The mechanical behavior of discrete atoms has been studied with molecular dynamics whose computational time is proportional to the square of the number of atoms, O(N²). Recently, a faster algorithm, Atomic-scale Finite Element Method (AFEM) with computational time proportional to the number of atoms, O(N), had been developed. The main idea of AFEM, compared with conventional finite element method is to replace nodes with atoms and elements with electric forces between atoms. When interpreting a non-linear system, it is necessary to use an iteration scheme. A simulation of molecular dynamics based on the Verlet's method was conducted in order to validate AFEM in one dimension. The speed of AFEM was investigated in one and two dimensional atomic systems. The results showed that the computational time of AFEM is approximately proportional to the number of atoms, and the absolute computation time appears to be small. The frameworks of AFEM not only for multi-body potential but also pair potential are presented. Finally, AFEM was applied to analyze and interpret the mechanical behavior of a carbon nanotube and a quartz. The buckling behavior of carbon nanotube showed a good agreement with the results illustrated in the original literature. / Master of Science

Artificial photosynthesis is used to harvest solar energy and store it in the form of chemical bonds. The system of interest in this study does this by splitting water into hydrogen and oxygen gas through a plasmon assisted process, collective oscillations from free electron gas. This is a renewable way to store energy that could be used as an alternative to fossil based fuel. In this study, a small part of this photo catalytic system is studied, namely the interaction between plasmonically active silver nanoparticles (Ag NPs) transferring photo-excited electrons via a linker molecule, 4-aminobenzoic acid (pABA). The pABA linker molecule transfers charge from the Ag surface to a semiconductor and a catalyst performing the water splitting. The pABA can bind in different ways onto the Ag-surface and the aim of this study is to examine which bond is strongest and which best enables charge transfer. To this purpose three systems where simulated quantum mechanically using a supercomputer. The total free energy of the systems was computed and compared. Out of the three studied binding sites, the hollow-site bond (pABA binding to three silver atoms) was found to have the lowest energy, meaningit's the strongest of the possible bonds. Additionally it was found that the band gap (the energy needed to transfer charge) for the pABA decreased when bound to the Ag-surface. The hollow-site bound pABA also had the smallest band gap, meaning it requires the least energy to transfer a charge and should therefore be the best bond fitted for the photo catalytic system. / Artificiell fotosyntes används för att absorbera solenergi och förvara den i formen av kemiska bindningar. Systemet som används i denna studie gör detta genom att splittra vatten till vätgas och syrgas genom en plasmon assisterad process. Detta är ett förnyelsebart sätt att förvara energi och kan användas som ett alternativ till fossila bränslen. I denna studie studeras en liten del utav detta fotokatalytiska system nämligen interaktionen där plasmonaktiva silvernanopartiklar (Ag NPs) överför foto-exciterade elektroner genom molekyllänken 4-aminobensoesyra (pABA). Molekyllänken pABA överför laddning från silverytan till en halvledare och en katalys som utför splittringen av vattnet. pABA kan binda på olika sätt tillen silveryta och denna studie syftar till att undersöka vilken utav bindningarna som är starkast och vilken som effektivast överför laddning. För att göra detta simulerades tre system kvantmekaniskt med hjälp av en superdator, ett system för varje sorts bindning. Den totala fria energin av systemen beräknades och jämfördes. Av de tre undersökta bindningarna hadehollow-site bindningen (pABA som binder till tre silveratomer) längst energi, vilket betyder att det är den starkaste av bindningarna. Utöver detta så visade det sig att bandgapet (energin som krävs för att överföra laddning) minskade för pABA när den var bunden till Ag-ytan. Hollow-site bundet pABA hade även minst bandgap, vilket betyder att den kräver minst energi för att överföra laddning och är därmed den mest effektiva bindningen för det fotokatalytiska systemet.

In order to understand the behaviour and function of proteins, their three dimensional structure needs to be known. Determination of macro-molecules’ structures is done using X-ray diffraction or electron microscopy, where the resulting diffraction pattern is used for molecular reconstruction. These methods are however limited by radiation damage.The aim of this work is to study radiation damage of peptides in proteins using computer simulations. Increased understanding of the atomic and molecular dynamics can contribute to an improvement of the method ofimaging biological molecules. To be able to describe the processes that take place as accurately as possible, the problem must treated quantum mechanically.Thus, the simulations are performed with molecular dynamics based on first principles. In order to capture the dynamics of the excited states of the molecule when exposed to X-rays, time-dependent density functional theory with delta self-consistent field is used. These simulations are compared to ground state simulations. The results of the thesis conclude that the excited and ground state simulations result in differences in the dynamics, which are most pronounced for lager molecules.

The department of Radiation Sciences at Umeå University has obtained an old linear accelerator, intended for educational purposes. The goal of this thesis was to find proper reinforced radiation protection in an intended bunker (a room with thick concrete walls), to ensure that the radiation outside the bunker falls within acceptable levels. The main method was with the use of Monte Carlo-simulations. To properly simulate the accelerator, knowledge of the energy distribution of emitted radiation was needed. For this, a novel method for spectra determination, using several depth dose measurements including off-axis, was developed. A method that shows promising results in finding the spectra when measurements outside the primary beam are included. The found energy spectrum was then used to simulate the accelerator in the intended bunker. The resulting dose distribution was visualized together with 3D CAD-images of the bunker, to easily see in which locations outside the bunker where the dose was high. An important finding was that some changes are required to ensure that the public does not receive too high doses of radiation on a public outdoor-area that is located above the bunker. Otherwise, the accelerator is only allowed to be run 1.8 hours per year. A workaround to this problem could be to just plant a thorn bush, covering the dangerous area of radius 3m. After such a measure has been taken, which is assumed in the following results, the focus moves to the radiation that leaks into the accelerator’s intended control room, which is located right outside the bunker’s entrance door. The results show that the accelerator is only allowed to be run for a maximum of 6.1 or 3.3 hours per year (depending on the placement of the accelerator in the room), without a specific extra reinforced radiation protection consisting mainly of lead bricks. With the specific extra protection added, the accelerator is allowed to be run 44 or 54 hours per year instead, showing a distinct improvement. However, the dose rate to the control room was still quite high, 13.7 μGy/h or 11.2 μGy/h, compared to the average dose received by someone living in Sweden, which is 0.27 μGy/h. Therefore, further measures are recommended. This is however a worst case scenario, since the leakage spectrum from the accelerator itself was simulated as having the same energy spectrum as the primarybeam at 0.1 % of the intensity, which is the maximum leakage dose according to the specifications for the accelerator. This is probably an overestimation of the intensity. Also, the energy spectra of the leakage is probably of lower energy than the primary beam in at least some directions. Implementing more knowledge of the leak spectra in future work, should therefore result in more allowed run hours for the accelerator.

Wellenleiter Quantenelektrodynamik (Wellenleiter QED) ist ein wichtiger Baustein in vielen zukünftigen, auf Quantenmechanik basierenden Technologien wie z.B. Quantencomputer. Ein typisches Modellsystem besteht aus einem Zwei-Niveau-System (two level system, TLS), das an einen eindimensionalen Wellenleiter gekoppelt wurde. Der Wellenleiter ist dabei durch eine Dispersionsrelation charakterisiert und kann unter anderem Bandkanten enthalten. Wir haben in der Dissertation einen neuartigen Zugang zur Wellenleiter QED präsentiert. Dieser Zugang basiert auf der Quantenfeldtheorie und ermöglicht die Berechnung Greenscher Funktionen im ein- und zwei-Anregungs Unterraum. Diese Greenschen Funktionen wurden benutzt um die Streumatrix und die spektrale Dichte in beiden Unterräumen zu berechnen. Desweiteren konnten wir mit Hilfe von Feynman-Diagrammen die physikalischen Prozesse in der Störungsreihe der Greenschen Funktionen identifizieren. Dies war besonders im zwei-Anregungs-Unterraum von Nutzen. In diesem Fall verhält sich das System nichtlinear, da das TLS nur eine Anregung absorbieren kann. Dadurch werden Effekte induziert wie photon bunching und die effiziente Anregung eines gebundenen Atom-Photon Zustandes. Es war uns möglich diese Effekte in der Störungsreihe der Greenschen Funktion wieder zu finden. Desweiteren haben wir die Greenschen Funktionen im Orts-Zeit-Raum benutzt um ein- und zwei-Photon-Wellenpakete zu propagieren. Es hat sich herausgestellt dass das Verhältnis von Pulsbreite zur spontanten Emissions-zeit sowohl das Streuverhalten als auch die maximale Anregung des TLS bestimmt. Letztendlich haben wir den Einfluss von Unordnung im Wellenleiter auf das Zerfallsverhalten des TLS untersucht. Wir haben entdeckt dass der gebundene Atom-Photon Zustand instabil wird sobald die Unordnung einen kritischen Wert erreicht. Darüberhinaus haben wir eine spezielle Klasse Feynman Diagramme identifiziert, die dem Zerfall eine nichtmarkovsche Dynamik verleihen. / Waveguide quantum electrodynamics (waveguide QED) can be considered as a building block for many prospective technologies like quantum computing. A prototypical system consists of a two-level system (TLS) coupled to a one-dimensional waveguide. The waveguide is characterized by its dispersion relation and can also feature a band edge/slow-light regime. In this thesis we have presented a new theoretical framework for waveguide QED, based on quantum field theory. The framework provides the Green''s functions of the system in the single- and two-excitation sectors for an arbitrary dispersion relation. We have calculated the scattering matrix and the spectral density in both sectors. Furthermore, we have also represented the Green''s functions in the form of Feynman diagrams, from which we can identify the underlying physical processes. A special property of the system is that it behaves nonlinear in the case of two or more photons. This is rooted in the structure of the TLS, which can at most absorb one excitation. The nonlinearity leads to two effects: photon bunching and the efficient excitation of an atom-photon bound state. We have found both effects within our framework and we were able to assign them individual terms in the perturbation series of the Green''s function. Furthermore, we have used the Green''s function in space-time domain to propagate Gaussian one- and two-photon wavepackets. Here, we have identified the ratio of the pulsewidth and the spontaneous emission time as the parameter which governs both the scattering behavior of the photons and the maximal TLS excitation. Eventually, we have investigated the effects of disorder in the waveguide on the decay properties of the TLS. We have found here that the atom-photon bound state is stable for small disorder, but breaks down at sufficiently strong disorder. Furthermore, we have identified a special class of diagrams which render the system non-Markovian even for energies far away from the band edge.

Cette thèse décrit l'observation expérimentale de l'effet Hong-Ou-Mandel avec une sourceatomique ultra-froide. L’expérience originale réalisée en 1987 par C. K. Hong, Z. Y. Ou et L. Mandel illustre de façon simple une interférence à deux particules explicable uniquement par la mécanique quantique : deux particules bosoniques et indiscernables, arrivant chacune sur une face d'entrée différente d'une lame semi-réfléchissante ressortent ensemble. Cet effet se traduit par une réduction du taux de détection en coïncidence entre les deux voies de sortie quand les particules arrivent simultanément sur la lame. Cette expérience fut originalement réalisée avec des photons et nous rapportons ici la première mise en oeuvre expérimentale avec des particules massives se propageant dans l’espace libre.Après présentation des différentes techniques nécessaires à sa réalisation, nous décrivons cette expérience et analysons les résultats obtenus. En particulier, la réduction du taux de coïncidence est suffisamment forte pour exclure toute interprétation classique ; l'observation de cet effet constitue une brique fondamentale dans le domaine de l’information quantique atomique. / In this thesis, we report the first realisation of the Hong–Ou–Mandel experiment with massive particles in momentum space. This milestone experiment was originally performed in quantum optics: two photons arriving simultaneously at the input ports of a 50:50 beam-splitter always emerge together in one of the output ports. The effect leads to a reduction of coincidence counts which translates into a dip when particles are indistinguishable. We performed the experiment with metastable helium atoms where the specificities of the Micro-Channel-Plate detector allows one to recover the momentum vector of each individual atom.After listing the necessary tools to perform this experiment with atoms, the experimental sequence is discussed and the results are presented. In particular we measured a coincidence count reduction that cannot be explained through any simple classical model. This corresponds to the signature of a two-particle interference, and confirms that our atomic pair source produces beams which have highly correlated populations and are well mode matched. This opens the prospect of testing Bell’s inequalities involving mechanical observables of massive particles, such as momentum, using methods inspired by quantum optics. It also demonstrates a new way to produce and benchmark twin-atom pairs that may be of interest for quantum information processing.

Thin-film solar cell research is central to the electricity production of the near future. Photovoltaic technologies based on silicon have a significant portion of the global market and installed capacity. Thin-film solar cells are port of the emerging photovoltaic technologies that are challenging silicon for a part of the electricity production based on solar power. These thin-film technologies, such as copper indium gallium selenide (CIGS) and cadmium telluride (CdTe), are lower cost and require less energy to produce, but also require rare materials. An alternative to these technologies are thin-film solar cells based on more abundant materials. To develop these new materials at Uppsala University, combinatorial synthesis is used. This method produces a significant amount of data across different measurement methods. The data needs to be analysed and combined to gather information about the characteristics of the materials being developed. To facilitate the analysis and combination of data, a database tool was created in MATLAB. The result is a program that allows its User to combine energy-dispersive X-ray spectroscopy (EDS), Raman spectroscopy and Photoluminescence spectroscopy measurements done on solar cell absorber layers. Absorber layers are the section of solar cells where sun lighet is absorbed, and electron-hole pairs are created. The program provides multiple figures and graphs combining the different data collected, enabling the User to draw conclusions about the characteristics of the sample and its suitability as an absorber layer. The combinatorial synthesis database tool created could be user for combinatorial synthesis analysis of other material samples that are not necessarily absorber layers for thin-film solar cells. This report describes both the development of the tool and the code itself.

Ce travail de thèse a consisté en l’étude de catalyseurs ultradispersés, composés de clusters nanométriques ou d’atomes isolés (single-atom catalysts, SACs) de métal, une nouvelle classe de catalyseurs faisant actuellement l’objet d’un engouement mondial. Les systèmes Pt/?-Al2O3 et Pt/TiO2 ont été préparés, caractérisés et testés en oxydation de CO et photogénération d’hydrogène, respectivement. Plusieurs méthodes d’imprégnation et de traitement thermique ont été comparées, notamment grâce à l’analyse de la dispersion du platine par microscopie électronique en transmission à balayage (STEM). Pour la préparation de SACs, notre choix s’est finalement porté sur l’imprégnation à humidité naissante d’une faible charge de précurseur Pt(NH3)4(NO3)2, suivie d’une calcination à l’air. L’étude des performances catalytiques et de l’évolution structurale des catalyseurs au cours des réactions a permis de montrer que les atomes isolés (cations) de platine étaient moins actifs que les clusters (réduits) pour les deux systèmes catalytiques étudiés. Dans le cas de Pt/?-Al2O3, des suivis par spectroscopie d’absorption X (XAS) operando en rayonnement synchrotron, spectroscopie infrarouge par réflexion diffuse (DRIFTS) operando et microscopie environnementale (E-STEM) ont montré la formation et la déstabilisation des SACs, cette dernière étant toutefois moindre en conditions oxydantes. En effet, l’oxygène stabilise le platine isolé via la formation de plusieurs liaisons Pt-O-Al comme montré par modélisation DFT, alors que la présence d’un composé réducteur (CO, H2) conduit à la formation de clusters, mobiles sur leur support. Ce travail met en évidence les limites possibles concernant la stabilisation et la mise en œuvre des SACs dans des réactions catalytiques impliquant des conditions réductrices / This PhD work is focused on the study of ultradispersed catalysts, composed of nanometer-sized clusters or isolated atoms (single-atom catalysts, SACs) of metal, a new class of catalysts which are currently the object of worldwide interest. The Pt/?-Al2O3 and Pt/TiO2 systems were prepared, characterized and evaluated for CO oxidation and hydrogen photogeneration, respectively.Several methods of impregnation and thermal treatment were compared, in particular through platinum dispersion analysis using scanning electron microscopy (STEM). For the preparation of SACs, our choice finally turned to the incipient wetness impregnation of Pt(NH3)4(NO3)2 precursor at low loading, followed by calcination in air.For the two catalytic systems of interest, the study of the performances and the structural evolution of the catalysts during the reactions shows that isolated Pt atoms (cations) are less active than their (reduced) cluster counterparts.In the case of Pt/?-Al2O3, operando X-ray absorption spectroscopy (XAS) using synchrotron radiation, operando diffuse reflectance infrared spectroscopy (DRIFTS), and environmental microscopy (E-STEM) allowed us to monitor the SAC formation and destabilization, the latter being however limited in oxidizing conditions. Indeed, the presence of oxygen stabilizes single Pt atoms via the formation of several Pt-O-Al bonds as shown by DFT modeling, whereas the presence of a reducing compound (CO, H2) leads to the formation of Pt clusters, mobile on their support.This work highlights the possible limitations in the stabilization and implementation of SACs for catalytic reactions involving reducing conditions

Ultra-cold dilute gases of neutral atoms are attractive candidates for creating controlled mesoscopic quantum systems. In particular, quantum degenerate gases of bosonic and fermionic atoms can be used to model the correlated many-body behaviour of Bose and Fermi condensed matter systems, and to study matter wave interference and coherence. This thesis describes the experimental realization and manipulation of Bose-Einstein condensates (BECs) of 87Rb and degenerate Fermi gases (DFGs) of 40K using static and dynamic magnetic atom chip traps. Atom chips are versatile modern tools used to manipulate atomic gases. The chips consist of micrometre-scale conductors supported by a planar insulating substrate, and can be used to create confining potentials for neutral atoms tens or hundreds of micrometres from the chip surface. We demonstrate for the first time that a DFG can be produced via sympathetic cooling with a BEC using a simple single-vacuum-chamber apparatus. The large 40K-87Rb collision rate afforded by the strongly confining atom chip potential permits rapid cooling of 40K to quantum degeneracy via sympathetic cooling with 87Rb. By studying 40K-87Rb cross-thermalization as a function of temperature, we observe the Ramsauer-Townsend reduction in the 40K-87Rb elastic scattering cross-section. We achieve DFG temperatures as low as T = 0.1TF , and observe Fermi pressure in the time-of-flight expansion of the gas. This thesis also describes the radio-frequency (RF) manipulation of trapped atoms to create dressed state double-well potentials for BEC and DFG.We demonstrate for the first time that RF-dressed potentials are species-selective, permitting the formation of simultaneous 87Rb double-well and 40K single-well potentials using a 40K-87Rb mixture. We also develop tools to measure fluctuations of the relative atom number and relative phase of a dynamically split 87Rb BEC. In particular, we observe atom number fluctuations at the shot-noise level using time-of-flight absorption imaging. These measurement tools lay the foundation for future investigations of number squeezing and matter wave coherence in BEC and DFG systems.

Ultra-cold dilute gases of neutral atoms are attractive candidates for creating controlled mesoscopic quantum systems. In particular, quantum degenerate gases of bosonic and fermionic atoms can be used to model the correlated many-body behaviour of Bose and Fermi condensed matter systems, and to study matter wave interference and coherence. This thesis describes the experimental realization and manipulation of Bose-Einstein condensates (BECs) of 87Rb and degenerate Fermi gases (DFGs) of 40K using static and dynamic magnetic atom chip traps. Atom chips are versatile modern tools used to manipulate atomic gases. The chips consist of micrometre-scale conductors supported by a planar insulating substrate, and can be used to create confining potentials for neutral atoms tens or hundreds of micrometres from the chip surface. We demonstrate for the first time that a DFG can be produced via sympathetic cooling with a BEC using a simple single-vacuum-chamber apparatus. The large 40K-87Rb collision rate afforded by the strongly confining atom chip potential permits rapid cooling of 40K to quantum degeneracy via sympathetic cooling with 87Rb. By studying 40K-87Rb cross-thermalization as a function of temperature, we observe the Ramsauer-Townsend reduction in the 40K-87Rb elastic scattering cross-section. We achieve DFG temperatures as low as T = 0.1TF , and observe Fermi pressure in the time-of-flight expansion of the gas. This thesis also describes the radio-frequency (RF) manipulation of trapped atoms to create dressed state double-well potentials for BEC and DFG.We demonstrate for the first time that RF-dressed potentials are species-selective, permitting the formation of simultaneous 87Rb double-well and 40K single-well potentials using a 40K-87Rb mixture. We also develop tools to measure fluctuations of the relative atom number and relative phase of a dynamically split 87Rb BEC. In particular, we observe atom number fluctuations at the shot-noise level using time-of-flight absorption imaging. These measurement tools lay the foundation for future investigations of number squeezing and matter wave coherence in BEC and DFG systems.