A great interest has been shown for self-assembled organic nano-structures that can be used in a variety of optoelectronic applications, from element detection to home electronics. It is known from experimental research that sexiphenyl (6P) grown on muscovite mica substrate form uniaxially self-assembled nanofibers which together with sexithiophene (6T) deposited on top gives the possibility to tune their polarized emission. A key to continue develop and explore the full potential of this technique is to understand the mechanisms behind the growth. This thesis investigate the initial growth of 6P and 6T on a 6Pˆ<img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?%5Cleft(11%20%5Cbar%7B1%7D%20%5Cright)%20%20%20" /> nanofiber substrate through Molecular Dynamics (MD) simulations. The adsorption of the molecules has been simulated with Simulated Annealing (SA) where 6P align perfectly with the substrate for all coverage while 6T starts to align after a certain amount of coverage. Both molecules show a monotonic increase in the adsorption energy per molecule with an increasing coverage. The surface diffusion of the molecules has been studied and shows a higher movement for both in the direction of the longmolecular axis. / Project P25154-N20 "Hetero-epitaxy of organic-organic nanofibers"

Molecular electronics is envisioned as a possible next step in device miniaturization. It is usually taken to mean the design and manufacturing of electronic devices and applications where organic molecules work as the fundamental functioning unit. It involves the measurement and manipulation of electronic response and transport in molecules attached to conducting leads. Organic molecules have the advantages over conventional solid state electronics of inherent small sizes, endless chemical diversity and ambient temperature low cost manufacturing. In this thesis we investigate the switching and conducting properties of photoswitching dithienylethene derivatives. Such molecules change their conformation in solution when acted upon by light. Photochromic molecules are attractive candidates for use in molecular electronics because of the switching between different states with different conducting properties. The possibility of optically controlling the conductance of the molecule attached to conducting leads may lead to new device implementations. The switching reaction is investigated with potential energy calculations for different values of the reaction coordinate between the closed and the open isomer. The electronic and atomic structure calculations are performed with Density Functional Theory (DFT). The potential energy barrier separating the open and closed isomer is investigated, as well as the nature of the excited states involved in the switching. The conducting properties of the molecule inserted between gold, silver and nickel leads is calculated within the Non Equilibrium Green Function theory (NEGF). The molecule is found to be a good conductor in both conformations, with the low-bias current for the closed one being about 20 times larger than that of the open in the case of gold contacts, and over 30 times larger in the case of silver contacts. For the Ni leads the current for the closed isomer is almost 40 times larger than that of the open. Importantly, the current-voltage characteristics away from the linear response is largely determined by molecular orbital re-hybridization in an electric field, in close analogy to what happens for Mn12 molecules. However in the case of dithienylethene attached to Au and Ag such a mechanism is effective also in conditions of strong electronic coupling to the electrodes. In reality these molecules are in constant motion, and the dynamical properties has to be considered. In this thesis such a line of work is initiated. In order to facilitate efficient and stable dynamical simulations of molecular systems the extended Lagrangian formulation of Born-Oppenheimer molecular dynamics have been implemented in two different codes. The extended Lagrangian framework enables the geometric integration of both the nuclear and electronic degrees of freedom. This provides highly efficient simulations that are stable and energy conserving even under incomplete and approximate self-consistent field (SCF) convergence. In the density functional theory code FreeON, different symplectic integrators up to the 6th order have been adapted and optimized. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements. Geometric integration schemes, including a weak dissipation to remove numerical noise, are developed and implemented in the self-consistent tight-binding code LATTE. We find that the inclusion of dissipation in the symplectic integration methods gives an efficient damping of numerical noise or perturbations that otherwise may accumulate from finite arithmetics in a perfect reversible dynamics. The modification of the integration breakes symplecticity and introduces a global energy drift. The systematic driftin energy and the broken symplecticity can be kept arbitrarily small without significant perturbations of the molecular trajectories. / QC 20101202

This thesis concerns quadratic response properties and their application to properties in Jablonski diagrams such as resonant two-photon absorption and excited state absorption. Our main interest lies in optical power limiting applications, and in this context, molecules containing heavy metal atoms prove superior. Therefore, we are interested in how relativity affects these properties, and in order to assess this, a four-component relativistic framework is adopted. To properly address the molecular properties of interest, both relativistic effects and electron correlation need to be accounted for. These two properties are not additive, and, therefore, correlation needs to be incorporated into the four-component framework. We present the implementation of quadratic response properties at the four-component density functional level of theory. For second-harmonic generation, we have, with numerical examples, demonstrated that correlation and relativity are indeed not additive and that the inclusion of noncollinear magnetization is of little importance. We report that both electron correlation as well as relativity strongly affect results for second-harmonic generation. For example, relativity alone reduces the µβ-response signal by 62% and 75% for meta- and ortho-bromobenzene, respectively, and enhances the same response by 17% and 21% for meta- and ortho-iodobenzene, respectively. In the four-component framework, we present the implementations of single and double residues of the quadratic response function, which allows for the evaluation of resonant two-photon absorption cross sections and excited state properties. Using these tools, we discuss different levels of approximation to the relativistic Hamiltonian and we demonstrate that for two-photon absorption, a proper treatment of relativistic effects qualitatively alters the spectrum. For example, already for an element as light as neon, significant differences are seen between the relativistic and nonrelativistic spectra as triplet transitions acquire substantial absorption cross sections in the former case. Finally, quantum mechanics in conjunction with electrodynamics is applied to determine clamping levels in macroscopic samples. The microscopic properties of the optically active chromophores are determined by response theory, and then, electrodynamics is used to describe the interactions between the chromophores and incident laser pulses. Using this approach a series of molecules have been investigated and their performances have been compared and ranked in order to find novel materials for optical power limiting applications.

In this thesis, quantum-mechanical calculations within density-functional theory on metallic systems are presented. The overarching goal has been to investigate effects of disorder. In particular, one of the properties investigated is the bindingenergy shifts for core electrons in binary alloys using different theoretical methods. These methods are compared with each other and with experimental results. One such method, the so-called Slater-Janak transition state method relies on the assumption that the single-particle eigenvalues within density-functional theory are linear functions of their respective occupation number. This assumption is investigated and it is found that while the eigenvalues to a first approximation show linear behavior, there are also nonlinearities which can influence the core-level binding energy shifts. Another area of investigation has been iron based alloys at pressures corresponding to those in the Earth’s inner core. This has been done for the hexagonal close packed and face entered cubic structures. The effects of alloying iron with magnesium and nickel on the equation of state as well on the elastic properties have been investigated. The calculations have shown that the hexagonal close packed structure in FeNi is more isotropic than the face-centered cubic structure, and that adding Mg to Fe has a large impact on the elastic properties. Finally, the effects of disorder due to thermal motion of the atoms have been investigated through ab-initio molecular dynamics simulations. Within the limits of this method and the setup, it is found that the face-centered cubic structure of molybdenum can be dynamically stabilized at high temperature, leading to a metastable structure, on the average. The dynamical stabilization of face-centered cubic molybdenum also rendered it possible to accurately calculate the lattice stability relative to the body-centered cubic phase. Inclusion of temperature effects for the lattice stability using ab-initio molecular dynamics simulations resolves the disagreement between ab-initio calculations and thermochemical methods.

The identity of dark matter is one of the key outstanding problems in both particle and astrophysics. In this thesis, I describe a number of complementary searches for particle dark matter. I discuss how the impact of dark matter on stars can constrain its interaction with nuclei, focussing on main sequence stars close to the Galactic Centre, and on the first stars as seen through the upcoming James Webb Space Telescope. The mass and annihilation cross-section of dark matter particles can be probed with searches for gamma rays produced in astronomical targets. Dwarf galaxies and ultracompact, primordially-produced dark matter minihalos turn out to be especially promising in this respect. I illustrate how the results of these searches can be combined with constraints from accelerators and cosmology to produce a single global fit to all available data. Global fits in supersymmetry turn out to be quite technically demanding, even with the simplest predictive models and the addition of complementary data from a bevy of astronomical and terrestrial experiments; I show how genetic algorithms can help in overcoming these challenges. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 5: Accepted. Paper 6: Submitted.

We are constantly struggling to understand how nature works, trying to identify recurrent events and looking for analogies and relations between objects or individuals. Knowing patterns of behavior is powerful and fundamental for survival of any species. In this thesis, datasets of diverse systems related to transportation, economics, sexual and social contacts, are characterized by using the formalisms of time series and network theory. Part of the results consists on the collection and analyzes of original network data, the rest focuses on the simulation of dynamical processes on these networks and to study how they are affected by the particular structures. The majority of the thesis is about temporal networks, i.e. networks whose structure changes in time. The new temporal dimension reveals structural dynamical properties that help to understand the feedback mechanisms responsible to make the network structure to adapt and to understand the emergence and inhibition of diverse phenomena in dynamic systems, as epidemics in sexual and contact networks. / Vi är ständigt kämpar för att förstå hur naturen fungerar, försöker identifier återkommande evenemang och söker analogier och relationer mellan objekt eller individer. Veta beteendemönster är kraftfull och grundläggande för överlevnad av arter. I denna avhandling, dataset av olika system i samband med transporter är ekonomi, sexuella och sociala kontakter, som kännetecknas av att använda formalismer av tidsserier och nätverk teori. En del av resultatet utgörs av insamling och analys av ursprungliga nätdata, fokuserar resten på simulering av dynamiska processer i dessa nätverk och att studera hur de påverkas av de särskilda strukturer. Huvuddelen av avhandlingen handlar om tidsmässiga nät, i.e. nät vars struktur förändringar i tid. Den nya tidsdimensionen avslöjar strukturella dynamiska egenskaper som hjälper till att förstå den feedback mekanismer som ansvarar för att göra nätverksstruktur att anpassa sig och förstå uppkomsten och hämning av olika företeelser i dynamiska system, epidemier i sexuella och kontaktnät. / Constantemente nos esforçamos para entender como a natureza funciona, tentando identificar eventos recorrentes e procurando por analogias e relações entre objetos ou indivíduos. Conhecer padrões de comportamento é algo poderoso e fundamental para a sobrevivência de qualquer espécie. Nesta tese, dados de sistemas diversos, relacionados a transporte, economia, contatos sexuais e sociais, são caracterizados usando o formalismo de séries temporais e teoria de redes. Uma parte dos resultados consiste na coleta e análise de dados de redes originais, a outra parte concentra-se na simulação de processos dinâmicos nessas redes e no estudo de como esses processos são afetados por determinadas estruturas. A maior parte da tese é sobre redes temporais, ou seja, redes cuja estrutura varia no tempo. A nova dimensão temporal revela propriedades estruturais dinâmicas que contribuem para o entendimento dos mecanismos de resposta responsáveis pela adaptação da rede, e para o entendimento da emergência e inibição de fenômenos diversos em sistemas dinâmicos, como epidemias em redes sexuais e de contato pessoal.

Detta arbete syftar till att utveckla ett förslag på ett utbildningsmaterial i form av en programmeringsorienterad fysik- och matematiklaboration. Målgruppen är i förstahand studenter som läser andra terminen i det ingenjörsförberedande programmet Tekniskt basår (KTH), men även studenter på motsvarande kunskapsnivå (tillexempel elever i gymnasiets naturvetenskapliga program). Laborationen konstruerades för att skapa förutsättningar för studenterna att:1) Visa på kritiskt tänkande,2) visa på kollaboration,3) öka ämnesförståelsen. Det föreslagna utbildningsmaterialet omfattar området beräkningsfysik, där en ickelinjärdifferentialekvation härled från en matematisk pendel ska lösas med hjälp avnumeriska metoder. Laborationens uppgifter formulerades med kritiskt tänkande som utgångspunkt och utfördes med parprogrammering som samarbetsform för kollaboration. I detta arbete undersöktes punkter 1) och 2) i en utbildningssituation med elever från andra terminen på Tekniskt basår. Fyra elevgruppers konversationer spelades in och en innehållsanalys utfördes på transkriberingen av ljudinspelningen. En mönsterjämförelsemetod användes för att stärka slutsatserna. Utifrån resultaten av undersökningsprojektet konstaterade vi att den teoretiska propositionen om att laborationskonstruktionen har medverkat till elevernas kollaboration och appliceringav kritiskt tänkande, har stärkts. / This work aims to develop a proposal for educational material in the form of a programming-oriented Physics and Mathematics lab. The target group is mainly students from the second semester in the Technical Preparatory Year program (KTH), but also students of equivalent knowledge level (for example, students in the upper secondary school- natural science program). The lab was designed to create opportunity for students to:1) apply critical thinking, 2) demonstrate collaboration, 3) increase subject understanding. The proposed educational material comprises computational physics, where a non linear differential equation derived from a mathematical pendulum is solved using numerical methods. The exercises in the lab were formulated with critical thinking in mind and pair programming was used as the context for collaboration. In this paper 1) and 2) were investigated in an educational setting with students from the second semester of the Technical Preporatory Year (KTH). The conversations of four student groups were recorded and a content analysis was performed on the transcriptions of the audio recordings. A pattern matching method was used to strengthen the conclusions. Based on the results of the research project, we found that the theoretical proposition that the construction of the laboratory work has contributed to the collaboration and application of critical thinking by the students,has been strengthened.

Detta arbete syftar till att utveckla ett förslag på ett utbildningsmaterial i form av en programmeringsorienterad fysik- och matematiklaboration. Målgruppen är i första hand studenter som läser andra terminen i det ingenjörsförberedande programmet Tekniskt basår (KTH), men även studenter på motsvarande kunskapsnivå (till exempel elever i gymnasiets naturvetenskapliga program). Laborationen konstruerades för att skapa förutsättningar för studenterna att: 1) Visa på kritiskt tänkande, 2) visa på kollaboration, 3) öka ämnesförståelsen. Det föreslagna utbildningsmaterialet omfattar området beräkningsfysik, där en ickelinjär differentialekvation härled från en matematisk pendel ska lösas med hjälp av numeriska metoder. Laborationens uppgifter formulerades med kritiskt tänkande som utgångspunkt och utfördes med parprogrammering som samarbetsform för kollaboration. I detta arbete undersöktes punkter 1) och 2) i en utbildningssituation med elever från andra terminen på Tekniskt basår. Fyra elevgruppers konversationer spelades in och en innehållsanalys utfördes på transkriberingen av ljudinspelningen. En mönsterjämförelsemetod användes för att stärka slutsatserna. Utifrån resultaten av undersökningsprojektet konstaterade vi att den teoretiska propositionen om att laborationskonstruktionen har medverkat till elevernas kollaboration och applicering av kritiskt tänkande, har stärkts. / This work aims to develop a proposal for educational material in the form of a programming-oriented Physics and Mathematics lab. The target group is mainly students from the second semester in the Technical Preparatory Year program (KTH), but also students of equivalent knowledge level (for example, students in the upper secondary school- natural science program). The lab was designed to create opportunity for students to: 1) apply critical thinking, 2) demonstrate collaboration, 3) increase subject understanding. The proposed educational material comprises computational physics, where a nonlinear differential equation derived from a mathematical pendulum is solved using numerical methods. The exercises in the lab were formulated with critical thinking in mind and pair programming was used as the context for collaboration. In this paper 1) and 2) were investigated in an educational setting with students from the second semester of the Technical Preporatory Year (KTH). The conversations of four student groups were recorded and a content analysis was performed on the transcriptions of the audio recordings. A pattern matching method was used to strengthen the conclusions. Based on the results of the research project, we found that the theoretical proposition that the construction of the laboratory work has contributed to the collaboration and application of critical thinking by the students, has been strengthened.

The experimentally obtained value of the critical exponent ν is presently in significant disagreement with current theoretical predictions for the λ-universality class. We suggest two novel approaches of determining the exponents ν and η by utilizing the effects of finite size scaling. The numerical computations are performed using Monte Carlo simulations of a 3D XY model, realized on a bc-lattice. Different sizes of systems are then either compared in pairs (pairwise fit) or all together (joint fit), in order to fit the correct value of the critical exponents to our sampled data. We find for the pairwise fitting procedure that ν = 0.6731(36) and η = 0.0351(39). Likewise, the joint fitting procedure yields ν = 0.6727(58) and η = 0.0349(49). The predictions for ν are very consistent with existing works, while the values for η are somewhat lower than expected from existing literature results. / Det experimentella värdet av den kritiska exponenten, ν, skiljer sig för närvarande från de teoretiska uppskattningarna som gjorts för λ-universalitetsklassen. Vi föreslår två nya metoder för att bestämma exponenterna ν och η, genom att använda effekterna från ändlig storleksskalning. De numeriska beräkningarna utförs med hjälp av Monte Carlo simulering av en tredimensionell XY-modell, realiserad på ett kubiskt gitter. Olika sys- temstorlekar jämförs sedan antingen parvis eller gemensamt, för att kunna anpassa värdet på de kritiska exponenterna till data. Vi erhåller ν = 0.6731(36) och η = 0.0351(39), för parvis anpassning, samt ν = 0.6727(58) and η = 0.0349(49) för gemensam anpassning. Det beräknade värdet på ν stämmer bra överens med andra arbeten, medan värdena på η är något lägre än förväntat från tidigare uppskattningar.

<p>A time-discrete formulation of the variational principle of mechanics is used to provide a consistent theoretical framework for the construction and analysis of low order integration methods. These are applied to mechanical systems subject to mixed constraints and dry frictional contacts and impacts---machines. The framework includes physics motivated constraint regularization and stabilization schemes. This is done by adding potential energy and Rayleigh dissipation terms in the Lagrangian formulation used throughout. These terms explicitly depend on the value of the Lagrange multipliers enforcing constraints. Having finite energy, the multipliers are thus massless ghost particles. The main numerical stepping method produced with the framework is called SPOOK.</p><p>Variational integrators preserve physical invariants globally, exactly in some cases, approximately but within fixed global bounds for others. This allows to product realistic physical trajectories even with the low order methods. These are needed in the solution of nonsmooth problems such as dry frictional contacts and in addition, they are computationally inexpensive. The combination of strong stability, low order, and the global preservation of invariants allows for large integration time steps, but without loosing accuracy on the important and visible physical quantities. SPOOK is thus well-suited for interactive simulations, such as those commonly used in virtual environment applications, because it is fast, stable, and faithful to the physics.</p><p>New results include a stable discretization of highly oscillatory terms of constraint regularization; a linearly stable constraint stabilization scheme based on ghost potential and Rayleigh dissipation terms; a single-step, strictly dissipative, approximate impact model; a quasi-linear complementarity formulation of dry friction that is isotropic and solvable for any nonnegative value of friction coefficients; an analysis of a splitting scheme to solve frictional contact complementarity problems; a stable, quaternion-based rigid body stepping scheme and a stable linear approximation thereof. SPOOK includes all these elements. It is linearly implicit and linearly stable, it requires the solution of either one linear system of equations of one mixed linear complementarity problem per regular time step, and two of the same when an impact condition is detected. The changes in energy caused by constraints, impacts, and dry friction, are all shown to be strictly dissipative in comparison with the free system. Since all regularization and stabilization parameters are introduced in the physics, they map directly onto physical properties and thus allow modeling of a variety of phenomena, such as constraint compliance, for instance.</p><p>Tutorial material is included for continuous and discrete-time analytic mechanics, quaternion algebra, complementarity problems, rigid body dynamics, constraint kinematics, and special topics in numerical linear algebra needed in the solution of the stepping equations of SPOOK.</p><p>The qualitative and quantitative aspects of SPOOK are demonstrated by comparison with a variety of standard techniques on well known test cases which are analyzed in details. SPOOK compares favorably for all these examples. In particular, it handles ill-posed and degenerate problems seamlessly and systematically. An implementation suitable for large scale performance and accuracy testing is left for future work.</p>