera logarítmica.Finalmente, se describen los resultados obtenidos por la implementación de los algoritmos anteriormente mencionados y se dan las conclusiones. / This Thesis has been motivated by the interest in applying deterministic global optimization procedures to problems in the real world with no special structures. We have focused on the Short-Term Hydrothermal Coordination of Electricity Generation Problem (also named Generation Problem in this Thesis) where the objective function and the nonlinear constraints are polynomials of degree up to four. In the Generation Problem there is no available d.c. representation of the involved functions and we cannot take advantage of any special structure of the problem either. Hence, a very general problem, such as the above-mentioned, does not seem to have any mathematical structure conducive to computational implementations. Nevertheless, when f(x) is a continuous function and S is a nonempty closed set the problem can be transformed into an equivalent problem expressed by minimize l(z) subject to z 2 D n intC (canonical d.c. program), where l(z) is a convex function (which is usually a linear function) and D and C are closed convex sets. A mathematical complementary convex structure such as D n int C is not always apparent and even when it is explicit, a lot of work still remains to be done to bring it into a form amenable to efficient computational implementations. The attractive feature of the mathematicalcomplementary convex structure is that it involves convexity. Thus, we can use analytical tools from convex analysis like sub differential and supporting hyper plane.On the other hand, since convexity is involved in a reverse sense, these tools must be used in some specific way and combined with combinatorial tools like cutting planes, branch and bound and outer approximation.We introduce the common general mathematical complementary convex structure underlying in global optimization problems and describe the Generation Problem, whose functions are d.c. functions because they are polynomials. Thus, by using the properties of the d.c. functions, we describe the Generation Problem as an equivalent canonical d.c. programming problem. From the structure of its functions the Generation Problem can be rewritten as a more suitable equivalent reverse convex program in order to obtain an adaptation for advantageous numerical implementations.Concepts and properties are introduced which allow us to obtain an explicit representation of a polynomial as a deference of convex polynomials, based on the fact that the set of mth powers of homogeneous polynomials of degree 1 is a generating set for the vector space of homogeneous polynomials of degree m.We also describe a new global optimization algorithm (adapted algorithm) in order to solve the Generation Problem. Since the equivalent reverse convex program is unbounded we use prismatical subdivisions instead of conical ones. Moreover, we prove the convergence of the adapted algorithm by using a prismatical subdivision process together with an outer approximation procedure.We enounce the Minimal Norm Problem by using the concept of Least Deviation Decomposition in order to obtain the optimal d.c. representation of a polynomial function, which allows a more efficient implementation, by reducing the number of iterations of the adapted algorithm.A quadratic semi-infinite algorithm is described. We propose a build-up and down strategy, introduced by Den Hertog (1997) for standard linear programs that uses a logarithmic barrier method.Finally, computational results are given and conclusions are explained.

In dieser Arbeit werden die zu einem m-sektoriellen Operator assoziierten Halbgruppen betrachtet, die die Lösungen des Anfangswertproblems der zugehörigen Evolutionsgleichung beschreiben. Es wird eine 1987 von Davies veröffentlichte Methode zur Abschätzung dieser Halbgruppen verallgemeinert. Einen Schwerpunkt bilden die zu Dirichlet-Formen assoziierten Markov-Halbgruppen. Für diese werden die Resultate spezialisiert und der Zusammenhang zur intrinsischen Metrik dargelegt. Die Arbeit schließt mit verschiedenen Beispielen, die zeigen, wie mit diesen Verallgemeinerungen von Davies Methode neue Anwendungsgebiete erschlossen werden können. / This thesis is about m-sectorial operators and their associated semigroups describing the solutions of the initial value problem of the corresponding evolution equation. We generalize a method published by Davies 1987 to estimate these semigroups. A focus is set on Markov semigroups associated with Dirchlet forms. The results are applied to them and the connection to the intrinsic metric is presented. The thesis ends with different examples showing how this generalization of Davies method can be applied into new fields of application.

Small molecule Zn(II) complexes containing N- and S- donor environments may serve as appropriate models for mimicking Zn protein sites, and thus, their reactions with heavy metal ions such as Pt(II) and W(0) may provide insight into possible adduct formation and zinc displacement. To study such possible interactions between zinc finger proteins and platinum-bound DNA, the ZnN2S2 dimeric complex, N,N?-bis(2- mercaptoethyl)-1,4-diazacycloheptane zinc (II), [Zn-1?]2, has been examined for Znbound thiolate reactivity in the presence of Pt(II) nitrogen ? rich compounds. The reactions yielded Zn/Pt di- and tri- nuclear thiolate-bridged adducts and metalexchanged products, which were initially observed via ESI-mass spectrometry (ESI-MS) analysis of reaction solutions, and ultimately verified by comparison to the ESI-MS analysis, 195Pt NMR spectroscopy, and X-ray crystallography of directly synthesized complexes. The isolation of Zn-(?-SR)-Pt-bridged [(Zn(bme-dach)Cl)(Pt(dien))]Cl adduct from these studies is, to our knowledge, the first Zn-Pt bimetallic thiolatebridged model demonstrating the interaction between Zn-bound thiolates and Pt(II). Additional derivatives involving Pd(II) and Au(III) have been explored to parallel the experiments executed with Pt(II). The [Zn-1?]2 was then modified by cleavage with Na+[ICH2CO2]- to produce (N- (3-Thiabutyl)-N?-(3-thiapentaneoate)-1,4-diazacycloheptane) zinc(II), Zn-1?-Ac or ZnN2SS?O, and 1,4-diazacycloheptane-1,4-diylbis(3-thiapentanoato) zinc(II), Zn-1?-Ac2 or ZnN2S?2O2, monomeric complexes (where S = thiolate, S? = thioether). The [Zn-1?]2 di- and Zn-1?-Ac mono-thiolato complexes demonstrated reactivity towards labile-ligand tungsten carbonyl species, (THF)W(CO)5 and (pip)2W(CO)4, to yield, respectively, the [(Zn-1?-Cl)W(CO)4]- complex and the [(Zn-1?-Ac)W(CO)5]x coordination polymer. With the aid of CO ligands for IR spectral monitoring, the products were isolated and characterized spectroscopically, as well as by X-ray diffraction and elemental analysis. To examine the potential for zinc complexes (or zinc-templated ligands) to possibly serve as a toxic metal remediation agents, Zn-1?-Ac and Zn-1?-Ac2 were reacted with Ni(BF4)2. The formation of Zn/Ni exchanged products confirmed the capability of ?free? Ni(II) to displace Zn(II) within the N-, S-, and O- chelate environment. The Zn/Ni exchanged complexes were analyzed by ESI-MS, UV-visible spectroscopy, IR spectroscopy of the acetate regions, and X-ray crystallography. They serve as foundation molecules for more noxious metal exchange / zinc displacement products.

The concept of LR-nets was introduced and investigated firstly by H.P. Lotz in [27] and by F. Raebiger in [30]. Therefore we call such nets Lotz-Raebiger nets, shortly LR-nets. In this thesis we treat two problems on asymptotic behavior of these operator nets. First problem is to generalize well known theorems for Ces`aro averages of a single operator to LR-nets, namely to generalize the Eberlein and Sine theorems. The second problem is related to the strong convergence of Markov LR-nets on L1-spaces. We prove that the existence of a lower-bound functions is necessary and sufficient for asymptotic stability of LR-nets of Markov operators.

In practice, a communication system works with finite blocklength codes because of the delay constraints and the information-theoretic bounds which are proposed for finite blocklength systems can be exploited to determine the performance of a designed system. In this thesis, achievable rates for given average error probabilities are considered for finite blocklength systems. Although classical bounds can be used to upper bound the error probability, these bounds require the optimization of auxiliary variables. In this work, a bound which is called the dependence testing (DT) bound that is free of any auxiliary variables is exploited. The DT bound is evaluated by introducing a normal approximation to the information density. Simulations carried out both for the Gaussian and discrete input alphabets show the proposed approximation enables very good prediction of the achievable rates. The proposed approximation is also used to calculate the average error probability for block fading channels. Simulations performed for Rayleigh block fading channels demonstrate that the total blocklength of the system in addition to the number of fading blocks should be accounted for especially when the number of fading blocks is large. A power allocation problem in block fading channels when the channel state information is available to the transmitting side is investigated in the final part of this work. The DT bound is optimized for a given channel state vector by allocating different power levels to each fading block by exploiting short-term power allocation. A simple power allocation algorithm is proposed which comes out with very similar results compared with the analytically computed values.

In this study, the effects of CBRT monetary policy decisions on the consumer, automobile, housing and commercial loans of the banks during the period from the early of 2004 to the middle of 2011 are examined. In order to perform this study, it is benefited from weekly weighted average loan interest rate data of the banks, which is the data having the highest frequency that could be obtained from the electronic data distribution system of CBRT. Monetary policy instruments of Central Bank may change in the course of time or monetary policy could be executed by more than one instrument. Therefore, as the political interest rate would be insufficient in the calculation of the effect of monetary policy on loan interest rates of the banks, Government Dept Securities&rsquo / premiums are used instead of the political interest rates in this study to make it reflect the policies of central bank more clearly as a whole. Among the Government Dept Securities that have different maturity structure, benchmark bonds that are adapted to the expected political interest rate changes and that react to the unexpected interest rate changes at the high rate (reaction coefficient 0.983) are used. In order to weight the cointegration relation between interest rates, unrestricted error correction model is established and it is determined by Bound Test that there is a long-term relation between each interest rate and interest rate of benchmark bond. After a cointegration relation is determined among the serials, autoregressive distributed lag model is used to determine the level of transitivity and it is determined that monetary policy decisions affect the banking interest rate at 77% level and by 13 weeks delay on average.

Higher Order Statistics (HOS) and Second Order Statistics (SOS) approaches have certain advantages and disadvantages in signal processing applications. HOS approach provides more statistical information for non-Gaussian signals. On the other hand, SOS approach is more robust to the estimation errors than the HOS approach, especially when the number of observations is small. In this thesis, HOS and SOS approaches are jointly used in order to take advantage of both methods. In this respect, the joint use of HOS and SOS approaches are introduced for online calibration of sensor arrays with arbitrary geometries. Three different problems in online array calibration are considered and new algorithms for each of these problems are proposed. In the first problem, the positions of the randomly deployed sensors are completely unknown except the two reference sensors and HOS and SOS approaches are used iteratively for the joint Direction of Arrival (DOA) and sensor position estimation. Iterative HOS-SOS algorithm (IHOSS) solves the ambiguity problem in sensor position estimation by observing the source signals at least in two different frequencies and hence it is applicable for wideband signals. The conditions on these frequencies are presented. IHOSS is the first algorithm in the literature which finds the DOA and sensor position estimations in case of randomly deployed sensors with unknown coordinates. In the second problem, narrowband signals are considered and it is assumed that the nominal sensor positions are known. Modified IHOSS (MIHOSS) algorithm uses the nominal sensor positions to solve the ambiguity problem in sensor position estimation. This algorithm can handle both small and large errors in sensor positions. The upper bound of perturbations for unambiguous sensor position estimation is presented. In the last problem, an online array calibration method is proposed for sensor arrays where the sensors have unknown gain/phase mismatches and mutual coupling coefficients. In this case, sensor positions are assumed to be known. The mutual coupling matrix is unstructured. The two reference sensors are assumed to be perfectly calibrated. IHOSS algorithm is adapted for online calibration and parameter estimation, and hence CIHOSS algorithm is obtained. While CIHOSS originates from IHOSS, it is fundamentally different in many aspects. CIHOSS uses multiple virtual ESPRIT structures and employs an alignment technique to order the elements of rows of the actual array steering matrix. In this thesis, a new cumulant matrix estimation technique is proposed for the HOS approach by converting the multi-source problem into a single source one. The proposed algorithms perform well even in the case of correlated source signals due to the effectiveness of the proposed cumulant matrix estimate. The iterative procedure in all the proposed algorithms is guaranteed to converge. Closed form expressions are derived for the deterministic Cram&acute / er-Rao bound (CRB) for DOA and unknown calibration parameters for non-circular complex Gaussian noise with unknown covariance matrix. Simulation results show that the performances of the proposed methods approach to the CRB for both DOA and unknown calibration parameter estimations for high SNR.

Xylanases are xylan-degrading enzymes, belong to glycosyl hydrolases (GH). Xylanases from the two major families 10 (GH10) and 11 (GH11) catalyze the hydrolysis of internal β-, bonds of xylan backbone. Xylan is the second most abundant polysaccharide in nature. Nearly one third of the dry weight of the higher plants is xylan and therefore, xylanases have an important role in biomass conversions. Currently, the most effective application of xylanases is in prebleaching of kraft pulp to minimize the use of environmentally hazardous chemicals in the subsequent treatment stages. In recent years, therefore, attention is focused on to isolate and/or engineer the xylanases for the industrial requirements. The desirable roperties of xylanases in paper industry are stability and activity at high temperatures and alkaline pH. While he factors responsible for the thermal stability of GH10 xylanases have been analyzed, factors governing the alkaline stability of GH10 xylanases remain poorly understood. The present thesis reports the crystal structures of an alkali thermostable GH10 extracellular endo-xylanase (BSX) from an alkalophilic organism, Bacillus sp. NG-27 in free and xylosaccharides-bound form. The enzyme was purified from the native organism and crystallized. The structure was solved by molecular replacement method. The 2.2 Å crystal structure of the native BSX enzyme is the first structure of an alkali thermostable GH10 family xylanase from an alkalophilic organism. It has unveiled unique protein properties that can form the basis for improving the thermal, alkaline stability and activity by site directed mutagenesis. The comparative study, especially in relation to GH10 xylanases, deciphered important structural features which are likely to be responsible for the alkaline stability of the enzyme. The work exemplifies the mechanism of adaptation of enzymes to function under polyextreme conditions through changes in the nature and composition of solvent-exposed residues. As apparent from the comparative study, the enhanced stability of the protein can be attributed to the surface rich in acidic residues and less number of solvent-exposed Asn as seen in BSX. This situation which may be roughly described as “acidic residues outside and Asn inside”, is a notable feature of alkali-stable GH10 xylanases from alkalophilic organisms. In addition, the candidate has carried out the comprehensive database analysis of the occurrence of C-H…O hydrogen bonds in helices and helix termini of globular proteins. The study provides a compelling evidence that the main-chain Cα and the side-chains CH which participate in C-H…O hydrogen bonds collectively augment the cohesive energy and thereby contribute together with the classical N-H…O hydrogen bonds and other interactions to the overall stability of helix and therefore of proteins. Chapter 1 starts with a brief introduction of xylanases, their classifications and overall folds. At present, a little more than a dozen of crystal structures of GH10 xylanases are known and described in the literature. A brief mention about these structures and their optimum pH and temperature is outlined under a separate section. In view of the industrial importance of the study enzyme, the potential industrial and biotechnological applications of xylanases are detailed in this Chapter. A section is dedicated to describe the present study enzyme BSX, an alkali thermostable endo-xylanase from an alkalophilic bacterium, Bacillus sp. NG-27. BSX has a molecular mass of ~41 kDa and is optimally active at 343 K and at a pH of 8.4. The alkaline thermostability of the wild type BSX is likely to be industrially important. At the end, the scope of the present work is detailed. Chapter 2 presents the purification of xylanase (BSX) from Bacillus sp. NG-27, the crystallization of the native and xylosaccharides-bound BSX, the X-ray diffraction data collection on these crystals and processing of the data. Repeated attempts to crystallize the protein expressed in the chloroplast of transgenic tobacco plant were unsuccessful. However, crystallization was achieved with the protein sample purified from the native source by hanging drop vapour diffusion method. Crystals were grown at both acidic (4.6) and basic pH (8.5). The corresponding crystallization conditions are 0.2 M MgCl2, 0.1 M sodium acetate pH 4.6 and 20% PEG 550 MME and 0.1 M aCl, 0.01 M MgCl2, 0.1 M Tris-HCl pH 8.5 and 15% PEG 8000. Crystals grown at acidic pH were not suitable for X-ray diffraction study. Subsequently, crystal obtained at a basic pH of 8.5 was used for X-ray data collection and it diffracted X-rays to better than 2.2 Å at the home source at cryo-temperature (100 K). Native BSX crystals belong to monoclinic space group C2 with unit cell parameters a = 174.5 Å, b = 54.7 Å, c = 131.5 Å and β = 131.2°. Crystals of xylosaccharides-bound enzyme were grown in a slightly modified crystallization condition of native, 0.1 M NaCl, 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.5 and 15% PEG 8000 and the enzyme was incubated with xylan prior to setting up the crystallization. Crystals belong to primitive orthorhombic space group P212121 with unit cell parameters a = 59.2 Å, b = 83.8 Å and c = 174.4 Å. A data set was collected using synchrotron radiation of wave length 1.0 Å from a cryo-cooled crystal at Spring-8 BL26B1 beam line, Japan. The Matthews coefficient VM for native and xylosaccharides- bound crystals was calculated to be 2.8 and 2.7 Å3 Da-1, respectively, suggesting two molecules in each crystal asymmetric unit. No twinning was detected in both the datasets and the overall quality of the data sets was found to be good. Chapter 3 details the application of molecular replacement method to the structure solution of native and xylosaccharides-bound BSX, the course of iterative model building and the refinement carried out, and the quality of the final protein structure models. The native-enzyme structure solution was obtained by the molecular replacement method using as a search model the crystal structure (PDB code 1hiz) of the closest homologous, extracellular xylanase (GSX) from Geobacillus stearothermophilus. No non- crystallographic symmetry (NCS) restraint was applied between the two independent molecules in the crystal asymmetric unit at the final round of refinement. The final positional refinement of native BSX converged to R factors of R = 19.4% and Rfree = 23.5% for data between 20.0 to 2.2 Å. The final native model consists of 5704 protein atoms, two Mg2+ ions and 721 solvent water molecules. The final native model was taken as the search structure for the xylosaccharides-bound BSX and a solution with a correlation coefficient of 70.7% and an R-factor of 32.1% was obtained from the molecular replacement calculation. Unlike the native structure refinement, NCS restraint was imposed at all stages of the refinement. Bound xylosaccharides were clearly visible inthe difference Fourier electron density maps. The last round of refinement gave a model with R and Rfree of 21.8% and 25.7%, respectively. The final xylosaccharides-bound model consists of 5766 protein atoms, four Mg2+ ions, 85 atoms belong to bound xylosaccharides and 523 solvent water molecules. No residues were found in the disallowed region of the Ramachandran (φ, ψ) map for both the structures. Chapter 4 describes the native and xylosaccharides-bound BSX crystal structures and the structural comparison of BSX with other GH10 family xylanase crystal structures for which the optimum temperature and pH are known in the literature. BSX folds as the ubiquitous (β/α)8-barrel, a common structural superfold characteristic of GH10 xylanases. The two active site glutamic acid residues, Glu149 and Glu259, are located on opposite sides of the active site cleft and their side-chains are at a distance of 5.5 Å apart suggesting the enzymatic reaction takes place by the retaining mechanism. From the structural superposition of other xylotriose-bound xylanase structures on to the xylosaccharides-bound BSX, structural plasticity in the xylotriose binding can be inferred, implying that the xylose recognition at the subsite -3 displays plasticity and is less specific as opposed to that at -1 and -2 subsites. The stacking interaction of one of the xylose moieties of the xylobiose with the Trp235 seen in BSX provides, for the first time, a structural evidence for the direct involvement of Trp235 in xylosaccharides binding. The crystal structure revealed a metal binding site, found at the C-terminal end of catalytic domain. The presence of metal binding site was not anticipated from earlier theoretically modeled structure and biochemical studies. Further, we have shown experimentally the requirement of Mg2+ ion for the enzyme activity. We havedescribed a novel WP sequence-structure-interaction motif which is present in the (+) side of the active site region and presumably helps in the efficient binding of the carbohydrate moiety of the xylan in the active site cleft of BSX. The structural comparison of BSX with other GH10 xylanases solved to date and characterized to be active at a pH close to neutral was done for the first time. The comparative study revealed the essential structural features which may responsible for the alkaline stability of GH10 xylanases.Briefly, the alkalophilic GH10 xylanases from alkalophilic organisms have surface abundant in acidic residues, the heat and alkaline susceptible residue Asn depleted on the protein surface and increased number of salt bridges. Our study has unveiled the role of the nature and composition of protein surface amino acids in the adaptation of enzymes to polyextreme conditions. The observations reported in the thesis provide important lessons for engineering alkaline stability in xylanases for industrial applications and in general for the understanding of alkaline stability in related proteins. A comparison of the surface features of the BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in polyextremophilicity of proteins, where understanding structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. Chapter 5 summaries the important findings of the present study from the crystal structural analysis of BSX and its comparison with non-alkalophilic GH10 xylanases. Separate sections are made on conclusions and future prospects for the study on BSX. Chapter 6 describes the comprehensive database analysis of C-H…O hydrogen bond in helices of globular proteins. The C-H…O hydrogen bonds found in helices are predominantly of type 5 → 1 or 4 → 1.Our analysis reveals that the Cγ and Cβ hydrogen atom(s) are frequently involved in such hydrogen bonds. A marked preference is noticed for aliphatic β-branched residue Ile to participate in 5 → 1 C- H…O hydrogen bonds involving methylene Cγ1 atom as donor in α-helices. In addition, C-H…O hydrogen bonds are present along with helix stabilizing salt bridges and to some extent compensate for the side-chain conformational entropy loss. Our analysis highlights that a multitude of local C-H…O hydrogen bondsformed by a variety of amino acid side-chains and Cα hydrogen atoms occur in helices and more so at the helix termini. A majority of the helix favouring residues, Met, Glu, Arg, Lys, Leu and Gln which also have large side-chains with more donatable CH groups, have significant propensity to form side-chain to main-chain C-H…O hydrogen bonds in helix. The large side-chains are marked by their ability to shield from the solvent the polar atoms of the peptide backbone and at the same time participate in weak cohesive C-H…O interactions in the helix. This chapter also details the identification for the first time a novel chain reversal motif stabilized by 1 → 5 Cα-H…O interactions. The importance of these hydrogen bonds with respect to helix stability is discussed in the final section of the chapter. Appendix A details the crystallographic and structural analyses oftwares used for the present thesis work. Appendix B describes, in addition to the crystal structure analysis of BSX, the work carried out by the candidate on a comparative study of a thermostable xylanase from Thermoascus aurantiacus, solved in our laboratory at atomic 1.11 Å (293 K) and ultrahigh 0.89 Å (100 K) resolutions. From the comparison, we have for the first time pointed out the possibility of plasticity of ion pairs in proteins with water molecules mediating some of the alternate arrangements. The αβ-loops are relatively less flexible than the βα-loops. The β-strands are least affected structurally with the increase in temperature. Thus the TIM barrel fold in the study enzyme, though having a single domain, may be dissected into parts based on the relative flexibility and described as having a rigid core constituted by the β-barrel and a less rigid exterior formed by the surrounding α-helices. Appendix C presents the crystallization and the preliminary X-ray characterization work done by the author of the thesis on an alkali thermostable cellulase enzyme from Thermomonospora sp. The protein is an extracellular enzyme with molecular mass of 14.2 kDa and interestingly, has the dual activity for both cellulose and xylan. The primary structure of the enzyme is not known. The enzyme was purified from the source organism and crystallized. A complete diffraction data set was collected and processed to 2.3 Å in an orthorhombic space group P212121. Appendix D contains tables which give details about the analysed 5 → 1 Cα- H…O hydrogen bonds in helices and a novel chain reversal motif with 1 → 5 Cα-H…O hydrogen bonds. Appendix E encloses reprints of publications which have resulted from the work reported in the thesis.

No description available.

<p>Spiral grain in trees causes trouble to the wood industry, since boards sawn from trees with large grain angle have severe problems with form stability. Measurements of the grain angle under bark enable the optimisation of the refining process. The main objective of this thesis is to study the potential in estimating the grain angle by using microwaves. To do this, electromagnetic modelling and sensitivity analysis are combined.</p><p>The dielectric properties of wood are different along and perpendicular to the wood fibres. This anisotropy is central for the estimation of the grain angle by means of microwaves. To estimate the grain angle, measurements are used together with electromagnetic modelling for the scattering from plane surfaces and cylinders. Measurement set-ups are proposed to determine the material parameters, such as the grain angle, for plane boards and cylindrical logs. For cylindrical logs both near-field and far-field measurements are investigated. In general, methods for determining material parameters exhibit large errors in the presence of noise. In this case, acceptable levels of these errors are achieved throug using few material parameters in the model: the grain angle and two dielectric parameters, characterising the electrical properties parallel and perpendicular to the fibres.</p><p>From the case with plane boards, it is concluded that it is possible to make use of the anisotropy of wood to estimate the grain angle from the reflected electromagnetic field. This property forms then the basis of the proposed methods for the estimation of the grain angle in cylindrical logs. For the proposed methods, a priori knowledge of the moisture content or temperature of the wood is not needed. Furthermore, since the anisotropy persist also for frozen wood, the method is valid for temperatures below zero degrees Celsius.</p><p>For the case with cylindrical logs, sensitivity analysis is applied to the near-field as well as the far-field methods, to analyse the parameter dependence with respect to the measurement model and the errors introduced by noise. In this sensitivity analysis, the Cram\'{e}r-Rao bound is used, giving the best possible variance for estimating the parameters. The levels of the error bounds are high, indicating a problematic estimation problem. However, the feasibility of accurate estimation will be improved through higher signal-to-noise ratios, repeated measurements, and better antenna gain. The sensitivity analysis is also useful as an analytical tool to understand the difficulties and remedies related to the method used for determining material parameters, as well as a practical aid in the design of a measurement set-up.</p><p>According to the thesis, grain angle estimation is possible with microwaves. The proposed methods are fast and suitable for further development for in-field use in the forest or in saw mills.</p> / <p>Träd med växtvridenhet orsakar problem i träindustrin eftersom brädor som sågats från träd med stor fibervinkel har problem med formstabiliteten och vrider sig då de torkas. Mätning av fibervinkeln under bark möjliggör optimering av förädlingsprocessen. I den här avhandlingen kombineras elektromagnetisk modellering och känslighetsanalys för att undersöka möjligheterna att bestämma fibervinkeln med mikrovågor.</p><p>De elektriska egenskaperna hos trä är olika längs med och vinkelrätt mot fibrerna. Den här anisotropin är utgångspunkten för att bestämma fibervinkeln med hjälp av mikrovågor. För att skatta fibervinkeln används mätningar tillsammans med elektromagnetisk modellering för spridningen från plana ytor och cylindrar. Mätuppställningar föreslås för problemet att skatta materialparametrar, såsom fibervinkeln, i plana brädor och cylindriska stockar. För cylindriska stockar undersöks både närfälts- och fjärrfältsmätningar. I allmänhet har metoder för skattning av materialparametrar stora fel då systemet innehåller brus. Här erhålls acceptabla fel genom att använda få materialparametrar i modelleringen. De materialparametrar som används är fibervinkeln och två dielektriska parametrar som karakteriserar de elektriska egenskaperna längs med och vinkelrätt mot träfibern.</p><p>Slutsatsen från fallet med plana brädor är att det är möjligt att använda anisotropin hos trä och dess påverkan på ett reflekterat elektromagnetiskt fält för att skatta fibervinkeln. Detta är grunden i de metoder som föreslås för cylindriska stockar. För samtliga metoder så gäller att varken fukthalt eller temperatur behöver vara kända på förhand. Eftersom anisotropin kvarstår också för fruset trä så är metoderna användbara även för temperaturer under noll grader Celsius.</p><p>För fallet med cylindriska stockar används känslighetsanalys på både närfälts- och fjärrfältsmetoderna för att analysera parameterberoendet i uppmätt data samt felen som introduceras av brus. I den här känslighetsanalysen används Cram\'{e}r-Rao gränsen som ger den bästa möjliga variansen för skattning av parametrarna. Nivåerna på gränserna är höga vilket indikerar att det är ett svårt estimeringsproblem. Möjligheterna att skatta parametrarna noggrant förbättras genom bättre signal-brus förhållande, upprepade mätningar samt ökad antennstyrka. Känslighetsanalysen är också användbar som ett analytiskt verktyg för ökad förståelse för problem och möjligheter relaterade till metoden för att skatta parametrarna och som ett praktiskt stöd för design av en mätuppställning.</p><p>Enligt avhandlingen är skattning av fibervinkel möjlig med mikrovågor. De föreslagna metoderna är snabba och lämpliga att utveckla vidare för användning i skogen eller i sågverk.</p>