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To gain a better understanding of complex mechanisms in biological systems, simultaneous control over multiple processes is key. To this purpose selective photouncaging has been developed. Photo-uncaging is an experimental scheme in which a molecule of interest has been inactivated synthetically and is activated by light. Usually a bond is cleaved and a leaving group is set free. The molecule which inactivates the molecule of interest and sets the leaving group free is called (photo-)cage. In a selective photo-uncaging scheme a number of leaving groups can be released independently, usually by irradiation with light of different wavelengths. This approach is, however, seriously limited in its applicability due to the properties of the involved cages and irradiation schemes. A major drawback is the usually quite broad UV-Vis absorption of the cages. This makes a selective activation by light difficult and limits the maximal number of independent cages severely.
Therefore, the aim of this thesis is to introduce the Vibrationally Promoted Electronic Resonance (VIPER) 2D-IR pulse sequence in a alternative selective uncaging scheme.
The VIPER 2D-IR pulse sequence is a spectroscopic tool which allows to generate 2D-IR signals whose lifetime are independent of the vibrational relaxation lifetime. It has been first used to monitor chemical exchange. It consists of a narrowband infared pump pulse, a subsequent UV-Vis pump pulse and a broadband infrared probe pulse. The UV-Vis pump pulse is off-resonant with regard to the UV-Vis absorption band. Electronic excitation becomes only possible, if the infrared pump pulse modulates the UV-Vis transition of the IR-excited molecule. This modulation brings the UV-Vis transition in resonance with the UV-Vis pump pulse. Thereby, only the molecules which were pre-excited with the infrared pulse can be excited into the electronically excited state. A computational prediction of the modulation was carried out by Jan von Cosel in the Burghardt group.
The narrowband infrared pump pulse can be used to selectively excite a subensemble of molecules in a mixture into an electronically excited state even if the UV-Vis spectra of all molecules are virtually identical. For this the sub-ensemble needs to exhibit an identifiable infrared spectrum. Combined with the introduction of isotope labels, which lead to changes in the infrared absorption spectra, the larger selectivity in the infrared region can be exploited for an alternative selective uncaging approach. In VIPER uncaging the infrared pump pulse selects the species and the subsequent UV-Vis pulse provides the energy needed for electronic excitation upon which the photo cleavage can occur.
After an introduction of the principle idea of uncaging and VIPER spectroscopy, the concept of VIPER uncaging is introduced and its limits and requirements are discussed. Some examples for possible VIPER cages are reviewed.
A coumarin molecule (7-diethylamino coumarin) which can release an azide group was chosen as a first test molecule for VIPER uncaging. Its isotopomers were characterized to determine suitable spectroscopic markers for successful uncaging and to find fitting experimental conditions. The chosen coumarin cage has an UV-Vis absorption band at approximately 380 nm and a steep flank on the high wavelength side of the band. The quantum yield for the azide compound is between 10-20 % depending on the solvent’s water content. The release was found to be on a picosecond timescale which is among the fastest known photo reactions, but the photo reaction mechanism has proven to be not straightforward. For the VIPER experiment on the mixture two isotopomers were chosen with a 13C atom at different positions. In one species a ring mode of the coumarin is changed by the 13C atom. In the other isotopomer the carbonyl stretching mode is influenced. The change in the ring mode region allows to select one species or the other with the infrared pre-excitation. Because of experimental difficulties only isotopomers with the same leaving group could be used. The successful selective electronic excitation of the individual isotopomers in a mixture was monitored by probing the carbonyl region.
As a second VIPER cage, para-hydroxyphenacyl (pHP) was chosen. A thiocyanate group was selected as leaving group. pHP cages have their electronic transition in the UV, with a maximum absorption at 290 nm. The shape of the spectrum is suitable and the quantum yield is very high, with values in the literature of up to 90 %. Also the photo reaction is well studied and the expected byproducts are well characterized. The chosen isotopologues were characterized spectroscopically. The resulting data on the photo reaction were in agreement with the mechanism proposed in the literature. The mixture for the VIPER experiment consisted of two isotopologues, where for one species all the C atoms in the ring were labelled and for the other the C-atom in the thiocyanate leaving group was labelled. Here the release of the different leaving groups, labelled and unlabelled thiocyanate, could be monitored selectively. This shows that it is possible to selectively release a molecule in a mixture of caged molecules by applying the VIPER pulse sequence.
The samples were synthesized by Matiss Reinfelds from the Heckel group and the VIPER experiments were done together with Carsten Neumann and with support
of the Bredenbeck group.
The leaving groups were chosen because of their infrared absorption which allowed to directly monitor the successful cleavage by spectroscopy. This was needed for the proof-of-concept experiment and to allow direct optimization of the experimental parameters but is not necessarily a requirement for VIPER uncaging.
Concerning the selectivity of the VIPER uncaging, the approach is at the moment mainly limited by the infrared pulse energy. The selective VIPER excitation is competing with unselective excitation directly by just the UV-Vis pulse. A more intense infrared pump pulse would increase only the selective VIPER excitation and thereby improve the contrast to the unspecific background.
To address this issue, the first steps towards an alternative infrared light generation are undertaken. In this alternative approach the infrared light for preexcitation is directly generated by difference frequency generation of the laser output, i.e. the high energy 800 nm fundamental, and the output of a non-collinear optical parametric amplifier (NOPA). To achieve a narrowband pump pulse the pulses are chirped before mixing. In the scope of this thesis a NOPA has been installed and the mixing has been tested with available test crystal medium. While infrared wavelength region and power were not in the aspired range with this alternative crystal the feasibility of mixing between a NOPA output and the fundamental could be shown.
Other possibilities to increase the contrast to the unspecific background excitation by the UV-Vis pump pulse are discussed. For most applications of selective VIPER uncaging the detection by fs-laser spectroscopy will not be needed and could be replaced by other methods e.g. chromatography. This will allow the experimental parameters of the VIPER pulse sequence to be changed in a way which reduces unspecific excitation i.e. reducing the UV-Vis-pump energy and result in much better contrast.
In conclusion, the experimental data in this thesis shows the VIPER pulse sequence to be applicable to selective uncaging schemes and indicates measures to arrive at the specificity necessary for uncaging applications. This thesis was focused on uncaging photo reactions with isotopomers and isotopologues, but other types of photo reactions could in principle be controlled in the same way. It should be possible to address different isomers in mixtures or different ground states of proteins selectively. The discussed experiments are a significant step towards control over photo reactions in mixtures.
Der Urknall vor ungefähr 13.8 Milliarden Jahren markiert die Entstehung des Universums. Die gesamte Energie und Materie war in einem Punkt konzentriert und expandiert seitdem kontinuierlich. Wenige Sekundenbruchteile nach dem Urknall war die Temperatur und Dichte dieser Materie extrem hoch und die erschaffenen Elementarteilchen, speziell Quarks und Gluonen, durchliefen einen Zustand den man als Quark-Gluon-Plasma (QGP) bezeichnet und innerhalb dessen die starke Wechselwirkung dominiert. Innerhalb dieses Plasmas können Quarks und Gluonen, welche sonst in Hadronen gebunden sind, sich frei bewegen. Die direkte Beobachtung des frühzeitlichen QGPs ist mit heutigen Mitteln nicht möglich. Allerdings ist es möglich die Dynamik und Kinematik innerhalb eines künstlich erzeugten QGPs zu erforschen und damit Rückschlüsse auf die Vorgänge während des Urknalls zu machen.
Um künstliche QGPs unter kontrollierten Bedingungen zu erzeugen, werden heutzutage ultrarelativistische Schwerionen zur Kollision gebracht. Der stärkste je gebaute Schwerionenbeschleuniger LHC befindet sich am Kernforschungzentrum CERN in der Nähe von Genf. Das ALICE Experiment, als eines der vier großen Experimente am LHC, wurde speziell gebaut um das QGP näher zu untersuchen. Vollständig ionisierte Bleikerne werden mit nahezu Lichtgeschwindigkeit in den Experimenten zur Kollision gebracht. Die deponierte Energie lässt die Temperatur der Quarks und Gluonen innerhalb der kollidierenden Nukleonen ansteigen bis eine kritische Temperatur überschritten wird und ein Phasenübergang in das QGP erfolgt. Im Laufe der Kollision kühlt das Medium ab und gelangt unter die kritische Temperatur. Nun werden aus den ehemals freien Quarks Hadronen gebildet. Diese Hadronen oder Zerfallsprodukte dieser Hadronen können daraufhin in die Detektoren des Experiments fliegen und werden dann dort gemessen.
Es gibt mehrere mögliche Observablen des QGP, die messbar mit dem ALICE Experiment sind. Die Observablen, die in dieser Arbeit detailliert untersucht werden, sind die invariante Masse und der Paartransversalimpuls eines Dielektrons. Ein Dielektron besteht aus einem Elektron und einem Positron, welche miteinander korreliert sind. Dielektronen sind ideale Sonden zur Vermessung des QGPs. Sie werden durch verschiedene Prozesse während allen Kollisionsphasen produziert, wie beispielsweise bei den initialen, harten Stößen der kollidierenden Nukleonen oder durch den elektromagnetischen Zerfall verschiedener Hadronen wie π0 und J/ψ. Zusätzlich strahlt das QGP Dielektronen abhängig von seiner Temperatur ab. Theoretisch erlaubt dies die direkte Temperaturmessung des QGPs. Ein weiterer Vorteil der Dielektronenmessung gegenüber der Messung von Hadronen liegt darin, dass Elektronen und Positronen keine Farbladungen tragen und somit auch nicht mit der dominierenden starken Wechselwirkung innerhalb des QGPs interagieren und somit unbeeinflusst Informationen über seine Dynamik liefern können.
In dieser vorliegenden Arbeit werden Dielektronenspektren als Funktion der invarianten Masse und des Paartransversalimpulses in Blei-Blei-Kollisionen mit einer Schwerpunktsenergie von √sNN = 5.02 TeV gemessen. Das erste Mal in Schwerionenkollisionen konnte an einem der großen LHC Experimente der minimale Transversalimpuls der gemessenen Elektronen und Positronen auf peT > 0.2 GeV/c minimiert werden. Dies gibt im Vergleich zu der publizierten Messung mit peT > 0.4 GeV/c die Möglichkeit auch sogenannte weiche Prozesse zu messen, erhöht aber auch den Komplexit ätsgrad der Messung durch massiv gesteigerten Untergrund. Zusätzlich ist die Messung zentralitäsabhängig durchgeführt. Zentralität ist ein Maß für den Abstand der beiden Bleikerne zum Zeitpunkt der Kollision. Je zentraler eine Kollision, desto größer ist die deponierte Energie und desto größer und heißer ist das erzeugte QGP und die daraus resultierenden Effekte.
Die gemessenen Dielektronenverteilungen werden mit dem erwarteten Beiträgen aus hadronischen Zerfällen verglichen. Die Messung ergibt, dass der Beitrag aus semileptonischen Zerfällen von Charmquarks gemessen im Vakuum, welcher mit der Anzahl der binären Nukleon-Nukleon-Kollisionen in Blei-Blei-Ereignissen hochskaliert ist, nicht das Dielektronenspektrum beschreibt. Eine Modifizierung des Beitrag gemäß des unabhängig gemessenen nuklearen Modifikationsfaktors für einzelne Elektronen aus Charm- und Beautyquarks verbessert die Beschreibung des Dielektronenspektrums. Zusätzlich wurde der Beitrag virtueller direkter Photonen abgeschätzt. Die gemessenen Werte sind vergleichbar mit vorangegangenen Messungen bei einer niedrigeren Schwerpunktsenergie. Ebenso ist es möglich in periphären Kollisionen einen Beitrag durch eine Quelle zu vermessen, die Dielektronen bei niedrigem Transversalimpuls pT,ee < 0.15 GeV/c aussendet.
Scanning probe microscopy (SPM) has become an essential surface characterization technique in research and development. By concept, SPM performance crucially depends on the quality of the nano-probe element, in particular, the apex radius. Now, with the development of advanced SPM modes beyond morphology mapping, new challenges have emerged regarding the design, morphology, function, and reliability of nano-probes. To tackle these challenges, versatile fabrication methods for precise nano-fabrication are needed. Aside from well-established technologies for SPM nano-probe fabrication, focused electron beam-induced deposition (FEBID) has become increasingly relevant in recent years, with the demonstration of controlled 3D nanoscale deposition and tailored deposit chemistry. Moreover, FEBID is compatible with practically any given surface morphology. In this review article, we introduce the technology, with a focus on the most relevant demands (shapes, feature size, materials and functionalities, substrate demands, and scalability), discuss the opportunities and challenges, and rationalize how those can be useful for advanced SPM applications. As will be shown, FEBID is an ideal tool for fabrication/modification and rapid prototyping of SPM-tipswith the potential to scale up industrially relevant manufacturing.
Focused electron and ion beam-induced deposition (FEBID/FIBID) are direct-write techniques with particular advantages in three-dimensional (3D) fabrication of ferromagnetic or superconducting nanostructures. Recently, two novel precursors, HCo 3 Fe(CO) 12 and Nb(NMe 3 ) 2 (N-t-Bu), were introduced, resulting in fully metallic CoFe ferromagnetic alloys by FEBID and superconducting NbC by FIBID, respectively. In order to properly define the writing strategy for the fabrication of 3D structures using these precursors, their temperature-dependent average residence time on the substrate and growing deposit needs to be known. This is a prerequisite for employing the simulation-guided 3D computer aided design (CAD) approach to FEBID/FIBID, which was introduced recently. We fabricated a series of rectangular-shaped deposits by FEBID at different substrate temperatures between 5 ∘ C and 24 ∘ C using the precursors and extracted the activation energy for precursor desorption and the pre-exponential factor from the measured heights of the deposits using the continuum growth model of FEBID based on the reaction-diffusion equation for the adsorbed precursor.
Suppression of light nuclei production in collisions of small systems at the Large Hadron Collider
(2019)
We show that the recently observed suppression of the yield ratio of deuteron to proton and of helium-3 to proton in p+p collisions compared to those in p+Pb or Pb+Pb collisions by the ALICE Collaboration at the Large Hadron Collider (LHC) can be explained if light nuclei are produced from the coalescence of nucleons at the kinetic freeze-out of these collisions. This suppression is attributed to the non-negligible sizes of deuteron and helium-3 compared to the size of the nucleon emission source in collisions of small systems, which reduces the overlap of their internal wave functions with those of nucleons. The same model is also used to study the production of triton and hypertriton in heavy-ion collisions at the LHC. Compared to helium-3 in events of low charged particle multiplicity, the triton is less suppressed due to its smaller size and the hypertriton is even more suppressed as a result of its much larger size.
We study how the mass and magnetic moment of the quarks are dynamically generated in nonequilibrium quark matter. We derive the equal-time transport and constraint equations for the quark Wigner function in a magnetized quark model and solve them in the semi-classical expansion. The quark mass and magnetic moment are self-consistently coupled to the Wigner function and controlled by the kinetic equations. While the quark mass is dynamically generated at the classical level, the quark magnetic moment is a pure quantum effect, induced by the quark spin interaction with the external magnetic field.
The plasma membrane (PM) is composed of a complex lipid mixture that forms heterogeneous membrane environments. Yet, how small-scale lipid organization controls physiological events at the PM remains largely unknown. Here, we show that ORP-related Osh lipid exchange proteins are critical for the synthesis of phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2], a key regulator of dynamic events at the PM. In real-time assays, we find that unsaturated phosphatidylserine (PS) and sterols, both Osh protein ligands, synergistically stimulate phosphatidylinositol 4-phosphate 5-kinase (PIP5K) activity. Biophysical FRET analyses suggest an unconventional co-distribution of unsaturated PS and phosphatidylinositol 4-phosphate (PI4P) species in sterol-containing membrane bilayers. Moreover, using in vivo imaging approaches and molecular dynamics simulations, we show that Osh protein-mediated unsaturated PI4P and PS membrane lipid organization is sensed by the PIP5K specificity loop. Thus, ORP family members create a nanoscale membrane lipid environment that drives PIP5K activity and PI(4,5)P2 synthesis that ultimately controls global PM organization and dynamics.
HADES (High Acceptance DiElectron Spectrometer), located at GSI, is a versatile detector for precise spectroscopy of e+ e- pairs and charged hadrons produced on a fixed target in a 1 to 3.5 AGeV kinetic beam energy region. The main experimental goal is to investigate properties of dense nuclear matter created in heavy ion collisions and learn about in-medium hadron properties.
In the HADES set-up 24 Mini Drift Chambers (MDC) allow for track reconstruction and determining the particle momentum by exploiting charged particle deflection in a magnetic field. In addition, the drift chambers contribute to particle identification by measuring the energy loss. The read-out concept foresees each sensing wire to be equipped with a preamplifier, analog pulse shaper and discriminator. In the current front-end electronics, the ASD-8 ASIC comprises the above modules. Due to limitations of the current on-board time to digital converters (TDC), especially regarding higher reaction rates expected at the future FAIR facility (HADES at SIS-100), the electronics need to be replaced by new board featuring multi-hit TDCs. Whereas ASD-8 chips cannot be procured anymore, a promising replacement candidate is the PASTTREC ASIC, developed by JU Krakow, which was tested w.r.t. suitability for MDC read-out in a variety of set-ups and, where possible, in direct comparison to ASD-8.
The timing precision, being the most crucial performance parameter of the joint system of detector and read-out electronics, was assessed in two different set-ups, i.e. a cosmic muon tracking set-up and a beam test at the COSY accelerator at Juelich using a minimum ionizing proton beam.
The beam test results were reproduced and can thus be quantitatively explained in a three dimensional GARFIELD simulation of a HADES MDC drift cell. In particular, the simulation is able to describe the characteristic dependence of the time precision on the track position within the cell.
A circuit simulation (SPICE) was used to closely model the time development of a raw drift chamber pulse, measured as a response to X-rays from a 55 Fe source. The insights gained from this model were used for attributing realistic charge values to the time over threshold values measured with the read-out ASICs in a charge calibration set-up. Furthermore, a high-level circuit simulation of the PASTTREC shaper is implemented to serve as a demonstration of the effect of the individual shaping and tail cancellation stages which are present in both ASICs.
The Compressed Baryonic Matter experiment (CBM) at FAIR and the NA61/SHINE experiment at CERN SPS aim to study the area of the QCD phase diagram at high net baryon densities and moderate temperatures using heavy-ion collisions. The FAIR and SPS accelerators cover energy ranges 2-11 and 13-150 GeV per nucleon respectively in laboratory frame for heavy ions up to Au and Pb. One of the key observables to study the properties of a matter created in such collisions is an anisotropic transverse flow of particles.
In this work, the performance of the CBM experiment for anisotropic flow measurements is studied with Monte-Carlo simulations using gold ions at SIS-100 energies employing different heavy-ion event generators. Also, procedures for centrality estimation and charged hadron identification are described and corresponding frameworks are developed.
The measurement of the reaction plane angle is performed with Projectile Spectator Detector (PSD), which is a hadron calorimeter located at a very forward angle. To prevent radiation damage by the high-intensity ion beam, the PSD has a hole in the center to let the beam pass through. Various combinations of CBM detector subsystems are used to investigate the possible systematic biases in flow and centrality measurements. Effects of detector azimuthal non uniformity and the PSD beam hole size on physics performance are studied. The resulting performance of CBM for flow measurements is demonstrated for identified charged hadron anisotropic flow as a function of rapidity and transverse momentum in different centrality classes.
The measurement techniques developed for CBM were also validated with the experimental data recently collected by the NA61/SHINE experiment at CERN SPS for Pb+Pb collisions at the beam momenta 30A GeV/c. Compared to the existing data from the NA49 experiment at the CERN SPS, the new data allows for a more precise measurement of anisotropic flow harmonics. The fixed target setup of NA61/SHINE also allows extending flow measurements available from the STAR at the RHIC beam energy scan (BES) program to a wide rapidity range up to the forward region where the projectile nucleon spectators appear. In this thesis, an analysis of the anisotropic flow harmonics in Pb+Pb collisions at beam momenta 30A GeV/c collected by the NA61/SHINE experiment in the year 2016 is presented. Flow coefficients are measured relative to the spectator plane estimated with the Projectile Spectators Detector (PSD). The flow coefficients are obtained as a function of rapidity and transverse momentum in different classes of collision centrality. The results are compared with the corresponding NA49 data and the measurements from the RHIC BES program.