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Institute
We prove that the projectivized strata of differentials are not contained in pointed Brill-Noether divisors, with only a few exceptions. For a generic element in a stratum of differentials, we show that many of the associated pointed Brill-Noether loci are of expected dimension. We use our results to study the Auel-Haburcak Conjecture: We obtain new non-containments between maximal Brill-Noether loci in Mg. Our results regarding quadratic differentials imply that the quadratic strata in genus 6 are uniruled.
IHMCIF: an extension of the PDBx/mmCIF data standard for integrative structure determination methods
(2024)
IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.
The spike protein of SARS-CoV-2 is a highly flexible membrane receptor that triggers the translocation of the virus into cells by attaching to the human receptors. Like other type I membrane receptors, this protein has several extracellular domains connected by flexible hinges. The presence of these hinges results in high flexibility, which consequently results in challenges in defining the conformation of the protein. Here, We developed a new method to define the conformational space based on a few variables inspired by the robotic field’s methods to determine a robotic arm’s forward kinematics. Using newly performed atomistic molecular dynamics (MD) simulations and publicly available data, we found that the Denavit-Hartenberg (DH) parameters can reliably show the changes in the local conformation. Furthermore, the rotational and translational components of the homogenous transformation matrix constructed based on the DH parameters can identify the changes in the global conformation of the spike and also differentiate between the conformation with a similar position of the spike head, which other types of parameters, such as spherical coordinates, fail to distinguish between such conformations. Finally, the new method will be beneficial for looking at the conformational heterogeneity in all other type I membrane receptors.
Precise intensity monitoring at CRYRING@ESR: on designing a Cryogenic Current Comparator for FAIR
(2023)
In the field of today’s beam intensity diagnostic there is a significant gap in the non-interceptive, calibrated measurement of the absolute intensity of continuous (unbunched) dc beams with current amplitudes below 1 μA. At the Facility for Antiproton and Ion Research (FAIR) low-intensity DC beams will occur during slow extraction from the synchrotrons as well as for coasting beams of highly-charged or exotic nuclei in the storage rings. The lack of adequate beam instrumentation limits the experimental program as well as the accuracy of experimental results.
The Cryogenic Current Comparator (CCC) can close the diagnostic gap with a high-precision dc current reading independent of ion-species and of beam parameters. However, the established detector design based on a core with high magnetic permeability and on a radial shield geometry has well-known weaknesses concerning magnetic shielding efficiency and intrinsic current noise. To eliminate these weaknesses, a novel coreless CCC with a co-axial shield was constructed and combined with a high-performance SQUID contributed by the Leibniz-Institute of Photonic Technology (Leibniz-IPHT Jena). The new axial CCC model was compared to a radial CCC with the established design provided by the Friedrich-Schiller-University Jena. According to numerical simulations prepared at TU Darmstadt and test measurements of the detectors in the laboratory, the new design offered a significant improvement of the shielding factor – from 75dB to 207dB at the required dimensions – and eliminated all noise contributions from the core material, promising an improved current resolution. Although the lower inductance of the pickup coil reduced the coupling to the beam significantly, the noise properties of the new CCC type were comparable to the classical version with a high-permeability core. However, the expected decrease of the low-frequency noise and thus an increase of the current resolution could not be observed at this stage of development.
Consequently, the classical CCC based on the radial shielding and high-permeability core had to be installed in CRYRING@ESR to provide best possible intensity measurements for the upcoming experimental campaign. In CRYRING the CCC was operated with beam currents between 1nA and 20μA and with different ion species (H, Ne, O, Pb, U). It was shown that the CCC provides a noise-limited current resolution of better than 3.2 nArms at a bandwidth of 200 kHz as well as a noise level below 40 pA/√Hz above 1 kHz. During the operation, the main noise sources of the accelerator environment had to be identified and suitable mitigation strategies were developed. Temperature and pressure fluctuations were suppressed with a newly-designed cryogenic support system based on a 70 l helium bath cryostat, developed and built in collaboration with the Institut für Luft- und Kältetechnik Dresden, in combination with a helium re-liquefier. The cryogenic operating time was restricted to around 7 days, which must be expanded significantly in the future. Digital filters were developed to remove the perturbations of the helium liquefier and of the neighboring dipole magnets. Given the promising results the CCC system can be considered as a prototype for future CCCs at FAIR.
Investigation of the kinematics involved in compton scattering and hard X-ray photoabsorption
(2023)
The present work investigates the kinematics of Compton scattering at gaseous, internally-cool helium and molecular nitrogen targets in the high- and the low-energy regime. Additionally, photoionization at molecular nitrogen with high-energy photons is investigated. These exeprimental regimes were previously inaccessible due to the extremely small cross sections involved. Nowadays, the third- and fourth-generation synchrotron machines produce sufficient photon flux, enabling the investiagtion of the above processes. The utilized cold-target recoil-ion momentum spectroscopy (COLTRIMS) technique further increases the detection efficiency of the observed processes, since it enables full-solid-angle detection by exploiting momentum conservation.
Compton scattering is investigated at both high (helium and N2) and low (helium) photon energies. In the high-energy regime, the impulse approximation is mostly valid, which is not the case for the low-energy regime. The impulse approximation assumes that the Compton-scattering process takes place at a free electron with a momentum distribution as if it was bound, thus ignoring the binding energy of the system. In the low-energy regime, the impulse approximation is not valid.
Photoionization is investigated at high photon energies, where the linear momentum of the photon cannot be neglected, as is the fashion of the commonly used dipole approximation.
Terahertz (THz) radiation lies between the micro and far-infrared range in the electromagnetic spectrum. Compared with microwave and millimeter waves, it has a larger signal bandwidth and extremely narrow antenna beam. Thus, it is easier to achieve high-resolution for imaging and detection applications. The unique properties, such as penetration for majority non-polar materials, non-ionizing characteristic and the spectral fingerprint of materials, makes THz imaging an appealing artifice in the military, biomedical, astronomical communications, and other areas. However, THz radiation’s current low power level and detection sensitivity block THz imaging system from including fewer optical elements than the visible or infrared range. This leads to imaging resolution, contrast, and imaging field of view degenerate and makes the aberration more serious. THz imaging based on the space Fourier spectrum detection is developed in this thesis to achieve high-quality imaging. The main concept of Fourier imaging is by recording the field distribution in the Fourier plane (focal plane) of the imaging system; the information of the target is obtained. The numerical processing method is needed to extract the amplitude and phase information of the imaged target. With additional process, three-dimensional (3D) information can be obtained based on the phase information. The novel recording and reconstructing ways of the Fourier imaging system enables it to have a higher resolution, better contrast, and broader field of view than conventional imaging systems such as microscopy and plane to plane telescopic imaging system.
The work presented in this thesis consists of two imaging systems, one is working at 300 GHz based on the fundamental heterodyne detection of the THz radiation, the other is operated at 600 GHz by utilizing the sub harmonic heterodyne detection technique. The realization and test of the heterodyne detection are based on the THz antenna-coupled field-effect transistor (TeraFET) detector developed by Dr. Alvydas Lisauskas. Both systems use two synchronized electronic multiplier chains to radiate the THz waves. One radiation works as the local oscillator (LO), the other works as illumination with a slight frequency shift, the radiations are mixed on the detector scanning in the Fourier plane to record the complex Fourier spectrum of the imaged target. The LO has the same frequency range as the illuminating radiation for fundamental heterodyne detection but half the frequency range for the sub-harmonic heterodyne detection. The 2-mm resolution, 60-dB contrast, and 5.5-cm diameter imaging area at 300 GHz and the of 500-μm resolution, 40-dB contrast, and 3.5-cm diameter imaging area at 600 GHz are achieved (the 300-GHz illuminating radiation has the approximate power of 600 μW , the 600-GHz illuminating radiation has the approximate power of 60 μW ).
The thesis consists of 6 parts. After the introduction, the second chapter expands on the topic of Fourier optics from a theoretical point of view and the simulations of the Fourier imaging system. First, the theory of the electromagnetic field propagation in free space and through an optical system are investigated to elicit the Fourier transform function of the imaging system. The simulation is used for theoretical considerations and the implementation of a Fourier optic script that allows for numerical investigations on reconstruction. The preliminary imaging field of view and resolution are also demonstrated. The third chapter describes the Fourier imaging system at 300 GHz based on the fundamental heterodyne detection, including the experimental setup, the 2D, and 3D imaging results. The following fourth chapter reports the integration of the TeraFET detector with two substrate lenses (one is a Si lens on the back-side Si substrate, the other is a wax/PTFE lens on the front side containing the bonding wires) for sub-harmonic heterodyne detection at 600 GHz. The characteristic of the wax/PTFE lens at THz range is presented. After that, the compared imaging results between the detector with and without the wax/PTFE lens are shown. The fifth chapter extends the demonstration on the lateral and depth resolution of the Fourier imaging system in detail and uses the experimental results at 600 GHz to validate the analytical predictions. The comparison of the resolution between the Fourier imaging system and the conventional microscopy system proves that the Fourier imaging system has better imaging quality under the same system configuration. The last chapter in this thesis concludes on the findings of the THz Fourier imaging and gives an outlook for the enhancement of the Fourier imaging system at THz range.