The present thesis is devoted to theoretical studies of light pulse propagation through different linear and nonlinear media. One dimensional holographic photonic crystals and one dimensional impurity band based photonic crystals are investigated as linear media. The effects of angular dependence of the band structures and pulse delay with respect to the light polarization are analyzed. A strict theory of nonlinear propagation of a few strong interacting light beams is presented and applied in the field of nonlinear optics. The key idea of this approach is a self-consistent solution of the nonlinear wave equation and the density matrix equations of the material beyond the so-called rotating wave approximation. The results of numerical studies led to a successful interpretation of recent experimental data [Nature, 415:767, 2002]. A theoretical study of the NO molecule by means of two-color infrared -- X-ray pump probe spectroscopy is presented. It was found that the phase of the infrared field strongly influences the trajectory of the nuclear wave packet, and hence, the X-ray spectrum. The dependence of the X-ray spectra on the delay time, the duration and the shape of the pulses are studied. / QC 20101207

The electronic structures of complex systems have been studied by theoretical calculations of soft x-ray spectroscopies like x-ray photoelectron spectroscopy, near edge x-ray absorption fine structure, and x-ray emission spectroscopies. A new approach based on time dependent density functional theory has been developed for the calculation of shake-up satellites associated with photoelectron spectra. This method has been applied to the phthalocyanine molecule, describing in detail its electronic structure, and revealing the origin of controversial experimental features. It is illustrated in this thesis that the theoretical intepretation plays a fundamental role in the full understanding of experimental spectra of large and complex molecular systems. Soft x-ray spectroscopies and valence band photoelectron spectroscopies have proved to be powerful tools for isomer identification, in the study of newly synthesized fullerene molecules, the azafullerene C48N12 and the C50Cl10 molecule, as well as for the determination of the conformational changes in the polymeric chain of poly(ethylene oxide). The dynamics of the core excitation process, revealed by the vibrational fine structure of the absorption resonances, has been studied by means of density functional and transition state theory approaches. / QC 20100929

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

<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>

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. 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. 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. / QC 20101123

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This thesis reports a state-of-the-art theoretical study of photophysical properties of organic charge-transfer aromatic molecules. These molecules are building blocks of molecular functional materials used in modern photonics technology and play essential roles in chemistry and biology in general. A good understanding of these systems is thus important. The theoretical results for permanent dipole moments of some substituted benzenes have been obtained using the coupled cluster singles and doubles (CCSD) method. The performance of density functional theory (DFT) for the geometry and electronic properties has been compared with that of traditional ab initio methods, such as Hartree-Fock, second-order Möller Plesset perturbation theory (MP2), CCSD and CCSD(T). Limitations of the DFT methods for charge transfer molecules have been demonstrated. The multi-configuration self-consistent field (MCSCF) method has been applied to understand properties of the triplet states of benzene derivatives by studying their phosphorescence with the inclusion of contributions from vibronic coupling. It has also been employed to calculate the photophysics of the thioxanthone molecule containing three benzene rings in combination with the CASPT2 method, resolving a long-standing problem concerning the possible stable conformations of the molecule. With knowledge of the building blocks a series of porphyrin derivatives with exceptionally large two-photon absorption cross sections were designed, and proposed for use in bioimaging applications. The static and dynamic properties of a few zinc and platinum organometallic compounds, being possible candidates for optical limiting devices, have also investigated. / QC 20101011

<p>The spin of an electron often misleadingly interpreted as the classical rotationof a particle. The quantum spin distinguishes itself from classicalrotation by possessing quantized states and can be detected by its magneticmoment. The properties of spin and its collective behavior with otherfundamental properties are fascinating in basic sciences. In many aspectsit offers scope for designing new materials by manipulating the ensemblesof spin. In recent years attention towards high density storage devices hasdriven the attention to the fundamental level were quantum physics rules.To understand better design of molecule based storage materials, studies onspin degrees of freedom and their coupling properties can not be neglected.</p><p>To account for many body effect of two or more electrons consistent withrelativity, an approximation like the Breit Hamiltonian(BH) is used in modernquantum chemical calculations, which is successful in explaining the splitin the spectra and corresponding properties associated with it. Often differenttactics are involved for a specific level of computations. For example themulti-configurational practice is different from the functional based calculations,and it depends on the size of the system to choose between resourcesand accuracy. As the coupling terms offers extra burden of calculating theintegrals it is literally challenging.</p><p>One can readily employ approximations as it suits best for the applicationoriented device computations. The possible methods available in the literatureare presented in chapter 2. The theoretical implementations of couplingfor the multi-reference and density functional method are discussed in detail.The multi-reference method precedes the density functional methodin terms of accuracy and generalizations, however it is inefficient in dealingvery large systems involving many transition elements, which is vital formolecule based magnets as they often possess open shell manifolds. On theother hand existing density functional method exercise perturbations techniqueswhich is extremely specialized for a specific system - highly coupledspins.</p><p>The importance of spin-spin coupling(SSC) in organic radical-Oxyallyl(OXA)was systematically studied with different basis sets and compared with asimilar isoelectronic radical(TMM). The method of spin-spin coupling implementationsare also emphasized. Similar coupling studies were carriedivout for the species HCP and NCN along with spin-orbit coupling(SOC).The splitting of the triplet states are in good agreement with experiments</p>