To understand the function of macromolecules like proteins it helps to know the structure of the molecule. Coherent diffraction imaging is an emerging method that might be used to figure out the structures of macromolecules. In this method diffraction patterns of the macromolecule are recorded by shining light on the molecule from many unknown orientations and detecting the pattern of the diffracted photons. By assembling the diffraction patterns in a specific way and finding the phase of the photons that gave rise to the diffraction patterns, it is theoretically possible to obtain the electronstructure of the molecule and thus the molecular structure. The assembling of several thousand diffraction patterns representing unknown orientations of the molecule is hard to do by hand, but there are several methods that can be used. The EMC (Expand-Maximize-Compress) algorithm is one of those methods. It is an iterative algorithm that tries to create a model describing the Fourier Transform of the electron density of the molecule by maximizing each diffraction patterns fit to the model. This work examines how sensitive the EMC algorithm is to datasets with few diffraction patterns or a low intensity of the light being diffracted by the molecule, for the proteins phytochrome and lysozyme. The result of the work could be used to make sure enough data in collected in real experiments. Diffraction patterns simulated with the program Condor is used in this work, instead of diffraction patterns from real experiments.EMC finds the correct model when the data set contains about 1/3 fewer photons for the smaller more symmetrical molecule lysozyme than it does for phytochrome. This might be because the shapes in lysozymes diffraction patterns are larger than in phyochrome’s patterns. For phytochrome the EMC algorithm assembled the diffraction patterns correctly, with fewest photons for the light intensity 0.764 J/μm2 and 1250 diffraction patterns. For lysozyme it was with an intensity 1.910 J/μm2 and 1425 diffraction patterns. More investigation of the data is needed to understand what factors that affect the EMC algorithms ability to assemble the diffraction patterns correctly. / För att förstå makromolekylers kemiska eller biologiska funktion so underlättar det om man känner till molekylens kemiska struktur. Med den nya tekniken “coherent diffraction imaging” ska det vara möjligt att lista ut makromolekylers struktur. I denna teknik detekterar man diffraktionsmönster av molekylen genom att belysa molekylen med ljus från många olika okända vinklar and registrera mönstret som skapas av det diffrakterade ljuset. Genom att sätta ihop alla dessa diffraktionsmönster på rätt sätt och sen återskapa fasen för ljuset i diffraktionsmönstret så kan man generera molekylens elektronstruktur och från elektronstrukturen kan man få tag i molekylens struktur. Att sätta ihop tio tusentals diffraktionsmönster med okända vinklar på rätt sätt är väldigt svårt att göra, men det finns flera olika metoder som kan användas. EMC (Expand-Maximize-Compress) är en sådan metod. EMC är en iterativ algoritm som skapar en modell av (Fourier transformen av) molekylens elektronstruktur genom att maximera hur bra diffraktionsmönstren passar med modellen. Detta arbete utreder hur bra EMC algoritmen är på att hitta rätt (Fourier transform av) elektronstruktur när väldigt få diffraktionsmönster används eller när intensiteten på ljuset som sprids av molekylen är lågt. Programmet Condor används för att generera teoretiska diffraktionsmönster för de 2 molekylerna lysozym och fytokrom. EMC används sedan med olika uppsättningar av intensitet och antal diffraktionsmönster för att skapa en modell av elektronstrukturen. EMC behövde ca 1/3 färre antal fotoner i sin modell för att hittar den rätta modellen av elektronstrukturen för den lilla symmetriskt formade molekylen lysozym än för fytokrom. Att det är lättare för EMC algoritmen att hitta den korrekta modellen för lysozym än fytokrom kan bero på att lysozyms diffraktionsmönster har större former/features eller på lysozyms storlek och form. EMC körningen som behövde minst antal fotoner för att hitta den korrekta elektronstrukturen för fytokrom hade intensiteten 0,764 J/μm2 på det inkommande ljuset och behövde 1250 diffraktionsmönster. För lysozym behövdes det 1,910 J/μm2 och 1425 diffraktionsmönster för att EMC algoritmen skulle hitta rätt modell av elektronstrukturen.

Advances in experimental physics, specifically light sources emitting at an attosecond time scale, has enabled the time resolution of atomic processes like photoionization. Recent developments have allowed these sources to produce light with non-linear polarization. There exists various theoretical methods that can simulate experimental set-ups that make use of these attosecond sources. The aim of this thesis project was to extend two of these methods to be able to simulate circularly polarized light in order to both better model experimental results and come up with new potentially interesting experiments. This has resulted in an extended version of the Random Phase Approximation with Exchange method capable of simulating an ionization process by light of arbitrary polarization, as well as well as an extended version of the NewStock package that is capable of time-resolved simulation of matter interactions with arbitrary light pulses.

I have investigated two different systems CO/Fe(100) and CO/Ru(0001), toobtain new information on the binding and desorption processes. The twodifferent systems have served as a model system, one for a static examination,CO on iron, and for the dynamic case, CO on ruthenium. To perform theseinvestigations, several types of techniques have been used such as, X-rayabsorption spectroscopy, X-ray emission spectroscopy, and femtosecond laserinduced desorption techniques such as two-pulse correlation. For the CO/Fe(100) system, we found that the on-top CO “<img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?%5Calpha" />1 phase” canbe described by the Blyholder-Nilsson-Pettersson model. The pre-dissociativephase of CO bound at hollow sites, “<img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?%5Calpha" />3 phase”, can be described in a Dewar-Chatt-Duncanson like picture. For the CO/Ru(0001) system, it was found that all our data could be fitted from an empirical friction heat bath model. Moreover, it turned out, thatthere is a strong frictional coupling to the substrate electrons and phonons.

Målet med det här projektet var att undersöka huruvida en XRF signalkan förbättras genom att filtrera denna genom en tunn skiva avantingen aluminium, bly eller molybden. För att undersöka dettaanvändes programmet MCNP6.2 för att simulera strålningsspektrat fråntvå olika strålkällor; ett röntgenrör av Wolfram som kan genererafotoner med energier så höga som 120keV, och ett radioaktivt Co-57preparat. Projektet visade på att detta är möjligt, och även attaluminium är att föredra i de flesta fall då det förbättrar XRFsignalenavsevärt, utan att behöva vara varken väldigt tjockt, elleroapplicerbart tunt. Utöver detta är aluminium även billigare samtlättare än de båda andra materialen. Även molybden kunde filtrerastrålningen på ett användbart vis när en Co-57 källa används. Dockbehövde filtret vara extremt tunt, därför rekommenderas ej molybden.Projektets slutsats var att ett 0,3 mm tjockt aluminiumfilterförbättrar signalen som mest när röntgenröret användes som källa,medans ett 0,8 mm tjockt aluminiumfilter fungerar bäst för Co-57 källan.

The ALPHA experiment at CERN is an ongoing project which tests fundamental symmetries between matter and antimatter by producing and trapping antihydrogen atoms in order to perform precision spectroscopic measurements. A logical next step is to form the antihydrogen molecular ion (consisting of one positron and two antiprotons). This system possesses net charge, and can therefore be trapped electrostatically, making repeated measurements possible. Moreover it has been suggested that the molecule has the potential to allow for higher-precision comparisons with ordinary matter than have been attained with the atom. Since both momentum and energy have to be conserved in a collision, a simple collision process between an antihydrogen atom (“Hbar”) and an antiproton (“pbar”) does not suffice in order to form the molecular ion. However it is possible, upon mixing of the two species, for a pbar colliding with an Hbar in the ground electronic state to form a metastable molecular state (i.e., a resonance) which is weakly coupled to a stable molecular state (i.e., a bound state) via spontaneous quadrupole transition. During the time a metastable ion exists, a second pbar can happen to undergo a Coulomb collision with the metastable molecular ion. The quadrupole electrostatic interaction with this secondary antiproton acts as a time-dependent perturbation on the molecular system which can strengthen the coupling between resonance and bound state. Hence a collision with a secondary pbar can induce a transition to a bound state whereby the excess energy is carried off by the secondary pbar. This work aims to determine the efficiency of the process just described. On the theoretical side, the following is done: a study is conducted on the topic of resonance scattering as it relates to the problem in consideration; building on this study a generalized time-dependent perturbation theory is constructed which is valid for transitions to and from resonant states as well as bound states. On the numerical side: the effective potential for pbar-Hbar scattering in the ground electronic state is obtained numerically within the adiabatic approximation; the energies and lifetimes of the resonant states of the molecular ion are estimated; a temperature-dependent rate coefficient is obtained for the process described which, in order to obtain a proper rate, needs to be multiplied by the square of the density of the antiproton plasma and by the number of antihydrogen atoms. It is concluded that at current capacity for trapping and storage of pbar and Hbar the process examined is not competitive with respect to other formation routes which have been proposed for the molecular ion.

In dieser Arbeit werden elektronische und strukturelle Dynamiken durch Femtosekundenpuls injizierte kleine Polaronen in Lithiumniobat betrachtet, sowie die Auswirkungen auf die nichtlineare Optik mit Schwerpunkt auf die Holographie und den mittleren infraroten Spektralbereich untersucht.

One way of realizing a quantum computer is to use an ion trap. The research group Trapped Ion Quantum Technologies at Stockholm university were operating an ion trap with strontium ions. To increase the coherence time they installed a magnetic field shielding. Therefore the experimental setup had to be partially rebuilt. A new 405 nm laser was installed in order to speed up the ionization step of neutral strontium atoms. The characterization of the laser was performed and it showed that the laser could be operated at the required wavelength. The wavelength was characterized with respect to temperature and power. A scan of the 422 nm Doppler cooling laser was also performed and it showed that the Doppler cooling worked as intended. Lastly, Rabi oscillations were performed to see if coherent manipulation of the ion's quantum state worked as intended. This experiment was also successful but it showed some differences between having the magnetic shielding door open or closed which should be investigated further.

Diese Arbeit befasst sich mit der Herstellung und Charakterisierung von lichtemittierenden Tunnelkontakten. Eine an diese Kontakte angelegte Spannung bewirkt einen Tunnelstrom. Die tunnelnden Elektronen regen wiederum Oberflächenplasmonen an, welche durch Streuung als Licht ins Fernfeld abgestrahlt werden. Oberflächenplasmonen sind Oszillationen der Elektronendichte an Metalloberflächen. Sie werden durch eine elektromagnetische Welle, welche an die Oberfläche gebunden ist und sich an der Grenzfläche entlang ausbreiten kann, beschrieben. Die Anregung dieser Oberflächenwellen wird in Experimenten meist durch Lichtquellen wie Lasern realisiert. Es ist jedoch auch möglich, Oberflächenplasmonen durch geladene Teilchen zu erzeugen. Diese Arbeit setzt sich mit dem Anregen von Oberflächenplasmonen durch inelastisches Elektronentunneln auseinander. Es werden hierfür Metall-Isolator-Metall- (MIM) und Metall-Isolator-Halbleiter-Tunnelkontakte (MIS) hergestellt und charakterisiert. Ein angeregtes Oberflächenplasmon kann durch Streuung als Photon abgestrahlt werden. Dieses Licht wird im Rahmen dieser Arbeit genutzt, um die ablaufenden Prozesse zu analysieren. In den Untersuchungen gelang es, die Tunnelkontakte so herzustellen, dass sich ein fester Tunnelstrom einstellt. Durch Optimierung der Präparation und Materialwahl wurde weiterhin eine zeitlich stabile Lichtemission erzielt. Mittels der Kombination von Siliciumwafern mit monokristallinen Goldplättchen, konnten die Stabilität und die optischen Eigenschaften des emittierten Lichts optimiert werden. Darüber hinaus wurde ein hoher Polarisationsgrad erreicht, der mit amorphen Goldelektroden nicht möglich war. Die atomar flachen Goldplättchen führen weiterhin zur Unterdrückung von ungewünschter Plasmonenstreuung, welche auf Oberflächenrauheit zurückzuführen ist. Ebenso konnte gezeigt werden, dass in einer strukturierten Metallelektrode lokalisierte Oberflächenplasmonen angeregt werden. Hierdurch verändern sich charakteristische spektrale Eigenschaften des abgestrahlten Lichts. Die gewonnenen Erkenntnisse können dafür genutzt werden, extrem kleine Plasmonenquellen zu realisieren, welche sich direkt mit anderen plasmonischen Bauelementen, wie Wellenleitern, auf Chip-Niveau kombinieren lassen. Ebenso stellen die lichtemittierenden Tunnelkontakte robuste und schnelle elektro-optische Koppler dar.:Zusammenfassung 7 Abstract 8 Abkürzungen 9 1 Einleitung 11 2 Theorie 15 2.1 Elektrische Eigenschaften von Tunnelkontakten 15 2.2 Optische Eigenschaften von Tunnelkontakten 21 2.2.1 Elektrodynamische Beschreibung und Dispersionsrelation von Oberflächenplasmonen 21 2.2.2 Plasmonenanregung 24 2.2.3 Feldverteilung und Dispersionsrelation in Tunnelkontakten 25 3 Experimentelle Methoden 31 3.1 Probenherstellung 31 3.1.1 Präparation der Substrate 31 3.1.2 Monokristalline Goldflakes 32 3.1.3 Beschichtung 35 3.1.4 Photolithographie 38 3.1.5 Interferenzlithographie 40 3.1.6 Focussed Ion Beam Milling 45 3.2 Elektrische Charakterisierung 47 3.3 Optische Charakterisierung 48 3.3.1 Invertiertes optisches Mikroskop: Axiovert 200 48 3.3.2 Abbildung von Bildebene und Brennebene 50 3.3.3 Spektroskopie 51 3.3.4 Spektraler Messbereich und Transferfunktion 52 4 Al-Al2O3-Au Tunnelkontakte 57 4.1 Aufbau 57 4.2 Elektrische Eigenschaften 58 4.2.1 Stabilität und Schaltbarkeit 62 4.3 Optische Eigenschaften 65 4.3.1 Spektrale Eigenschaften 67 4.3.2 Emissionszentren 71 4.4 Morphologische Veränderungen 73 4.5 Zusammenfassung 76 5 Si-SiO2-Au Tunnelkontakte 79 5.1 Aufbau 79 5.2 Elektrische Eigenschaften 80 5.2.1 Ohmscher Kontakt zu Silicium 81 5.2.2 Einfluss der Dotierung 83 5.2.3 Einfluss des Isolatormaterials 85 5.2.4 Stabilität 86 5.3 Optische Eigenschaften 89 5.3.1 Spektrale Eigenschaften 90 5.3.2 Abstrahlcharakteristik und -mechanismus 92 5.3.3 Emission unterhalb des Quantenlimits 95 5.3.4 Emissionszentren 97 5.3.5 Stabilität der Emission 103 5.3.6 Strukturierte Tunnelkontakte 104 5.4 Zusammenfassung 114 6 Monokristalline Goldflakes 117 6.1 Besonderheiten der Goldflakes 117 6.2 Aufbau 120 6.3 Optische Eigenschaften 122 6.3.1 Spektrale Eigenschaften 125 6.3.2 Vergleich zu Si-SiO2-Au Tunnelkontakten 126 6.4 Tunnelkontakte mit strukturierten Flakes 128 6.5 Zusammenfassung 133 7 Zusammenfassung und Ausblick 135 Literatur 145 / This thesis deals with the fabrication and characterization of light emitting tunnel junctions. A voltage applied to these structures causes a tunneling current. The tunneling electrons in turn excite surface plasmons, which are scattered into photons that are emitted into the far field. Surface plasmon resonances are the collective oscillation of the electron density at a metal interface. Associated with them is an electromagnetic wave which is bound to the interface and can propagate along it. The excitation of these surface waves in experiments is often achieved by lightsources like lasers. It is, however, also possible to generate surface plasmons by charged particles. This work deals with the excitation of surface plasmons by inelastic electron tunneling. To investigate this, metal-insulator-metal (MIM) and metal-insulator-semiconductor (MIS) tunnel junctions are produced and characterized. The excited surface plasmons can be scattered and emitted as photons. This light is used to study the underlying processes. It was possible to produce the tunnel junctions in such a way that a stable tunnel current is achieved. By optimizing the preparation and choice of materials, a continous light emission without fluctuations was achieved. By combining silicon wafers with monocrystalline gold platelets, the stability and optical properties of the emitted light was optimized. Moreover, a high degree of polarization was achieved, which was not possible with amorphous gold electrodes. The atomically flat gold platelets further lead to the suppression of unwanted plasmon scattering, which is caused by surface roughness. It has also been shown that localized surface plasmons are excited in a structured metal electrode, which changes characteristic spectral properties of the emitted light. The knowledge gained can be used to realize extremely small plasmon sources, which can be combined directly with other plasmonic components, such as waveguides, on the chip level. Likewise, the light-emitting tunnel junctions are robust and fast electro-optical couplers.:Zusammenfassung 7 Abstract 8 Abkürzungen 9 1 Einleitung 11 2 Theorie 15 2.1 Elektrische Eigenschaften von Tunnelkontakten 15 2.2 Optische Eigenschaften von Tunnelkontakten 21 2.2.1 Elektrodynamische Beschreibung und Dispersionsrelation von Oberflächenplasmonen 21 2.2.2 Plasmonenanregung 24 2.2.3 Feldverteilung und Dispersionsrelation in Tunnelkontakten 25 3 Experimentelle Methoden 31 3.1 Probenherstellung 31 3.1.1 Präparation der Substrate 31 3.1.2 Monokristalline Goldflakes 32 3.1.3 Beschichtung 35 3.1.4 Photolithographie 38 3.1.5 Interferenzlithographie 40 3.1.6 Focussed Ion Beam Milling 45 3.2 Elektrische Charakterisierung 47 3.3 Optische Charakterisierung 48 3.3.1 Invertiertes optisches Mikroskop: Axiovert 200 48 3.3.2 Abbildung von Bildebene und Brennebene 50 3.3.3 Spektroskopie 51 3.3.4 Spektraler Messbereich und Transferfunktion 52 4 Al-Al2O3-Au Tunnelkontakte 57 4.1 Aufbau 57 4.2 Elektrische Eigenschaften 58 4.2.1 Stabilität und Schaltbarkeit 62 4.3 Optische Eigenschaften 65 4.3.1 Spektrale Eigenschaften 67 4.3.2 Emissionszentren 71 4.4 Morphologische Veränderungen 73 4.5 Zusammenfassung 76 5 Si-SiO2-Au Tunnelkontakte 79 5.1 Aufbau 79 5.2 Elektrische Eigenschaften 80 5.2.1 Ohmscher Kontakt zu Silicium 81 5.2.2 Einfluss der Dotierung 83 5.2.3 Einfluss des Isolatormaterials 85 5.2.4 Stabilität 86 5.3 Optische Eigenschaften 89 5.3.1 Spektrale Eigenschaften 90 5.3.2 Abstrahlcharakteristik und -mechanismus 92 5.3.3 Emission unterhalb des Quantenlimits 95 5.3.4 Emissionszentren 97 5.3.5 Stabilität der Emission 103 5.3.6 Strukturierte Tunnelkontakte 104 5.4 Zusammenfassung 114 6 Monokristalline Goldflakes 117 6.1 Besonderheiten der Goldflakes 117 6.2 Aufbau 120 6.3 Optische Eigenschaften 122 6.3.1 Spektrale Eigenschaften 125 6.3.2 Vergleich zu Si-SiO2-Au Tunnelkontakten 126 6.4 Tunnelkontakte mit strukturierten Flakes 128 6.5 Zusammenfassung 133 7 Zusammenfassung und Ausblick 135 Literatur 145

According to Bröstcancer förbundet, mammography is not efficient at detecting tumors in dense breast tissue or diagnosing breast cancer at its early stages. Ultrasound-optical tomography (UOT) is an imaging technique in development and has the potential for deep-tissue imaging. If ultrasound-optical tomography were implemented, it would be easier to differentiate between malignant, benign, and healthy tissue from any type of breast tissue. UOT is an imaging technique that takes advantage of high penetration depth and high spatial resolution of ultrasound imaging and optical imaging. In UOT, a laser light and an ultrasound pulse propagate through the tissue simultaneously at a frequency f$_L$ and f$_{US}$, respectively. The light will scatter while it propagates through the tissue and some of this scattered light will become frequency shifted by ultrasound pulse due to the acousto-optic effect. The tagged light will have the frequency $f_T = f_L + f_{US}$. The tagged (frequency shifted) light can be separated from the untagged light (unshifted light) using a thulium-doped lithium niobate, Tm$^{3+}$:$~$LiNbO$_3$, crystal as a filter. The crystal is kept at a temperature close to zero kelvin because then it exhibits unique characteristics, e.g. it has a narrow linewidth and long-lived hyperfine levels at this temperature. The filter is created by a method known as spectral hole burning (SHB). A laser beam is used to transfer electrons from the ground state to the excited state to create a hole at a specific wavelength. The spectral hole is created at the frequency of the tagged light and hence a narrow bandpass filter is constructed inside the crystal. The tagged light is fully transmitted through the filter while it highly attenuates untagged light. The tagged light is detected with a photodiode and processed in MATLAB after it has been transferred to an oscilloscope. This thesis aims to model and design a phantom probe that minimizes vibration and other unwanted movements or disturbances during measurements. The automated phantom holder will be used for the recording of 3D images. Another task of the thesis was to obtain the absorption spectrum of a 0.005$\%$ Tm$^{3+}$:$~$LiNbO$_3$ crystal when it is cooled down to 3$~$K to ensure that the crystal has the same absorption characteristics as predicted in literature. The absorption line at $\sim$ 800$~$nm is of interest since oxyhemoglobin and deoxyhemoglobin have similar absorption coefficients at $\sim$ 800$~$nm. Optical absorption and scattering information will help determine if the sample contains a cancerous region. The phantom probe was modeled in Solid Works and manufactured through 3D printing. In this setup, the sample holder was chosen to be translated while the ultrasound transducer was stationary to generate less blurry images. The design of the probe has to accommodate two detection schemes, reflection and transmission mode. The phantom probe was automated using a linear servo actuator since it was controlled with pulse-width modulation (PWM). It used a square signal as an input that could be generated with an Arbitrary signal generator (AWG). Using a device that operates with a signal was important because it would make it easier to integrate it into the experimental setup. The whole phantom probe was constructed in a cost-efficient way and in a way that it could be easily incorporated into the experimental setup. The absorption spectrum showed that the crystal has an absorption line at $\sim$ 794.3$~$nm. This absorption spectrum was compared to an absorption spectrum taken at 8$~$K on the same crystal and captured with a different method. Both absorption spectra had the same absorption peaks at almost the same wavelengths but they also showed few discrepancies that may depend on the temperature difference and the recording method. In this thesis, the absorption spectrum data taken was captured by sweeping the wavelength. The signal was captured with a photodiode, transferred to an oscilloscope, and then processed in MATLAB. The absorption spectrum data at 8$~$K was obtained using a Fourier transform spectrometer, resulting in data with little noise and well resolved peaks. To conclude, a functional and robust phantom probe was designed and manufactured that could withstand vibration and other undesired movements. An absorption spectrum of Tm$^{3+}$:$~$LiNbO$_3$ crystal was obtained at 3$~$K and compared to absorption taken at 8$~$K and compared to literature and previous measurements under similar conditions.

Plasmonic effects in nanosized particles enhance the interaction between light and matter due to the localized surface plasmon resonance, with potential applications such as all-optical transistors and optical computers. Commonly, the dynamics of nanoparticles’ optical properties are assessed via pump-probe spectroscopy, where a plasmonic structure is exited by an initial laser, the pump. Thereafter a second, less intense laser, a probe, interacts with the now excited structure at a time delay. Through measurements of the probelight transmitted by the matter, the optical dynamics of the structure are monitored. Similar methodologies can potentially be used for other applications as well, such as all-optical switching. This study focuses on an implementation of a numerical finite element method model simulating a pump-probe experiment to predict the effects of different geometries and evaluate experimental data. The simulations are split into three parts. Initially, periodically spaced nanoparticles are excited by the pump laser. Then the model estimates the internal thermal dynamics of the excited nanoparticles and in turn, determines the change in complex permittivity. Lastly, the probe-matter interaction is modeled. To evaluate the model, a comparison with another model was performed. Furthermore, simulations of periodically spaced gold dimer nanoparticles in air were done to investigate how dimers affect transmitted light. For a probe light polarization rotated 45◦ against the axis parallel to the dimer, a change in rotation of 6◦ over 35 fs was induced by the pump, indicating a potential switching mechanism.