<p>Gamma ray bursts are flashes of gamma rays, associated with high energy explosions at cosmological distances. The main sources of gamma ray bursts are imploding stars. These bursts are mostly observed as thin beams ejecting out of these imploding stars. These beams ejecting out of the stars results in forming extremely hot electrons, ions and strong electromagnetic fields. This report presents the thesis work on visualizing the raw electron, proton and electromagnetic data. Pre-computed data of same electrons and protons are also visualized. The whole simulation data visualized is very large. The raw electron, proton and electromagnetic data are taken as 56 time steps each. The pre-computed electron and proton data taken for visualization are 269 and 282 time steps respectively. The raw data is of 4D that is the data consists of position and 3 momenta. This data have been visualized by dividing the data into 3D subsets. Using the raw data densities are calculated. These densities are visualized by volume rendering technique. The Pre-computed data consists of densities, which are directly using volume rendering technique. VtK is used for volume rendering the data. The work is done on scaling the data for volume rendering. Different components are developed in Vtk for better visualization and analyzation of the data. The magnetic field data is of 3D and electric field is of 2D. These data are visualized as points in 3D space and connected these points’ throug lines. The magnetic and electric field data are visualized in same space. A smooth simulation movie is made from the pre-computed data using windows-movie maker.</p>

<p>There are many different codes available for making molecular dynamic simulation. Most of these are focused on high performance mainly. We have moved that focus towards modularity, flexibility and user friendliness. Our goal has been to design a software that is easy to use, can handle many different kind of simulations and is easily extendable to meet new requirements.</p><p>In the report we present you with the theory that is needed to understand the principles of a molecular dynamics simulation. The four different potentials we have used in the software are presented. Further we give a detailed description of the design and the different design choices we have made while constructing the software.</p><p>We show some examples of how the software can be used and discuss some aspects of the performance of the implementation. Finally we give our thoughts on the future of the software.</p>

<p>Real world modeling has become a very useful tool when new designs and applications are tested before they are introduced on the market. A field that recently has discovered the possible use of modeling is reliability prediction. The reliability and lifetime of a component has until recently been based on months and years of testing. In order to shorten the test time it is possible to simulate the environmental effect on the components. Another advantage of modeling is that changes of large systems where many different components work together can easily be studied. Without modeling the reliability has to be tested over and over again if the system is redesigned since it is impossible to know how the new change will affect the reliability.</p><p>Since electronic circuits are being made smaller and smaller with the increasing demand of faster technology the circuits are very vulnerable to corrosion. A trend in the automotive industry is also to move the electronic devices from the benign environment in the cab to the hash environment on the driveline or the chassi. The most common way to protect the electronics from the hash environment is to put it into a protective covering, also called Electronic Control Unit (ECU). Even though the ECU is sealed, water can still enter the ECU in several ways and cause serious damages by corrosion. The corrosion rate of a component is among others depending of the environmental humidity and temperature. Knowing the humidity and temperature are therefore very important to be able to eliminate corrosion problems. In order to achieve a better understanding of the physics behind the failure and to improve the reliability of the ECU a model of the temperature and humidity penetration is built in this thesis.</p><p>There are several components in the ECU which all responds differently to water vapour. By measuring the humidity penetration in the ECU while components were added one by one, the physical properties of the components could be determined. Some properties were also determined through additional solubility measurements. The humidity penetration of the ECU is then predicted by inserting these properties into mathematical models in Simulink^Ó.</p><p>The conclusion is that it is possible to model the humidity penetration and the temperature changes in the ECU. After the physical properties of the components were determined, the diffusion model agreed well with measurements. The numerical method used in this thesis has been found to be fast and stable. The length of the time-steps has been varied from a couple of minutes to more than an hour in the numerical model. A few physical properties has to be examined more in detailed and the model is then going to be a good foundation on which corrosion and other damaging processes can be modelled.</p>

Real world modeling has become a very useful tool when new designs and applications are tested before they are introduced on the market. A field that recently has discovered the possible use of modeling is reliability prediction. The reliability and lifetime of a component has until recently been based on months and years of testing. In order to shorten the test time it is possible to simulate the environmental effect on the components. Another advantage of modeling is that changes of large systems where many different components work together can easily be studied. Without modeling the reliability has to be tested over and over again if the system is redesigned since it is impossible to know how the new change will affect the reliability. Since electronic circuits are being made smaller and smaller with the increasing demand of faster technology the circuits are very vulnerable to corrosion. A trend in the automotive industry is also to move the electronic devices from the benign environment in the cab to the hash environment on the driveline or the chassi. The most common way to protect the electronics from the hash environment is to put it into a protective covering, also called Electronic Control Unit (ECU). Even though the ECU is sealed, water can still enter the ECU in several ways and cause serious damages by corrosion. The corrosion rate of a component is among others depending of the environmental humidity and temperature. Knowing the humidity and temperature are therefore very important to be able to eliminate corrosion problems. In order to achieve a better understanding of the physics behind the failure and to improve the reliability of the ECU a model of the temperature and humidity penetration is built in this thesis. There are several components in the ECU which all responds differently to water vapour. By measuring the humidity penetration in the ECU while components were added one by one, the physical properties of the components could be determined. Some properties were also determined through additional solubility measurements. The humidity penetration of the ECU is then predicted by inserting these properties into mathematical models in SimulinkÓ. The conclusion is that it is possible to model the humidity penetration and the temperature changes in the ECU. After the physical properties of the components were determined, the diffusion model agreed well with measurements. The numerical method used in this thesis has been found to be fast and stable. The length of the time-steps has been varied from a couple of minutes to more than an hour in the numerical model. A few physical properties has to be examined more in detailed and the model is then going to be a good foundation on which corrosion and other damaging processes can be modelled.

There are many different codes available for making molecular dynamic simulation. Most of these are focused on high performance mainly. We have moved that focus towards modularity, flexibility and user friendliness. Our goal has been to design a software that is easy to use, can handle many different kind of simulations and is easily extendable to meet new requirements. In the report we present you with the theory that is needed to understand the principles of a molecular dynamics simulation. The four different potentials we have used in the software are presented. Further we give a detailed description of the design and the different design choices we have made while constructing the software. We show some examples of how the software can be used and discuss some aspects of the performance of the implementation. Finally we give our thoughts on the future of the software.

Gamma ray bursts are flashes of gamma rays, associated with high energy explosions at cosmological distances. The main sources of gamma ray bursts are imploding stars. These bursts are mostly observed as thin beams ejecting out of these imploding stars. These beams ejecting out of the stars results in forming extremely hot electrons, ions and strong electromagnetic fields. This report presents the thesis work on visualizing the raw electron, proton and electromagnetic data. Pre-computed data of same electrons and protons are also visualized. The whole simulation data visualized is very large. The raw electron, proton and electromagnetic data are taken as 56 time steps each. The pre-computed electron and proton data taken for visualization are 269 and 282 time steps respectively. The raw data is of 4D that is the data consists of position and 3 momenta. This data have been visualized by dividing the data into 3D subsets. Using the raw data densities are calculated. These densities are visualized by volume rendering technique. The Pre-computed data consists of densities, which are directly using volume rendering technique. VtK is used for volume rendering the data. The work is done on scaling the data for volume rendering. Different components are developed in Vtk for better visualization and analyzation of the data. The magnetic field data is of 3D and electric field is of 2D. These data are visualized as points in 3D space and connected these points’ throug lines. The magnetic and electric field data are visualized in same space. A smooth simulation movie is made from the pre-computed data using windows-movie maker.

<p>The main purpose of this thesis is to implement the Gauss--Legendre quadrature for the dispersion coefficient. This has been done and can be now be made with different number of points. The calculations with this implementation has shown that the relativistic impact on helium, neon, argon and krypton is largest for krypton, that has the highest charge of its nucleus. It was also seen that the polarizability of neon as a function of the imaginary angular frequency decreases monotonically from a static value.</p>

<p>The absorption properties of the Pt1 chromophore at room temperature have been studied. Stretch, bend and torsion parameters for Pt(II), P, C (type 1, 2 and 4) and H have been parameterized for use in the MM3 force field. Parameters were fitted to energies computed at the B3LYP level of theory. The parameterized model was used to perform molecular dynamics simulations at room temperature. This was done for several environments and for time periods of up to 200 ps. Absorption properties were computed for snapshots from the dynamics, from which average absorption spectra were created. A conformational broadening of around 40 nm was found in the theoretical spectra, which is in good agreement with experiments. Due to a lack of solvent-solute interactions and the use of a less extensive basis set, a systematic blue shift of 40 nm is evident in the computed spectra.</p>

The X-ray absorption spectrum of silicon in of SiCl4 has been calculated for the LIII and LII edges. The resulting spectrum has been vibrationally resolved by considering the symmetric stretch vibrational mode and the results has been compared to experiment [4]. One peak from the experiment was found to be missing in the calculated vibrationally resolved spectrum. The other calculated peaks could be matched to the corresponding experimental peaks although significant basis set effects are present. An investigation of one peak beyond the Franck–Condon principle shows it to be a good approximation in the case of the studied system.

The work presented in this thesis concerns the dynamics in π-conjugated hydrocarbon systems. Due to the molecular bonding structure of these systems there exists a coupling between the electronic system and the phonons of the lattice. If this interaction, which is referred to as the electron-phonon (e-ph) coupling, is sufficiently strong it may cause externally introduced charge carriers to self-localize in a polarization cloud of lattice distortions. These quasi-particles are, if singly charged, termed polarons, the localization length of which, aside from the e-ph coupling strength, also depend upon the structural and energetic disorder of the system. In disordered systems localization is strong and transport is facilitated by nonadiabatic hopping of charge carriers from one localized state to the next, whereas in well-ordered systems, where extended states are formed, adiabatic transport models apply.Despite great academic efforts a unified model for charge transport in π-conjugated systems is still lacking and further investigations are necessary to uncover the basic physics at hand in these systems. The call for such efforts has been the main guidelines for the work presented in this thesis and are related to the topics of papers I-IV. In order to capture the coupled electron-lattice dynamics, we use a methodological approach where we obtain the time-dependence of the electronic degrees of freedom from the solutions to the time-dependent Schrödinger equation and determine the ionic motion in the evolving charge density distribution by simultaneously solving the lattice equation of motion within the potential field of the ions. The Hamiltonian used to describe the system is derived from an extension of the famous Su-Schrieffer-Heeger (SSH) model extended to three-dimensional systems.In papers I-III we explore the impact of phenylene ring torsion on delocalization and transport properties in poly(para-phenylene vinylene) (PPV). The physics that we are particularly interested in relates to the reduced electron transfer integral strength across the interconnection between the phenylene rings and the vinylene groups upon ring torsion. Keeping this in mind, we demonstrate in paper I the impact of static ring torsion on intrachain mobility and provide a detailed analysis of the influence of the potential barriers (due to consecutive ring torsion) on the nature of charge carrier propagation. In paper II we extend our initial approach to include also the dynamics of ring torsion. We show that without any externally applied electric field, this type of dynamics is the dominant property controlling intrachain propagation, but that when an external electric field is applied, charge carriers may traverse the potential barriers through a process that involves nonadiabatic effects and a temporary delocalization of the polaron state. Finally, in paper III we study the impact of the lattice dynamics on the electron localization properties in PPV and show that the phenylene ring torsion modes couples strongly to the electronic wave function which gives rise to electron localization at room temperature.In papers IV and V we focus on the dynamics of molecular crystals using a stack of pentacene molecules in the single crystal configuration as a model system, but study, in paper IV, the transport as a function of the intermolecular interaction strength, J. We observe a smooth transition from a nonadiabatic to an adiabatic polaron drift process over the regime 20&lt;J&lt;120 meV. For intermolecular interaction strengths above J≈120 meV the polaron is no longer stable and transport becomes band-like. In paper V, finally, we study the internal conversion processes in these systems, which is the dominant relaxation channel from higher lying states. This process involves the transfer of energy from the electronic system to the lattice. Our results show that this process is strongly nonadiabatic and that the relaxation time associated with large energy excitations is limited by transitions made between states of different bands. / I dagens samhälle är elektroniken ett allt viktigare och större inslag i vår vardag. Vi ser på TV, talar i mobiltelefoner, och arbetar på datorer. I hjärtat av denna teknologi finner vi diskreta komponenter och integrerade kretsar utformade främst för att styra strömmen av elektroner genom halvledande material. Traditionellt sett har kisel eller olika former av legeringar använts som det aktiva materialet i dessa komponenter och kretsar, men under de senaste 20 åren har såväl transistorer som solceller och lysdioder realiserats där det aktiva materialet är organiskt, d.v.s., kolbaserat.Vi befinner oss för tillfället mitt uppe i det kommersiella genombrottet för organisk elektronik. Redan idag säljs många MP3-spelare och mobiltelefoner med små skärmar där varje pixelelementen utgörs av organiska ljusemitterande dioder (OLEDs), men teknologin håller redan på att introduceras i mer storskaliga produkter som datorskärmar och TV-apparater som därigenom skulle kunna göras energieffektivare, tunnare, flexiblare och på sikt också billigare. Andra tekniska tillämpningsområden för organisk elektronik som förutspås en lysande framtid är RFID-märkning, organiska solceller, och elektronik tryckt på papper, men även smarta textiler och bioelektronik har stor utvecklingspotential.Den kanske största utmaningen kvarstår dock, att skapa elektroniska kretsar och komponenter uppbyggda kring enskilda molekyler, s.k. molekylär elektronik. Mycket snart närmar vi oss den fysikaliska gränsen för hur små komponenter som vi kan realisera med traditionella icke-organiska material som kisel och en stor drivkraft bakom forskningen på halvledande organiska material har varit just visionen om molekylär elektronik som inte är mer än några miljondelars milimeter stora. För detta ändamål krävs en mycket nogrann kontroll av tillverkningsprocesserna liksom en detaljförståelse för hur molekylerna leder ström och hur denna förmåga kan manipuleras för att realisera såväl traditionella som nya komponenter.I denna avhandling presenteras en översikt av den fysik som möjliggör ledningsförmåga hos särskilda klasser av organiska material, s.k. π-konjugerade system, samt de forskningsresultat som utgör mitt bidrag till denna disciplin. En av utmaningarna på området är den komplexitet som de organiska materialen erbjuder: laddningsprocesserna påverkas nämligen av en rad olika faktorer såsom laddningstäthet, temperatur, pålagd spänning, samt molekylernas former och inbördes struktur. I detta arbete har jag utifrån en vidareutveckling av existerande modeller genom numeriska datasimuleringar undersökt effekten av de senare tre faktorerna på elektronstrukturen, laddnigstransporten och energidissipation i denna klass av material. / Center of Organic Electronics (COE)