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<p>Mechanical properties of solids are governed by crystal imperfections. Computational materials science is largely concerned with the modelling of such defects, e.g. their formation, migration, and interaction energies. Atomistic simulations of systems containing lattice defects are inherently difficult because of the generally complicated geometrical structure of the defects, the need for large simulation cells, etc.</p><p>In this thesis, the role of lattice defects in the mechanism behind homogeneous melting is demonstrated. Also, a generic calculational scheme for studying atomic vibrations close to extended defects (applied to a dislocation) has been considered. Furthermore, heat capacities in the solid and liquid phases of aluminium have been calculated, as well as various thermophysical defect properties.</p><p>The work was carried out using classical atomistic simulations, mainly molecular dynamics, of aluminium and copper. The interatomic forces were modelled with effective interactions of the embedded-atom type.</p><p>The main results of this thesis are the following:</p><p>• The thermal fluctuation initiating melting is an aggregate typically with 6-7 interstitials and 3-4 vacancies.</p><p>• In the initial stage of melting, no signs of a shear modulus melting mechanism, or the presence of line-like defects (dislocations), can be seen.</p><p>• The typical time interval from when melting initiates to the time at which the liquid phase is fully developed is of the order of 1000τ, where the period τ corresponds to the maximum vibrational frequency in the solid.</p><p>• The solid-liquid boundary advances at a pace comparable to that of thermal transport by vibrating atoms in the crystal at high temperatures.</p><p>• The seemingly small anharmonic effect in the heat capacity of aluminium is caused by a partial cancellation of the low-order term linear in the temperature and anharmonic terms of higher order in the temperature.</p><p>• The core region of an edge dislocation in face-centred cubic aluminium has compressed and expanded regions. The excess volume associated with the dislocation core is small, about 6 percent of the atomic volume, as a result of a partial cancellation between the volume changes of the compressed and expanded regions.</p><p>• The compressed and expanded regions of the edge dislocation core give negative and positive contributions, respectively, to the excess vibrational entropy. The overall effect is a positive vibrational excess entropy of the dislocation core which is about 2<i>k</i>B per atomic repeat length along the dislocation core.</p><p>• The atomic vibrations near the dislocation core are modelled by considering an atomic cluster with about 500-1000 atoms containing the core of dislocation, embedded in a large discrete, but relaxed, lattice of about 23 000 atoms. An atomic region that is four atomic layers thick and about 18 atomic diameters long in the direction parallel to the Burgers vector, accounts for most of the excess entropy.</p><p>• The constant-pressure heat capacity of aluminium shows a minimum as a function of temperature in the liquid phase. </p>

<p>Denna uppsats presenterar en undersökning om gymnasieelevers kunskaper i derivata. Undersökningen syftar till att jämföra både elevernas teoretiska förståelse samt deras praktiska kunskaper med de krav som anges av kursplaner, läroböcker samt rådande undervisningspraxis. Undersökningen syftar också till att utreda om det råder något samband mellan elevernas teoretiska förståelse av derivata och deras praktiska kunskaper på området.</p><p>Undersökningen är bedriven i provform där eleverna under två tillfällen besvarar två olika prov, ett av teoretisk karaktär samt ett av praktiskt beräknande karaktär. Proven är gjorda så att de representerar de rådande kursplanernas krav på godkänd nivå. Det teoretiska provet är upplagt så att eleverna språkligt ska förklara en rad grundläggande teorier och användningsområden inom derivata. Det praktiska provet består av räkneuppgifter av samma karaktär som eleverna är vana vid från lokala samt nationella prov. Undersökningsgruppen består av 22 stycken elever som går det tekniska programmet i årskurs tre.</p><p>Resultaten visar att det i undersökningsgruppen råder ett samband mellan teoretisk förståelse och praktisk kunskap. Detta samband är beräknat mellan de olika provdelarnas resultat och är statistiskt säkerställt. Frågan om eleverna kan sägas ha visat tillräckliga kunskaper för att enligt kursplanen anses vara godkända är behandlad i diskussionsform och presenteras i slutet av rapporten. Där återfinns även en diskussion om undersökningens brister och generaliserbarhet.</p>

HTML clipboardIn this thesis, dynamic effects on electron transport in molecular electronic devices are presented. Special attention is paid to the dynamics of atomic motions of bridged molecules, thermal motions of surrounding solvents, and many-body electron correlations in molecular junctions. In the framework of single-body Green’s function, the effect of nuclear motions on electron transport in molecular junctions is introduced on the basis of Born-Oppenheimer approximation. Contributions to electron transport from electron-vibration coupling are investigated from the second derivative of current-voltage characteristics, in which each peak is corresponding to a normal mode of the vibration. The inelastic-tunneling spectrum is thus a useful tool in probing the molecular conformations in molecular junctions. By taking account of the many-body interaction between electrons in the scattering region, both time-independent and time-dependent many-body Green’s function formula based on timedependent density functional theory have been developed, in which the concept of state of the system is used to provide insight into the correlation effect on electron transport in molecular devices. An effective approach that combines molecular dynamics simulations and first principles calculations has also been developed to study the statistical behavior of electron transport in electro-chemically gated molecular junctions. The effect of thermal motions of polar water molecules on electron transport at different temperatures has been found to be closely related to the temperature-dependent dynamical hydrogen bond network. / QC20100630

Because of the generation of polaritons, which are quasiparticles possessing the characteristics of both photonics and electronics, active photonic materials offer a possible solution to transfer electromagnetic energy below the diffraction limit and further increase the density of photonic integrated circuits. A theoretical investigation of these exciting materials is, therefore, very important for practical applications. Four different kinds of polaritons have been studied in this thesis, (1) surface polaritons of negative-index-material cylindric rods, (2) exciton polaritons of semiconductor quantum dots, (3) localized plasmon polaritons of metallic nanoshells, and (4) surface plasmon polaritons of subwavelength hole arrays in thin metal films. All these types of polaritons were found to strongly affect the optical properties of the studied active photonic materials. More specifically, (1) for two-dimensional photonic crystals composed of negative-index-material cylindric rods, the coupling among surface polaritons localized in the rods results in dispersionless anti-crossing bands; (2) for three-dimensional diamond-lattice quantum-dot photonic crystals, the exciton polariton resonances lead to the formation of complete band gaps in the dispersion relationships; (3) for metallic nanoshells, the thickness of the metal shell strongly modifies the localized plasmon polaritons, and therefore influences the degree of localization of the electromagnetic field inside the metallic nanoshells; (4) for subwavelength hole arrays in thin metal films, high-order surface-polariton Bloch waves contribute significantly to the efficient transmission. To numerically simulate these active photonic materials, we introduced three approaches, (1) an extended plane-wave-based transfer-matrix approach for negative- index-material media, (2) a plane-wave method for semiconductor quantum-dot photonic crystals, and (3) an auxiliary-differential-equation finite-difference time- domain approach for semiconductor quantum-dot arrays. A brief perspective is also given at the end of this thesis. / QC 20100825

In this thesis, quantum chemistry, in particular the B3LYP density functional method, is used to investigate a number of methyl transfer enzymes. Quantum chemical methodology is today a very important tool in the elucidation of properties and reaction mechanisms of enzyme active sites. The enzymes considered in this thesis are the S-adenosyl L-methionine-dependent enzymes - glycine N-methyltransferase, guanidinoacetate methyltransferase, phenylethanolamine N-methyltransferase, and histone lysine methyltransferase. In addition, the reaction mechanism of the DNA repairing enzyme O6-methylguanine methyltransferase is studied. Active site models of varying sizes were designed and stationary points along the reaction paths were optimized and characterized. Potential energy surfaces for the reactions were calculated and the feasibility of the suggested reaction mechanisms was able to be judged. By systematically increasing the size of the models, deeper insight into the details of the reactions was obtained, the roles of the various active site residues could be analyzed, and, very importantly, the adopted modeling strategy was evaluated. / QC 20100927

Mechanical properties of solids are governed by crystal imperfections. Computational materials science is largely concerned with the modelling of such defects, e.g. their formation, migration, and interaction energies. Atomistic simulations of systems containing lattice defects are inherently difficult because of the generally complicated geometrical structure of the defects, the need for large simulation cells, etc. In this thesis, the role of lattice defects in the mechanism behind homogeneous melting is demonstrated. Also, a generic calculational scheme for studying atomic vibrations close to extended defects (applied to a dislocation) has been considered. Furthermore, heat capacities in the solid and liquid phases of aluminium have been calculated, as well as various thermophysical defect properties. The work was carried out using classical atomistic simulations, mainly molecular dynamics, of aluminium and copper. The interatomic forces were modelled with effective interactions of the embedded-atom type. The main results of this thesis are the following: • The thermal fluctuation initiating melting is an aggregate typically with 6-7 interstitials and 3-4 vacancies. • In the initial stage of melting, no signs of a shear modulus melting mechanism, or the presence of line-like defects (dislocations), can be seen. • The typical time interval from when melting initiates to the time at which the liquid phase is fully developed is of the order of 1000τ, where the period τ corresponds to the maximum vibrational frequency in the solid. • The solid-liquid boundary advances at a pace comparable to that of thermal transport by vibrating atoms in the crystal at high temperatures. • The seemingly small anharmonic effect in the heat capacity of aluminium is caused by a partial cancellation of the low-order term linear in the temperature and anharmonic terms of higher order in the temperature. • The core region of an edge dislocation in face-centred cubic aluminium has compressed and expanded regions. The excess volume associated with the dislocation core is small, about 6 percent of the atomic volume, as a result of a partial cancellation between the volume changes of the compressed and expanded regions. • The compressed and expanded regions of the edge dislocation core give negative and positive contributions, respectively, to the excess vibrational entropy. The overall effect is a positive vibrational excess entropy of the dislocation core which is about 2kB per atomic repeat length along the dislocation core. • The atomic vibrations near the dislocation core are modelled by considering an atomic cluster with about 500-1000 atoms containing the core of dislocation, embedded in a large discrete, but relaxed, lattice of about 23 000 atoms. An atomic region that is four atomic layers thick and about 18 atomic diameters long in the direction parallel to the Burgers vector, accounts for most of the excess entropy. • The constant-pressure heat capacity of aluminium shows a minimum as a function of temperature in the liquid phase. / QC 20101013

Denna uppsats presenterar en undersökning om gymnasieelevers kunskaper i derivata. Undersökningen syftar till att jämföra både elevernas teoretiska förståelse samt deras praktiska kunskaper med de krav som anges av kursplaner, läroböcker samt rådande undervisningspraxis. Undersökningen syftar också till att utreda om det råder något samband mellan elevernas teoretiska förståelse av derivata och deras praktiska kunskaper på området. Undersökningen är bedriven i provform där eleverna under två tillfällen besvarar två olika prov, ett av teoretisk karaktär samt ett av praktiskt beräknande karaktär. Proven är gjorda så att de representerar de rådande kursplanernas krav på godkänd nivå. Det teoretiska provet är upplagt så att eleverna språkligt ska förklara en rad grundläggande teorier och användningsområden inom derivata. Det praktiska provet består av räkneuppgifter av samma karaktär som eleverna är vana vid från lokala samt nationella prov. Undersökningsgruppen består av 22 stycken elever som går det tekniska programmet i årskurs tre. Resultaten visar att det i undersökningsgruppen råder ett samband mellan teoretisk förståelse och praktisk kunskap. Detta samband är beräknat mellan de olika provdelarnas resultat och är statistiskt säkerställt. Frågan om eleverna kan sägas ha visat tillräckliga kunskaper för att enligt kursplanen anses vara godkända är behandlad i diskussionsform och presenteras i slutet av rapporten. Där återfinns även en diskussion om undersökningens brister och generaliserbarhet.

<p>The present thesis is a theoretical study of several x-ray spectroscopies { x-ray absorption, xray photoelectron, radiative and non-radiative resonant Raman scattering spectroscopy. The main focus point is investigating the role of the nuclear dynamics in molecules (naphthalene, biphenyl, the water dimer, HCl) on these spectra.</p><p>The theoretical tools we use consist of the basic equations of the relevant x-ray spectroscopy. Wave packet methods are also used. The molecular parameters needed for our simulations are obtained through suitable quantum chemical calculations, mainly based on either wave function or density functional methods. Our simulations are compared with experimental data, where available.</p><p>Simulations of x-ray absorption and x-ray photoionization spectra for naphthalene and biphenyl show that the spectral shapes are heavily inuenced by the joint e ect of two factors { chemical shifts and excitations of vibrational progression. In both of the studied molecules, similar vibrational modes are excited, giving rise to a signi cant vibrational broadening of the spectra. Comparison between the two molecules and also comparison to the reference case { benzene, provides useful insight into the molecular behavior under core excitation.</p><p>In a further step, we consider the O1s x-ray photoelectron spectrum of the water dimer. A substantial broadening of the two bands originating from the donor and the acceptor oxygen is found. It is caused by excitations of soft intermolecular vibrational modes, associated with the hydrogen bond.</p><p>Another strong inuence of the nuclear dynamics is clearly seen in the resonant x-ray Raman scattering of HCl. Vibrational collapse is observed experimentally and con rmed theoretically for two cases: resonant excitation of the K line and o -resonant excitation of the elastic peak. These two collapses can be strictly realized for excitations in the hard x-ray region. Our considerations show that using this technique, one can eliminate the broadenings caused by the lifetime of the core excited state and the vibrational broadening, and hence, considerably increase the spectral resolution.</p><p>Finally, we predict an interference e ect in the resonant Auger scattering from xed-inspace molecules. By exciting a molecule to a dissociative state and measuring the angular distribution of the Auger electrons in coincidence with the molecular ion, one can observe this e ect. The interference pattern can be used after Fourier transformation for extracting structural data about the studied system.</p>

<p>This licentiate thesis deals with quantum chemistry methods for large systems. In particular, the thesis focuses on the efficient construction of the Coulomb and exchange matrices which are important parts of the Fock matrix in Hartree--Fock calculations.The methods described are also applicable in Kohn--Sham Density FunctionalTheory calculations, where the Coulomb and exchange matrices areparts of the Kohn--Sham matrix. Screening techniques for reducing the computational complexity of bot Coulomb and exchange computations are discussed, as well as the fast multipole method, used for efficient computation of the Coulomb matrix.</p><p>The thesis also discusses how sparsity in the matrices occurring in Hartree--Fock and Kohn--Sham Density Functional Theory calculations can be used to achieve more efficient storage of matrices as well as more efficient operations on them.</p><p>As an example of a possible type of application, the thesis includes a theoretical study of Heisenberg exchange constants, using unrestricted Kohn--Sham Density Functional Theory calculations.</p>