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Institute
The gas-phase reaction of O + H₃⁺ has two exothermic product channels: OH+ + H2 and H2O+ + H. In the present study, we analyze experimental data from a merged-beams measurement to derive thermal rate coefficients resolved by product channel for the temperature range from 10 to 1000 K. Published astrochemical models either ignore the second product channel or apply a temperature-independent branching ratio of 70% versus 30% for the formation of OH+ + H2 versus H2O+ + H, respectively, which originates from a single experimental data point measured at 295 K. Our results are consistent with this data point, but show a branching ratio that varies with temperature reaching 58% versus 42% at 10 K. We provide recommended rate coefficients for the two product channels for two cases, one where the initial fine-structure population of the O(3PJ) reactant is in its J = 2 ground state and the other one where it is in thermal equilibrium.
Electronic and magnetic properties of the RuX3 (X=Cl, Br, I) family: two siblings - and a cousin?
(2022)
Motivated by reports of metallic behavior in the recently synthesized RuI3, in contrast to the Mott-insulating nature of the actively discussed α-RuCl3, as well as RuBr3, we present a detailed comparative analysis of the electronic and magnetic properties of this family of trihalides. Using a combination of first-principles calculations and effective-model considerations, we conclude that RuI3, similarly to the other two members, is most probably on the verge of a Mott insulator, but with much smaller magnetic moments and strong magnetic frustration. We predict the ideal pristine crystal of RuI3 to have a nearly vanishing conventional nearest-neighbor Heisenberg interaction and to be a quantum spin liquid candidate of a possibly different kind than the Kitaev spin liquid. In order to understand the apparent contradiction to the reported resistivity ρ, we analyze the experimental evidence for all three compounds and propose a scenario for the observed metallicity in existing samples of RuI3. Furthermore, for the Mott insulator RuBr3, we obtain a magnetic Hamiltonian of a similar form to that in the much-discussed α-RuCl3 and show that this Hamiltonian is in agreement with experimental evidence in RuBr3.
Gasdermin-D (GSDMD) is the ultimate effector of pyroptosis, a form of programmed cell death associated with pathogen invasion and inflammation. After proteolytic cleavage by caspases, the GSDMD N-terminal domain (GSDMDNT) assembles on the inner leaflet of the plasma membrane and induces the formation of membrane pores. We use atomistic molecular dynamics simulations to study GSDMDNT monomers, oligomers, and rings in an asymmetric plasma membrane mimetic. We identify distinct interaction motifs of GSDMDNT with phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) and phosphatidylserine (PS) headgroups and describe their conformational dependence. Oligomers are stabilized by shared lipid binding sites between neighboring monomers acting akin to double-sided tape. We show that already small GSDMDNT oligomers support stable, water-filled, and ion-conducting membrane pores bounded by curled beta-sheets. In large-scale simulations, we resolve the process of pore formation from GSDMDNT arcs and lipid efflux from partial rings. We find that high-order GSDMDNT oligomers can crack under the line tension of 86 pN created by an open membrane edge to form the slit pores or closed GSDMDNT rings seen in atomic force microscopy experiments. Our simulations provide a detailed view of key steps in GSDMDNT-induced plasma membrane pore formation, including sublytic pores that explain nonselective ion flux during early pyroptosis.
During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examine structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally test candidate structural motifs and identify several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs may act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assemble co-translationally in only some but not all of the relevant biogenesis pathways. Our results highlight the regulatory complexity of assembly pathways.
The electrical and computational properties of neurons in our brains are determined by a rich repertoire of membrane-spanning ion channels and elaborate dendritic trees. However, the precise reason for this inherent complexity remains unknown. Here, we generated large stochastic populations of biophysically realistic hippocampal granule cell models comparing those with all 15 ion channels to their reduced but functional counterparts containing only 5 ion channels. Strikingly, valid parameter combinations in the full models were more frequent and more stable in the face of perturbations to channel expression levels. Scaling up the numbers of ion channels artificially in the reduced models recovered these advantages confirming the key contribution of the actual number of ion channel types. We conclude that the diversity of ion channels gives a neuron greater flexibility and robustness to achieve target excitability.
Focused ion beam induced deposition (FIBID) is a direct-write technique enabling the growth of individual nanostructures of any shape and dimension with high lateral resolution. Moreover, the fast and reliable writing of periodically arranged nanostructures can be used to fabricate devices for the investigation of collective phenomena and to design novel functional metamaterials. Here, FIBID is employed to prepare dc-Josephson junction arrays (dc-JJA) consisting of superconducting NbC dots coupled through the proximity effect via a granular metal layer. The fabrication is straightforward and allows the preparation of dc-JJA within a few seconds. Microstructure and composition of the arrays are investigated by transmission electron microscopy and energy dispersive X-ray spectroscopy. The superconductor-to-metal transition of the prepared dc-JJA is studied in a direct way, by tuning the Josephson junction resistance in 70 nm-spaced superconducting NbC dots. The observed magnetoresistance oscillations with a period determined by the flux quantum give evidence for the coherent charge transport by paired electrons. Moreover, the measured resistance minima correspond to two fundamental matching configurations of fluxons in the dc-JJA, caused by magnetic frustration. The robust properties of the prepared dc-JJA demonstrate the opportunities for a fast preparation of complex device configurations using direct-write approaches.
More than 75% of surface and secreted proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, influencing protein dynamics and interactions with other molecules. Glycan conformational freedom impairs complete structural elucidation of glycoproteins. Computer simulations may be used to model glycan structure and dynamics. However, such simulations typically require thousands of computing hours on specialized supercomputers, thus limiting routine use. Here, we describe a reductionist method that can be implemented on personal computers to graft ensembles of realistic glycan conformers onto static protein structures in a matter of minutes. Using this open-source pipeline, we reconstructed the full glycan cover of SARS-CoV-2 Spike protein (S-protein) and a human GABAA receptor. Focusing on S-protein, we show that GlycoSHIELD recapitulates key features of extended simulations of the glycosylated protein, including epitope masking, and provides new mechanistic insights on N-glycan impact on protein structural dynamics.
We experimentally investigated the quasifree mechanism (QFM) in one-photon double ionization of He and H2 at 800 eV photon energy and circular polarization with a COLTRIMS reaction microscope. Our work provides new insight into this elusive photoionization mechanism that was predicted by Miron Amusia more than four decades ago. We found the distinct four-fold symmetry in the angular emission pattern of QFM electrons from H2 double ionization that has previously only been observed for He. Furthermore, we provide experimental evidence that the photon momentum is not imparted onto the center of mass in quasifree photoionization, which is in contrast to the situation in single ionization and in double ionization mediated by the shake-off and knock-out mechanisms. This finding is substantiated by numerical results obtained by solving the system’s full-dimensional time-dependent Schrödinger equation beyond the dipole approximation.
The stellar nucleosynthesis of elements heavier than iron can primarily be attributed to neutron capture reactions in the s and r process. While the s process is considered to be well understood with regards to the stellar sites, phases and conditions where it occurs, nucleosynthesis networks still need accurate neutron capture cross sections
with low uncertainties as input parameters. Their quantitative outputs for the isotopic abundances produced in the s process, coupled with the observable solar abundances, can be used to indirectly infer the expected r process abundances. The two stable gallium isotopes, 69Ga and 71Ga, have been shown in sensitivity studies to have considerable impact on the weak s process in massive stars. The available experimental data, mostly derived from neutron activation measurements for quasi-stellar neutron spectra at kBT = 25 keV, show disagreements up to a factor of three.
Determining the differential neutron capture cross section can provide input data for the whole range of astrophysically relevant energies. To that end, a neutron time of flight experimental campaign at the n_TOF facility at CERN was performed for three months, using isotopically enriched samples of both isotopes. The data taken at the EAR1 experimental area covered a wide neutron energy range from thermal to several hundred keV. The respective differential and spectrum averaged neutron capture cross sections for 69Ga and 71Ga were determined in this thesis. They show good agreement with the evaluated cross sections for 71Ga, but reproduce the deviations from the evaluated data that other, more recent activation measurements showed for 69Ga.
Tracking influenza a virus infection in the lung from hematological data with machine learning
(2022)
The tracking of pathogen burden and host responses with minimal-invasive methods during respiratory infections is central for monitoring disease development and guiding treatment decisions. Utilizing a standardized murine model of respiratory Influenza A virus (IAV) infection, we developed and tested different supervised machine learning models to predict viral burden and immune response markers, i.e. cytokines and leukocytes in the lung, from hematological data. We performed independently in vivo infection experiments to acquire extensive data for training and testing purposes of the models. We show here that lung viral load, neutrophil counts, cytokines like IFN-γ and IL-6, and other lung infection markers can be predicted from hematological data. Furthermore, feature analysis of the models shows that blood granulocytes and platelets play a crucial role in prediction and are highly involved in the immune response against IAV. The proposed in silico tools pave the path towards improved tracking and monitoring of influenza infections and possibly other respiratory infections based on minimal-invasively obtained hematological parameters.
Die vorliegende Arbeit befasst sich mit der Untersuchung der Transporteigenschaften inklusive Ladungsträgerdynamik von quasi-zweidimensionalen organischen Ladungstransfersalzen. Diese Materialien besitzen eine Schichtstruktur und weisen eine hohe Anisotropie der elektrischen Leitfähigkeit auf. Aufgrund der geringen Bandbreite und der niedrigen Ladungsträgerkonzentration gehören die Materialien zu den stark-korrelierten Elektronensystemen, wobei sich die elektronischen Eigenschaften leicht durch chemische Modifikationen oder äußere Parameter beeinflussen lassen. Die starken Korrelationen resultieren in Metall-Isolator-Übergängen, die sich beim Mott-isolierenden Zustand in einer homogenen Verteilung und beim ladungsgeordneten Zustand in einer periodischen Anordnung der lokalisierten Ladungsträger manifestieren.
Mithilfe der Fluktuationsspektroskopie, die sich mit der Analyse der zeitabhängigen Widerstandsfluktuationen befasst, konnten im Rahmen dieser Arbeit neue Erkenntnisse über die Ladungsträgerdynamik in den verschiedenen elektronischen Zuständen gewonnen werden. Die Metall-Isolator-Übergänge in den untersuchten Systemen, die auf den Molekülen BEDT-TTF (kurz: ET) bzw. BEDT-TSF (kurz: BETS) basieren, sind von der Stärke der strukturellen Dimerisierung abhängig und wurden durch die Kühlrate, eine Zugbelastung sowie durch die Ausnutzung des Feldeffekts beeinflusst.
In den Systemen κ-(BETS)₂Mn[N(CN)₂]₃, κ-(ET)₂Hg(SCN)₂Cl und κ-(ET)₂Cu[N(CN)₂]Br sind die Donormoleküle als Dimere angeordnet, sodass aufgrund der effektiv halben Bandfüllung bei genügender Korrelationsstärke häufig ein Mott-Übergang auftritt. In κ-(ET)₂Hg(SCN)₂Cl führt eine schwächere Dimerisierung jedoch zu einem Ladungsordnungsübergang, der mit elektronischer Ferroelektrizität einhergeht. Dabei wird die polare Ordnung durch eine Ladungsdisproportionierung innerhalb der Dimere verursacht. Die Widerstandsfluktuationen zeigen am ferroelektrischen Übergang einen starken Anstieg der spektralen Leistungsdichte, eine Abhängigkeit vom angelegten elektrischen Feld sowie Zeitabhängigkeiten, die auf räumliche Korrelationen der fluktuierenden Prozesse hindeuten. Diese Eigenschaften wurden ebenfalls für das System κ-(BETS)₂Mn[N(CN)₂]₃ beobachtet. Hierbei wurden mithilfe der dielektrischen Spektroskopie ebenfalls Hinweise auf Ferroelektrizität gefunden, während durch die Analyse der stromabhängigen Widerstandsfluktuationen die Größe der polaren Regionen abgeschätzt werden konnte. Das System κ-(ET)₂Cu[N(CN)₂]Br, das in einer Feldeffekttransistor-Struktur vorliegt, erlaubt neben der Untersuchung des Bandbreiten-getriebenen Mott-Übergangs durch die Zugbelastung eines Substrats auch die Beeinflussung der elektronischen Eigenschaften durch die Änderung der Bandfüllung mittels elektrostatischer Dotierung. Hierbei wurden starke Abhängigkeiten des Widerstands von der Gatespannung beobachtet und Ähnlichkeiten der Ladungsträgerdynamik zu herkömmlichen Volumenproben gefunden.
Bei den Systemen θ-(ET)₂MM'(SCN)₄ mit MM'=CsCo, RbZn, TlZn tritt ein Ladungsordnungsübergang auf, der eine starke Abhängigkeit von der Kühlrate zeigt. Durch schnelles Abkühlen lässt sich der Phasenübergang erster Ordnung kinetisch vermeiden, wodurch ein Ladungsglaszustand realisiert wird. Dieser metastabile Zustand zeigt neuartige physikalische Eigenschaften mit Ähnlichkeiten zu herkömmlichen Gläsern und wurde als Folge der geometrischen Frustration der Ladung auf einem Dreiecksgitter diskutiert. Im Rahmen dieser Arbeit konnte die Ladungsträgerdynamik in den verschiedenen Ladungszuständen von unterschiedlich frustrierten Systemen verglichen werden. Zur Realisierung sehr schneller Abkühlraten wurde dafür eine Heizpulsmethode verwendet und weiterentwickelt. Der Ladungsglaszustand zeigte dabei für verschiedene Systeme ein deutlich niedrigeres Rauschniveau als der ladungsgeordnete Zustand. In Kombination mit Messungen der thermischen Ausdehnung und kühlratenabhängiger Transportmessungen wurde in den Systemen mit der stärksten Frustration die Existenz eines strukturellen Glasübergangs nachgewiesen, der von einer starken Verlangsamung der Ladungsträgerdynamik begleitet wird. Diese Erkenntnisse werfen ein neues Licht auf die bisherige rein elektronische Interpretation des Ladungsglaszustands und heben den Einfluss der strukturellen Freiheitsgrade hervor.
Gasdermin-D (GSDMD) is the ultimate effector of pyroptosis, a form of programmed cell death associated with pathogen invasion and inflammation. After proteolytic cleavage by caspases activated by the inflammasome, the GSDMD N-terminal domain (GSDMDNT) assembles on the inner leaflet of the plasma membrane and induces the formation of large membrane pores. We use atomistic molecular dynamics simulations to study GSDMDNT monomers, oligomers, and rings in an asymmetric plasma membrane mimetic. We identify distinct interaction motifs of GSDMDNT with phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) and phosphatidylserine (PS) head-groups and describe differential lipid binding between the pore and prepore conformations. Oligomers are stabilized by shared lipid binding sites between neighboring monomers acting akin to double-sided tape. We show that already small GSDMDNT oligomers form stable, water-filled and ion-conducting membrane pores bounded by curled beta-sheets. In large-scale simulations, we resolve the process of pore formation by lipid detachment from GSDMDNT arcs and lipid efflux from partial rings. We find that that high-order GSDMDNT oligomers can crack under the line tension of 86 pN created by an open membrane edge to form the slit pores or closed GSDMDNT rings seen in experiment. Our simulations provide a detailed view of key steps in GSDMDNT-induced plasma membrane pore formation, including sublytic pores that explain nonselective ion flux during early pyroptosis.
Transport of lipids across membranes is fundamental for diverse biological pathways in cells. Multiple ion-coupled transporters take part in lipid translocation, but their mechanisms remain largely unknown. Major facilitator superfamily (MFS) lipid transporters play central roles in cell wall synthesis, brain development and function, lipids recycling, and cell signaling. Recent structures of MFS lipid transporters revealed overlapping architectural features pointing towards a common mechanism. Here we used cysteine disulfide trapping, molecular dynamics simulations, mutagenesis analysis, and transport assays in vitro and in vivo, to investigate the mechanism of LtaA, a proton-dependent MFS lipid transporter essential for lipoteichoic acid synthesis in the pathogen Staphylococcus aureus. We reveal that LtaA displays asymmetric lateral openings with distinct functional relevance and that cycling through outward- and inward-facing conformations is essential for transport activity. We demonstrate that while the entire amphipathic central cavity of LtaA contributes to lipid binding, its hydrophilic pocket dictates substrate specificity. We propose that LtaA catalyzes lipid translocation by a ‘trap-and-flip’ mechanism that might be shared among MFS lipid transporters.
Intrinsically disordered regions (IDRs) are essential for membrane receptor regulation but often remain unresolved in structural studies. TRPV4, a member of the TRP vanilloid channel family involved in thermo- and osmosensation, has a large N-terminal IDR of approximately 150 amino acids. With an integrated structural biology approach, we analyze the structural ensemble of the TRPV4 IDR and identify a network of regulatory elements that modulate channel activity in a hierarchical lipid-dependent manner through transient long-range interactions. A highly conserved autoinhibitory patch acts as a master regulator by competing with PIP2 binding to attenuate channel activity. Molecular dynamics simulations show that loss of the interaction between the PIP2-binding site and the membrane reduces the force exerted by the IDR on the structured core of TRPV4. This work demonstrates that IDR structural dynamics are coupled to TRPV4 activity and highlights the importance of IDRs for TRP channel function and regulation.
This work is focused on the anomalous skin effect in copper and how it affects the efficiency of copper-cavities in the temperature range 40-50 K. The quality factor Q of three coaxial cavities was measured over the temperature range from 10 K to room temperature in the experiment. The three coaxial cavities have the same structure, but different lengths, which correspond to resonant frequencies: around 100 MHz, 220 MHz and 340 MHz. Furthermore, the effects of copper-plating and additional baking in the vacuum oven on the quality factor Q are studied in the experiment. The motivation is to check the feasibility of an efficient, pulsed, ion linac, operated at cryogenic temperatures.
We fabricated memristive devices using focused electron beam-induced deposition (FEBID) as a direct-writing technique employing a Pt/TiO2/Pt sandwich layer device configuration. Pinching in the measured current-voltage characteristics (i-v), the characteristic fingerprint of memristive behavior was clearly observed. The temperature dependence was measured for both high and low resistive states in the range from 290 K down to about 2 K, showing a stretched exponential behavior characteristic of Mott-type variable-range hopping. From this observation, a valence change mechanism of the charge transport inside the TiO2 layer can be deduced.
The photoelectric effect describes the ejection of an electron upon absorption of one or several photons. The kinetic energy of this electron is determined by the photon energy reduced by the binding energy of the electron and, if strong laser fields are involved, by the ponderomotive potential in addition. It has therefore been widely taken for granted that for atoms and molecules, the photoelectron energy does not depend on the electron’s emission direction, but theoretical studies have questioned this since 1990. Here, we provide experimental evidence that the energies of photoelectrons emitted against the light propagation direction are shifted toward higher values, while those electrons that are emitted along the light propagation direction are shifted to lower values. We attribute the energy shift to a nondipole contribution to the ponderomotive potential that is due to the interaction of the moving electrons with the incident photons.
Proton-powered c-ring rotation in mitochondrial ATP synthase is crucial to convert the transmembrane protonmotive force into torque to drive the synthesis of ATP. Capitalizing on recent cryo-EM structures, we aim at a structural and energetic understanding of how functional directional rotation is achieved. We performed multi-microsecond atomistic simulations to determine the free energy profiles along the c-ring rotation angle before and after the arrival of a new proton. Our results reveal that rotation proceeds by dynamic sliding of the ring over the a-subunit surface, during which interactions with conserved polar residues stabilize distinct intermediates. Ordered water chains line up for a Grotthuss-type proton transfer in one of these intermediates. After proton transfer, a high barrier prevents backward rotation and an overall drop in free energy favors forward rotation, ensuring the directionality of c-ring rotation required for the thermodynamically disfavored ATP synthesis. The essential arginine of the a-subunit stabilizes the rotated configuration through a salt-bridge with the c-ring. Overall, we describe a complete mechanism for the rotation step of the ATP synthase rotor, thereby illuminating a process critical to all life at atomic resolution.
Proton-powered c-ring rotation in mitochondrial ATP synthase is crucial to convert the transmembrane protonmotive force into torque to drive the synthesis of ATP. Capitalizing on recent cryo-EM structures, we aim at a structural and energetic understanding of how functional directional rotation is achieved. We performed multi-microsecond atomistic simulations to determine the free energy profiles along the c-ring rotation angle before and after the arrival of a new proton. Our results reveal that rotation proceeds by dynamic sliding of the ring over the a-subunit surface, during which interactions with conserved polar residues stabilize distinct intermediates. Ordered water chains line up for a Grotthuss-type proton transfer in one of these intermediates. After proton transfer, a high barrier prevents backward rotation and an overall drop in free energy favors forward rotation, ensuring the directionality of c-ring rotation required for the thermodynamically disfavored ATP synthesis. The essential arginine of the a-subunit stabilizes the rotated configuration through a salt-bridge with the c-ring. Overall, we describe a complete mechanism for the rotation step of the ATP synthase rotor, thereby illuminating a process critical to all life at atomic resolution.
Cryo-electron tomography (CryoET) resolves individual macromolecules inside living cells. However, the complex composition and high density of cells challenge the faithful identification of features in tomograms. Here, we capitalize on recent advances in electron tomography and demonstrate that 3D template matching (TM) localizes a wide range of structures inside crowded eukaryotic cells with confidence 10 to 100-fold above the noise level. We establish a TM pipeline with systematically tuned parameters for automated, objective and comprehensive feature identification. High-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, lipid membranes and microtubules, and individual subunits, demonstrate that TM is generic. We resolve ~100-kDa proteins, connect the functional states of complexes to their cellular localization, and capture vaults carrying ribosomal cargo in situ. By capturing individual molecular events inside living cells with defined statistical confidence, high-confidence TM greatly speeds up the CryoET workflow and sets the stage for visual proteomics.
This article summarizes some of the current theoretical developments and the experimental status of hypernuclei in relativistic heavy-ion collisions and elementary collisions. In particular, the most recent results of hyperhydrogen of mass A = 3 and 4 are discussed. The highlight at SQM2022 in this perspective was the discovery of the anti-hyperhydrogen-4 by the STAR Collaboration, in a large data set consisting of different collision systems. Furthermore, the production yields of hyperhydrogen-4 and hyperhelium-4 from the STAR Collaboration can be described nicely by the thermal model when the excited states of these hypernuclei are taken into account. In contrast, the production measurements in small systems (pp and p–Pb) from the ALICE Collaboration tends to favour the coalescence model over the thermal description. New measurements from STAR, ALICE and HADES Collaborations of the properties, e.g. lifetime, of A = 3 and 4 hypernuclei give similar results of these properties. Also the anti-hyperhydrogen-4 lifetime is in rather good agreement with previous measurements. Interestingly, the new STAR measurement on the R3 value, that is connected to the branching ratio, points to a Λ separation energy that is below 100 keV but definitely consistent with the value of 130 keV assumed since the 70s.
We show examples of the impact of the Maxwellian averaged capture cross sections determined at n_TOF over the past 20 years on AGB stellar nucleosynthesis models. In particular, we developed an automated procedure to derive MACSs from evaluated data libraries, which are subsequently used as input to stellar models computed by means of the FuNS code. In this contribution, we present a number of s-process abundances obtained using different data libraries as input to stellar models, with a focus on the role of n_TOF data.
This thesis investigates exotic phases within effective models for strongly interacting matter.
The focus lies on the chiral inhomogeneous phase (IP) that is characterized by a spontaneous breaking of translational symmetry and the moat regime, which is a precursor phenomenon exhibiting a non-trivial mesonic dispersion relation.
These phenomena are expected to occur at non-zero baryon densities, which is a parameter region that is mostly non-accessible to first-principle investigations of Quantum chromodynamics (QCD).
As an alternative approach, we consider the Gross-Neveu (GN) and Nambu-Jona-Lasinio (NJL) model within the mean-field approximation, which can be regarded as effective models for QCD.
We focus on two aspects of the moat regime and the IP in these models.
First, we investigate the influence of the employed regularization scheme in the (3+1)-dimensional NJL model, which is nonrenormalizable, i.e., the regulator cannot be removed.
We find that the moat regime is a robust feature under change of regularization scheme, while the IP is sensitive to the specific choice of scheme.
This suggests that the moat regime is a universal feature of the phase diagram of the NJL model, while the IP might only be an artifact of the employed regulator.
Second, we study the influence of the number of spatial dimensions on the emergence of the IP.
To this end, we investigate the GN model in noninteger spatial dimensions d.
We find that the IP and the moat regime are present for d < 2, while they are absent for d > 2.
This demonstrates the central role of the dimensionality of spacetime and illustrates the connection of previously obtained results in this model in integer number of spatial dimensions.
Moreover, this suggests that the occurrence of these phenomena in three spatial dimensions is solely caused by the finite regulator.
In summary, this thesis contributes to advancing our understanding of the phase structure of QCD, particularly regarding the existence and characteristics of inhomogeneous phases and the moat regime.
Even though the investigations are performed within effective models, they provide valuable insight into the aspects that are crucial for the formation of an inhomogeneous chiral condensate in fermionic theories.
In this thesis, we present a detailed consideration of both qualitative and quantitative properties of static spherically symmetric solutions of the Einstein equations with self-interacting scalar fields. Our focus is on solutions with naked singularities. We study the qualitative properties of the solutions of the Einstein equations with real static self-interacting $N$ scalar fields, making some assumptions on self-interaction. We provide a rigorous proof that the corresponding solutions will be regular up to $r=0$. Furthermore, we find the rigorous form of asymptotic solutions near the singularity and at spatial infinity. We construct some examples of spherical-like naked singularities at $r=r_s\neq0$ in curvature coordinates.
We analyze the stability of the previously considered solutions against odd-parity gravitational perturbations and also examine the fundamental quasi-normal modes spectra. For the general class of the self-interaction potential, we demonstrate well-posedness of the initial problem and stability for positively defined potentials. As an example, we numerically study the case of the scalar field with power-law self-interaction potential and find the fundamental quasi-normal modes frequencies. We demonstrate that they differ from the standard Schwarzschild black hole case.
We study in detail the motion of particles in the vicinity of previously considered solutions. Mainly, we are interested in considering properties of the distribution of stable circular orbits around the corresponding configurations and images of the accretion disk for a distant observer. For all cases, we find possible types of stable circular orbit distributions and domains of parameters where they are realized.
We also demonstrate that the presence of self-interaction can lead to a new type of circular orbit distributions, which is absent in the linear massless scalar field case. We build Keplerian disk images in the plane of a distant observer and demonstrate the possibility to mimic the shadows of black holes.
By combining two unique facilities at the Gesellschaft fuer Schwerionenforschung (GSI), the Fragment Separator (FRS) and the Experimental Storage Ring (ESR), the first direct measurement of a proton capture reaction of stored radioactive isotopes was accomplished. The combination of well-defined ion energy, an ultra-thin internal gas target, and the ability to adjust the beam energy in the storage ring enables precise, energy-differentiated measurements of the (p,gamma) cross sections. The new setup provides a sensitive method for measuring (p,gamma) reactions relevant for nucleosynthesis processes in supernovae, which are among the most violent explosions in the universe and are not yet well understood. The cross sections of the 118Te(p,gamma) and 124Xe(p,gamma) reactions were measured
at energies of astrophysical interest. The heavy ions were stored with energies of 6 MeV/nucleon and 7 MeV/nucleon and interacted with a hydrogen gas-jet target.
The produced proton-capture products were detected with a double-sided silicon strip detector. The radiative recombination process of the fully stripped ions and electrons from the hydrogen target was used as a luminosity monitor.
Additionally, post-processing nucleosynthesis simulations within the NuGrid [1] research platform have been performed. The impact of the new experimental results on the p-process nucleosynthesis around 124Xe and 118Te in a core-collapse supernova was investigated. The successful measurement of the proton capture cross sections of radioactive isotopes rises the motivation to proceed with experiments in lower energy regions.
[1] M. Pignatari and F. Herwig, “The nugrid research platform: A comprehensive simulation approach for nuclear astrophysics,” Nuclear Physics News, vol. 22, no. 4, pp. 18–23, 2012.
In this thesis, the early time dynamics in a heavy ion collision of Pb-Nuclei at LHC center-of-mass energies of 5 TeV is studied. Right after the collision the system is out-of-equilibrium and essentially gluon dominated, with their density saturating at a specific momentum scale Q_s. Based on a separation of scales for the soft and hard gluonic degrees of freedom, the initial state is given from an effective model, known as the Color Glass Condensate. Within this model, the soft gluons behave classical to leading order, making it possible to study their dynamics in gauge invariant fashion on a three dimensional lattice, solving Hamiltonian field equations of motion, keeping real time. Quark-Antiquark pairs are produced in the gluonic medium, known as the Glasma and manifest themselves as a source of quantum fluctuations.
They enter the dynamics of the gluons as a current, making the system semi-classical. In lattice simulations, the non-equilibrium system is tested for pressure isotropization, which is a necessary ingredient to reach a local thermal equilibrium (LTE), making a hydrodynamical description at a later stage possible. In addition, the occupation of energy modes is studied with its implications on thermalization and classicality.
Das Experiment ALICE (A Large Ion Collider Experiment) am CERN (Conseil Européen pour la Recherche Nucléaire) LHC (Large Hadron Collider) fokussiert sich auf die Untersuchung stark wechselwirkender Materie unter extremen Bedingungen. Solche Bedingungen existierten wenige Mikrosekunden nach dem Urknall, als die Temperaturen so hoch waren, dass Partonen (Quarks und Gluonen) nicht zu farbneutralen Hadronen gebunden waren. In solch einem Quark-Gluon-Plasma können sich die Partonen frei bewegen, wobei sie allerdings mit anderen Partonen aus dem Medium stark wechselwirken. Am LHC werden Bleikerne auf ultra-relativistische Energien von bis zu 2.68 TeV beschleunigt und zur Kollision gebracht, wobei für weniger als 10 fm/c ein QGP entsteht, das schnell expandiert. Die Partonen hadronisieren, wenn das QGP sich auf Temperaturen von weniger als der Phasenübergangstemperatur von ≈155MeV abkühlt. Die finalen Teilchen- und Impulsverteilungen werden werden vom ALICE Detektor gemessen und geben Aufschluss auf elementare Prozesse im QGP.
Die TPC (Time Projection Chamber ) ist eines der wichtigsten Detektorsysteme von ALICE. Sie trägt maßgeblich zur Rekonstruktion von Teilchenspuren und zur Identifikation der Teilchensorten bei mittleren Rapiditäten bei. Die TPC ist eine große zylindrische Spurendriftkammer und besteht aus einem 88mˆ3 großen Gasvolumen, das von der zentralen Hochspannungselektrode in zwei Seiten geteilt wird. Durchquert ein Teilchen das Gasvolumen, ionisiert es entlang seiner Spur eine spezifische Menge von Gasatomen. Die Ionisationselektronen driften entlang des extrem homogenen elektrischen Feldes zu den Auslesekammern an den Endkappen auf beiden Seiten der TPC. Die Messung der Position und der Menge der Ionisationselektronen erlaubt die Rekonstruktion der Teilchenspur sowie, in Kombination mit der Impulsmessungen über die Krümmung der Teilchenspur im Magnetfeld, die Bestimmung der Teilchensorte über den spezifischen Energieverlust pro Wegstrecke im Gas. Das Gasvolumen der TPC war in LHC Run 1 (2010–2013) mit Ne-CO_2 (90-10) gefüllt. Die Gasmischung wurde zu Ar-CO_2 (88-12) für Run 2 (2015–2018) geändert. Als Auslesekammern wurden Vieldrahtproportionalkammern verwendet, die aus einer segmentierten Ausleseebene, einer Anodendrahtebene, einer Kathodendrahtebene und einem Gating-Grid (GG) bestehen. Das GG is eine zusätzliche Drahtebene, die durch zwei verschiedene Spannungseinstellungen transparent oder undurchlässig für Elektronen und positive Ionen geschaltet werden kann.
In den ersten Daten von Run 2 bei hohen Interaktionsraten wurden große Verzerrungen der gemessenen Spurpunkte beobachtet, die auf Grund von Verzerrungen des Driftfeldes auftreten und nicht von Daten aus Run 1 bekannt waren. Diese Verzerrungen treten nur sehr lokal an den Grenzen von manchen der inneren Auslesekammern (IROCs) auf. Zudem wurden auch große Verzerrungen in einer (C06) der äußeren Auslesekammern (OROCs) festgestellt, die sich bei einem bestimmten Radius über die ganze Breite der Kammer erstrecken. Die Ergebnisse dieser Arbeit befassen sich mit der Untersuchung jener Verzerrungen und ihrer Ursache, sowie mit der Entwicklung von Strategien um die Verzerrungen zu minimieren.
Messungen der Verzerrungen in den IROCs und Vergleiche mit Simulationen lassen darauf schließen, dass die Verzerrungen von positiver Raumladung hervorgerufen werden, die durch Gasverstärkung an sehr begrenzten Regionen der Auslesekammern entsteht und sich durch das Driftvolumen bewegt. Es werden charakteristische Abhängigkeiten von der Interaktionsrate sowie systematische Veränderungen bei Umkehrung der Orientierung des Magnetfeldes gemessen. Eine erneute Analyse von Run 1 Daten mit den Methoden aus Run 2 zeigt, dass die Verzerrungen bereits in Run 1 auftraten, jedoch durch die Ne-Gasmischung und niedrigere Interaktionsraten um eine Größenordnung kleiner waren. Neue Daten aus Run 2, für die die Gasmischung zeitweise wieder von Ar-CO_2 zu Ne-CO_2- N_2 geändert wurde, bestätigen die Ergebnisse der Run 1 Datenanalyse. Der Ursprung der Raumladung wird systematisch eingegrenzt. Es werden einzelne IROCs identifiziert, an deren Anodendrähten die Raumladung entsteht. Physikalische Modelle ermöglichen es, die Entstehung der Raumladung auf das Volumen zurückzuführen, das sich zwischen zwei IROCs befindet. Damit besteht die Vermutung, dass einzelne Spitzen von Anodendrähten am äußeren Rand dieser IROCs in das Gasvolumen hineinragen und somit hohe elektrische Felder erzeugen, an denen Gasverstärkung stattfindet. Die positiven Ionen können dann ungehindert in das Driftvolumen gelangen. Um diesen Effekt zu unterdrücken, wird das Potential der Cover-Elektroden angepasst, die sich auf den Befestigungsvorrichtungen der Drahtebenen an den Kammerrändern befinden. Dadurch kann die Menge von Ionisationselektronen, die in das Volumen zwischen zwei IROCs hineindriftet und vervielfacht wird, eingeschränkt werden. Über elektro-statische Simulationen und Messungen wird eine Einstellung für das Cover-Elektroden-Potential gefunden, mit der die Verzerrungen auf 30 % reduziert werden können. Die Verzerrungen in OROC C06 entstehen durch positive Ionen, die aus der Verstärkungsregion in das Driftvolumen gelangen, da an dieser bestimmten Stelle zwei aufeinanderfolgende GG-Drähte den Kontakt verloren haben. Die Verzerrungen werden um mehr als einen Faktor 3 reduziert, indem die Hochspannung der Anodendrähte um 50 V und somit der Gasverstärkungsfaktor um einen Faktor 2 verringert wird und indem das Potential der noch funktionierenden GG-Drähte erhöht wird.
Zusammenfassend konnten die lokalen Raumladungsverzerrungen für die letzte Pb−Pb Strahlzeit von Run 2 auf weniger als 1cm bei den höchsten Interaktionsraten verringert werden. Zudem wurde der Anteil des von Raumladungsverzerrungen betroffenen Volumens der TPC signifikant verringert, sodass die ursprüngliche Auflösung der Spurrekonstruktion wieder erreicht werden konnte.
Lattice QCD and functional methods are making significant progress in constraining the QCD phase diagram. As an important milestone, the chiral phase transition with massless u, d-quarks at zero density is now understood to be of second order for all strange quark masses, and a smooth crossover as soon as mu,d, ≠ 0. Together with information on fluctuations and refined reweighted simulations, this bounds a possible critical point to be at µB/T ≲3. On the other hand, an approximately chiral-spin symmetric temperature window has been discovered above the chiral crossover, Tch<T ≳3Tch, with distinct correlator multiplet patterns and a pion spectral function suggesting resonance-like degrees of freedom, which dissolve graduallly with temperature.
Prediction for hyper nuclei multiplicities from GSI to LHC energies from the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model combined with a final state coalescence approach is presented and compared to the thermal model. The influence of the coalescence radius on the collision energy and centrality dependence of the Λ3H/ΛΛ3H/Λ ratio is discussed.
Subensemble is a type of statistical ensemble which is the generalization of grand canonical and canonical ensembles. The subensemble acceptance method (SAM) provides general formulas to correct the cumulants of distributions in heavy-ion collisions for the global conservation of all QCD charges. The method is applicable for an arbitrary equation of state and sufficiently large systems, such as those created in central collisions of heavy ions. The new fluctuation measures insensitive to global conservation effects are presented. The main results are illustrated in the hadron resonance gas and van der Waals fluid frameworks.
Present nuclear reaction network computations for astrophysical simulations involve many different types of rates, including neutron-capture reactions of interest for the modeling of heavy-element nucleosynthesis. While for many of them we still have to rely on theoretical calculations, an increasing number of experimentally-determined cross sections have now become available. In this contribution, we present “ASTrophysical Rate and rAw data Library” (ASTRAL), a new online database for neutron-capture cross sections based on experimental results, mainly obtained through activation and timeof-flight measurements. For the evaluation process, cross sections were re-calculated starting from raw data and by considering recent changes in physical properties of the involved isotopes (e.g., half-life and γ-ray intensities). We show the current status of the database, the techniques adopted to derive the recommended Maxwellian-averaged cross sections, and future developments.
Results on proton and Λ flow, calculated with the UrQMD model that incorporates different realistic density dependent equations of state, are presented. It is shown that the proton and hyperon flow shows sensitivity to the equation of state and especially to the appearance of a phase transition at densities below 4n0. Even though qualitatively hyperons and protons exhibit the same beam energy dependence of the flow, the quantitative results are different. In this context it is suggested that the hyperon measurements can be used to study the density dependence of the hyperon interaction in high density QCD matter.
We study equilibrium as well as out-of-equilibrium properties of the strongly interacting QGP medium under extreme conditions of high temperature T and high baryon densities or baryon chemical potentials μB within a kinetic approach. We present the thermodynamic and transport properties of the QGP close to equilibrium in the framework of effective models with Nf=3 active quark flavours such as the Polyakov extended Nambu-Jona Lasinio (PNJL) and dynamical quasiparticle model with the CEP (DQPM-CP). Considering the transport coefficients and the EoS of the QGP phase, we compare our results with various results from the literature. Furthermore, out-of equilibrium properties of the QGP medium and in particular, the effect of a μB- dependence of thermodynamic and transport properties of the QGP are studied within the Parton-Hadron-String-Dynamics (PHSD) transport approach, which covers the full evolution of the system during HICs. We find that bulk observables and flow coefficients for strange hadrons as well as for antiprotons are more sensitive to the properties of the QGP, in particular to the μB - dependence of the QGP interactions.
Presolar grain isotopic ratios as constraints to nuclear physics inputs for s-process calculations
(2023)
The isotopic abundances in presolar SiC grains of AGB origin provide important and precise constraints to those star nucleosynthesis models. By comparing the values of the s-element abundances resulting from calculations with the ones measured in these dust grains, it turns out that new measurements of weak-interaction rates in ionized plasmas, as well as of neutron-capture cross sections, are needed, especially in the region near the neutron magic numbers 50 and 82.
This thesis aims to investigate the properties of hadronic matter by analyzing fluctuations of conserved charges. A transport model (SMASH) is used for these studies to achieve this. The first part of this thesis focuses on examining transport coefficients, specifically the diffusion coefficients of conserved charges and the shear viscosity. The second part investigates equal-time correlations of particle numbers in the form of cumulants. The last chapter studies different aspects of the isobar collision systems Ru and Zr.
As a first step, the hadronic medium and interactions between its constituents are introduced, and simultaneously, their impact on transport coefficients is investigated. The methodology is verified by comparing the results of SMASH with Chapman-Enskog calculations, followed by examining 3-to-1 multi-particle reactions, revealing their influence on shear viscosity and electrical diffusion. The analysis of the full hadron gas considers angle-dependent cross-sections and additional elastic cross-sections via the AQM description, showing significant impacts on transport coefficients. The dependency on the number of degrees of freedom is explored, with noticeable effects on diffusion coefficients but a smaller influence on the shear viscosity. At non-zero baryon chemical potential, the diffusion coefficients are strongly influenced, while the shear viscosity remains unaffected. Overall, the study underscores the importance of individual cross-sections and the modeling of interactions on transport coefficients.
The following chapter explores fluctuations of conserved charges, crucial for understanding phase transitions in heavy-ion collision from the quark-gluon plasma to the hadronic phase. Using SMASH, the impact of global charge conservation on particle number cumulants in subvolumes of boxes simulating infinite matter is studied. Comparisons with simpler systems highlights the influence of hadronic interactions on cumulants, especially via charge annihilation processes and the results from SMASH shows agreement with analytical calculations. Calculations at finite baryon chemical potential reveals a transition from a Poisson to Skellam distribution within the net proton cumulants. It is shown that an unfolding procedure to obtain the net baryon fluctuations from the net proton ones deviates from the actual net baryon result, particularly in larger volumes. Finally, net proton correlations at vanishing baryon chemical potential align with ALICE measurements and the net proton cumulants are unaffected by deuteron formation.
In the next step, the goal is to investigate critical fluctuations in the hadronic medium. Therefore, the hadronic system is initialized with critical equilibrium fluctuations by coupling the hadron resonance gas with the 3D Ising model. The single-particle probability distributions are derived from the principle of maximum entropy. Evolving these distributions in SMASH, their development in an expanding sphere adjusted to experimental conditions can be analyzed. It reveals resonance decay and formations as the primary source that affects the particle cumulants. Because of isospin randomization processes, critical fluctuations are better preserved in net nucleon numbers. However, for the strongest coupling investigated in this work, correlations of the critical field are still present in the final state of the evolution in the net proton fluctuations. Examining cumulant dependence on rapidity windows shows a non-monotonic trend.
In the third part, collisions involving the isobars Ru and Zr are studied at a center-of-mass energy of 200 GeV. Initially, SMASH is used to study the initial conditions to hydrodynamical simulations, emphasizing the importance of the nuclear structure of isobars on the geometry of the collision area. It is found that the deformation parameters notably influence the initial state. Correlations between nucleon-nucleon pairs on eccentricity fluctuations yield no significant effect. Subsequently, the hydrodynamic model vHLLE evolves the previously explored initial conditions and for the transition between the hydrodynamic and kinetic descriptions, the Cooper-Frye formula is used. Usage of the canonical ensemble ensures the exact conservation of the conserved charges B, Q, and S. The neutron skin effect, which changes the charge distribution within Ru nuclei, is additionally considered. Fluctuations are assessed, revealing suppression in large rapidity windows due to global charge conservation. The hadronic phase modifies fluctuations of net pions, net kaons, and net protons via annihilation processes, yet fluctuations remain unaffected by the neutron skin effect.
The core of this work is represented by the investigation of the chiral phase transition, using Monte Carlo simulations and unimproved staggered fermions, both in the weak and strong coupling regimes of Quantum Chromodynamics. Based on recent results from Monte Carlo simulations, both using unimproved staggered fermions and Wilson fermions, the chiral phase transition in the continuum and chiral limit shows compatibility with a second-order phase transition for Nf (number of flavours) in range [2:7], at zero baryon chemical potential. This achievement relies on the analytic continuation of Nf to non-integer values on the lattice, which allows to make use of extrapolation techniques to the chiral limit, where simulations are not possible. Furthermore, these results provide a resolution to the ambiguous scenario for Nf = 2 in the chiral limt. The first part of this thesis is devoted to the investigation of the chiral phase transition when a non-zero imaginary baryon chemical potential is involved, whose value corresponds to the 81% of the Roberge-Weiss one. Using the same extrapolation techniques aforementioned, the order of the chiral phase transition in the continuum and chiral limit shows compatibility with a second-order phase transition for Nf in range [2:6], highlighting a lack of dependence of the order of the chiral phase transition on the imaginary baryon chemical potential value. The second part of this thesis is about the study of the extension of the first-order chiral region in the strong coupling regime, at zero baryon chemical potential. Using Monte Carlo techniques, this can be done by investigating the Z2 boundary on a coarse lattice, whose temporal extent reads Nt = 2, and simulations are realised for Nf = 4, 8. The results in the weak coupling regime show, for $Nt = 8, 6, 4 and fixed Nf value, an inflating first-order chiral region. As in the strong coupling limit a second-order chiral phase transition is expected, the first-order chiral region has to shrink as the strong coupling regime is approached, resulting in a non-monotonic behaviour of the Z2 boundary. For Nf = 8, a critical mass on the Z2 boundary has been obtained, confirming the expected non-monotonic behaviour. For Nf = 4 the results do not provide a unique conclusion: Either a Z2 boundary at extremely low bare quark mass or a second-order chiral phase transition in the O(2) universality class in the chiral limit can take place. In addition to the two main topics, the performances of the second-order minimum norm integrator (2MN) and the fourth-order minimum norm integrator (4MN) have been compared, after implementing the 4MN one in the CL2QCD code used to realise our simulations. The 2MN integrator had already been implemented in the code since the first version was released. The two integrators belong to the class of symplectic integrators and represent an essential component of the RHMC algorithm, involved in our investigation. This step is extremely important, in order to guarantee the best quality when collecting data from simulations, and the results of the comparison suggested to favor the 2MN integrator, for both the topics.
Cryo-electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyse biomolecules in situ by subtomogram averaging (STA). Specimen thickness is a key factor affecting cryo-ET data quality. Cells that are too thick for transmission imaging can be thinned by cryo-focused-ion-beam (cryo-FIB) milling. However, optimal specimen thickness for cryo-ET on lamellae has not been systematically investigated. Furthermore, the ions used to ablate material can cause damage in the lamellae, thereby reducing STA resolution. Here, we systematically benchmark the resolution depending on lamella thickness and the depth of the particles within the sample. Up to ca. 180 nm, lamella thickness does not negatively impact resolution. This shows that there is no need to generate very thin lamellae and thickness can be chosen such that it captures major cellular features. Furthermore, we show that gallium-ion-induced damage extends to depths of up to 30 nm from either lamella surface.
Experiments on Vibrational Energy Transfer (VET) in proteins contribute to our understanding of fundamental biological processes such as allostery, dissipation of excess energy, and possibly enzymatic catalysis. While these processes have been studied for a long time, many questions remain unanswered. The aim of this work was to expand the application of existing spectroscopic techniques to investigate VET, seeking tailored solutions for the diversity of proteins and amino acid environments. Additionally, new target proteins were to be established to broaden the spectrum of VET experiments towards the role of VET and low-frequency protein modes (LFMs).
To test their suitability as VET sensors, the non-canonical amino acids (ncAAs) Azidoalanine (N3Ala), azido-L-Homoalanine (Aha), p-azido-Phenylalanine (N3Phe), p-cyano-Phenylalanine (CNPhe), and 4-cyano-Tryptophan (CNTrp) were coupled to the VET donor β-(1-azulenyl)-L-Alanine (AzAla) in dipeptides. Their spectral properties were compared using FTIR and VET spectra in H2O, dimethyl sulfoxide, and tetrahydrofuran.
The solvent strongly influences the measured VET signals, which can be explained by the direct interaction of the solvent with the dipeptides. Additionally, the peak time within the subgroups of azide and nitrile sensors increased with the size of the side chain, indicating the dependence between peak time and the distance between VET donor and sensor. When incorporated into a protein, solvent interactions are less dominant. Therefore, Aha, N3Phe, and CNPhe were additionally incorporated at two different positions in the PDZ protein domain and investigated. Due to Fermi resonances, signals from azide sensors are challenging to predict, unlike those of the nitrile sensors.
Overall, the experiments showed that nitrile groups can serve well as VET sensors, as their lower extinction coefficient is compensated for by a narrower bandwidth. This expands the number of potential target proteins, and sensor incorporation can be less disruptive at various protein locations.
Since the VET donor AzAla can inject the energy of a photon into a protein as vibrational energy at a specific location, it can also be used for the targeted excitation of LFMs. If these modes are involved in an enzymatic reaction, a direct influence on activity is expected. This hypothesis has long existed but has not been definitively verified. Some studies have found evidence for the involvement of LFMs in formate dehydrogenase (FDH) catalysis. Therefore, FDH was chosen for the investigation of LFMs in enzymes. This specific system additionally allows the use of a natural VET sensor: it forms a stable complex with NAD+ and N3-, an excellent IR marker. Thus, it provided the opportunity to test low-molecular-weight non-covalent ligands as VET sensors.
After ensuring sufficient AzAla supply through the internal establishment of an enzymatic synthesis, AzAla could be incorporated at various positions in FDH. Despite spectral overlap between free and bound N3-, the latter could be identified by its narrower FWHM. For some variants, no binding could be observed. Circular dichroism spectra showed that these variants structurally deviate slightly from other variants and the wild type (WT). VET could be observed over 22 Å from two regions of the protein to the N3- bound in the active center, at protein concentrations of below 2 mM. Unbound N3- did not generate signals, allowing it to be added in excess ensuring the saturation of the protein in VET experiments.
The activity of FDH WT and four AzAla mutants was investigated under substrate saturation without and with AzAla excitation. In these experiments, a slight reduction in activity under illumination was observed, even for the WT, who is not expected to interact with the excitation light. So far, a difference in sample temperature cannot be excluded as the cause for this decline.
The presented experiments with FDH illustrate the potential of low-molecular-weight ligands as VET sensors, with N3- being particularly attractive due to its simple structure (preventing Fermi resonances) and its high extinction coefficient. Its use can add many metalloproteins as potential targets for VET experiments and allows investigation without a VET sensor ncAA. Additionally, initial experiments were conducted to measure light-dependent FDH activity. By specifically exciting protein LFMs, this project could contribute in the future to answering longstanding questions about the extraordinary catalytic efficiency of enzymes.
Im Clusterprojekt ELEMENTS arbeiten Physiker*innen verschiedenster Fachgebiete eng mit einander zusammen, um die Entstehung schwerer Elemente im Universum zu erforschen. Nur durch diese interdisziplinäre Kollaboration kann das komplexe Zusammenspiel mikroskopischer und makroskopischer Ereignisse entschlüsselt werden. Dabei bilden Theorie, Experiment und Beobachtung die drei großen Pfeiler des Forschungsvorhabens.
DIE ARCHITEKTUR DER ZELLE : Wie sehen die Bausteine des Lebens genau aus, wie interagieren die zellulären Akteure miteinander? Im Rahmen der Exzellenzcluster-Initiative SCALE (Subcellular Architecture of Life) wollen Frankfurter Wissenschaftlerinnen und Wissenschaftler diesen wichtigen Fragen nachgehen. Das Projekt ist interdisziplinär: Mehrere Forschungsgruppen, deren Schwerpunkt Biophysik ist, arbeiten zusammen. Der Biophysiker Achilleas Frangakis und die Bioinformatikerin Kathi Zarnack sind auch dabei. Sie verfolgen im Rahmen des Projekts große Ziele.
Continued advances in quantum technologies rely on producing nanometer-scale wires. Although several state-of-the-art nanolithographic technologies and bottom-up synthesis processes have been used to engineer these wires, critical challenges remain in growing uniform atomic-scale crystalline wires and constructing their network structures. Here, we discover a simple method to fabricate atomic-scale wires with various arrangements, including stripes, X-junctions, Y-junctions, and nanorings. Single-crystalline atomic-scale wires of a Mott insulator, whose bandgap is comparable to those of wide-gap semiconductors, are spontaneously grown on graphite substrates by pulsed-laser deposition. These wires are one unit cell thick and have an exact width of two and four unit cells (1.4 and 2.8 nm) and lengths up to a few micrometers. We show that the nonequilibrium reaction-diffusion processes may play an essential role in atomic pattern formation. Our findings offer a previously unknown perspective on the nonequilibrium self-organization phenomena on an atomic scale, paving a unique way for the quantum architecture of nano-network.
DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2
(2023)
More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.
Neutron stars are unique laboratories for the investigation of the high density properties of bulk matter. In this work, the astrophysical constraints for a phase transition from hadronic matter to deconfined quark matter are examined thoroughly. A scheme for relating known astrophysical observables such as mass, radius and tidal deformability to the parameter space of such a transition is devised and applied to the set of data currently available.
In order to span a wide parameter space, a highly parameterizable relativistic mean field equation in compliance with chiral effective field theory results is used, where the stiffness of the equation of state can be varied via the effective mass at saturation density. The phase transitions are modelled using a Maxwell construction and assumed to be of first order, with a constant speed of sound quark matter model. The resulting equations of state are analyzed and divided into four categories, which can be used to constrain the parameter space that allows phase transition. It is highlighted, that a subset of this parameter space would even be detectable without the need of higher precision measurements. A phase transition at high densities is shown to be particularly promising in this regard. Finally, the groundwork is laid to apply the equation of state used in this work for supernova or merger simulations, by extending it to non-zero temperatures.
Asymptotic giant branch (AGB) stars are responsible for the production of the main component of the solar s-process distribution. Despite enormous progress in the theoretical modeling of these objects over the last few decades, many uncertainties remain. The still-unknown mechanism leading to the production of 13C neutron source is one example. The nucleosynthetic signature of AGB stars can be examined in a number of stellar sources, from spectroscopic observations of intrinsic and extrinsic stars to the heavy-element isotopic composition of presolar grains found in meteorites. The wealth of available observational data allows for constraining the processes occurring in AGB interiors. In this view, we discuss recent results from new AGB models including the effects of mixing triggered by magnetic fields, and show comparisons of the related s-process nucleosynthesis with available observations.
We investigate the development of the directed, v1, and elliptic flow, v2, in heavy ion collisions in mid-central Au+Au reactions at Elab=1.23A GeV. We demonstrate that the elliptic flow of hot and dense matter is initially positive (v2>0) due to the early pressure gradient. This positive v2 transfers its momentum to the spectators, which leads to the creation of the directed flow v1. In turn, the spectator shadowing of the in-plane expansion leads to a preferred decoupling of hadrons in the out-of-plane direction and results in a negative v2 for the observable final state hadrons. We propose a measurement of v1−v2 flow correlations and of the elliptic flow of dileptons as methods to pin down this evolution pattern. The elliptic flow of the dileptons allows then to determine the early-state EoS more precisely, because it avoids the strong modifications of the momentum distribution due to shadowing seen in the protons. This opens the unique opportunity for the HADES and CBM collaborations to measure the Equation-of-State directly at 2-3 times nuclear saturation density.
Transient receptor potential (TRP) ion channels are among the most well-studied classes of temperature-sensing molecules. Yet, the molecular mechanism and thermodynamic basis for the temperature sensitivity of TRP channels remains to this day poorly understood. One hypothesis is that the temperature-sensing mechanism can simply be described by a difference in heat capacity between the closed and open channel states. While such a two-state model may be simplistic it nonetheless has descriptive value, in the sense that it can be used to to compare overall temperature sensitivity between different channels and mutants. Here, we introduce a mathematical framework based on the two-state model to reliably extract temperature-dependent thermodynamic potentials and heat capacities from measurements of equilibrium constants at different temperatures. Our framework is implemented in an open-source data analysis package that provides a straightforward way to fit both linear and nonlinear van ‘t Hoff plots, thus avoiding some of the previous, potentially erroneous, assumptions when extracting thermodynamic variables from TRP channel electrophysiology data.
The Heidelberg Ion-Beam Therapy Centre (HIT) provides proton, helium, and carbon-ion beams with different energies and intensities for cancer treatment and oxygen-ion beams for experiments. For several experiments and possible future applications, such as helium ion beam radiography, a low-intensity ion beam monitor integrated into the dose delivery feedback system for the accelerator control is a necessary pre-requisite. The updated 2D prototype for this purpose consists of scintillating fibres with enhanced radiation hardness, silicon photomultipliers (SiPMs) to amplify the emitted light, and a dedicated front-end readout system (FERS) to process and record the generated signals. This setup was tested successfully on monitoring ion-beam position and profile horizontally and vertically, as well as the beam intensity, for all four ion types with energies from 50 to 430 MeV/u and intensities from 1E2 to 1E7 ions/s. Additionally, time-of-arrival (ToA) measurements on single ions have been successfully performed for a limited intensity range, allowing for ion tracking in a further update. This will reduce noise, and will also improve the accuracy and usability of ion radiography.
In the framework of the LHC Injectors Upgrade Project (LIU), the CERN Proton Synchrotron Booster (PSB) went through major upgrades resulting in new effects to study, challenges to overcome and new parameter regimes to explore. To assess the achievable beam brightness limit of the machine, a series of experimental and computational studies in the transverse planes were performed. In particular, the new injection scheme induces optics perturbations that are strongly enhanced near the half-integer resonance. In this thesis, methods for dynamically measuring and correcting these perturbations and their impact on the beam performance will be presented. Additionally, the quality of the transverse beam distributions and strategies for improvement will be addressed. Finally, the space charge effects when dynamically crossing the half-integer resonance will be characterized. The results of these studies and their broader significance beyond the PSB will be discussed.