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The rapid spread of the Coronavirus (COVID-19) confronts policy makers with the problem of measuring the effectiveness of containment strategies, balancing public health considerations with the economic costs of social distancing measures. We introduce a modified epidemic model that we name the controlled-SIR model, in which the disease reproduction rate evolves dynamically in response to political and societal reactions. An analytic solution is presented. The model reproduces official COVID-19 cases counts of a large number of regions and countries that surpassed the first peak of the outbreak. A single unbiased feedback parameter is extracted from field data and used to formulate an index that measures the efficiency of containment strategies (the CEI index). CEI values for a range of countries are given. For two variants of the controlled-SIR model, detailed estimates of the total medical and socio-economic costs are evaluated over the entire course of the epidemic. Costs comprise medical care cost, the economic cost of social distancing, as well as the economic value of lives saved. Under plausible parameters, strict measures fare better than a hands-off policy. Strategies based on current case numbers lead to substantially higher total costs than strategies based on the overall history of the epidemic.
Living cells constantly remodel the shape of their lipid membranes. In the endo-plasmic reticulum (ER), the reticulon homology domain (RHD) of the reticulophagy regulator 1 (RETR1/FAM134B) forms dense autophagic puncta that are associated with membrane removal by ER-phagy. In molecular dynamics (MD) simulations, we find that FAM134B-RHD spontaneously forms clusters, driven in part by curvature-mediated attraction. At a critical size, the FAM134B-RHD clusters induce the formation of membrane buds. The kinetics of budding depends sensitively on protein concentration and bilayer asymmetry. Our MD simulations shed light on the role of FAM134B-RHD in ER-phagy and show that membrane asymmetry can be used to modulate the kinetics barrier for membrane remodeling.
Living cells constantly remodel the shape of their lipid membranes. In the endoplasmic reticulum (ER), the reticulon homology domain (RHD) of the reticulophagy regulator 1 (RETR1/FAM134B) forms dense autophagic puncta that are associated with membrane removal by ER-phagy. In molecular dynamics (MD) simulations, we find that FAM134B-RHD spontaneously forms clusters, driven in part by curvature-mediated attractions. At a critical size, as in a nucleation process, the FAM134B-RHD clusters induce the formation of membrane buds. The kinetics of budding depends sensitively on protein concentration and bilayer asymmetry. Our MD simulations shed light on the role of FAM134B-RHD in ER-phagy and show that membrane asymmetry can be used to modulate the kinetic barrier for membrane remodeling.
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport. Their intricate 120 MDa architecture remains incompletely understood. Here, we report a near-complete structural model of the human NPC scaffold with explicit membrane and in multiple conformational states. We combined AI-based structure prediction with in situ and in cellulo cryo-electron tomography and integrative modeling. We show that linker Nups spatially organize the scaffold within and across subcomplexes to establish the higher-order structure. Microsecond-long molecular dynamics simulations suggest that the scaffold is not required to stabilize the inner and outer nuclear membrane fusion, but rather widens the central pore. Our work exemplifies how AI-based modeling can be integrated with in situ structural biology to understand subcellular architecture across spatial organization levels.
Direct laser acceleration (DLA) of electrons in a plasma of near-critical electron density (NCD) and the associated synchrotron-like radiation are discussed for moderate relativistic laser intensity (normalized laser amplitude a0 ≤ 4.3) and ps length pulse. This regime is typical of kJ PW-class laser facilities designed for high-energy-density (HED) research. In experiments at the PHELIX facility, it has been demonstrated that interaction of a 1019 W/cm2 sub-ps laser pulse with a sub-mm length NCD plasma results in the generation of high-current well-directed super-ponderomotive electrons with an effective temperature ten times higher than the ponderomotive potential [Rosmej et al., Plasma Phys. Controlled Fusion 62, 115024 (2020)]. Three-dimensional particle-in-cell simulations provide good agreement with the measured electron energy distribution and are used in the current work to study synchrotron radiation from the DLA-accelerated electrons. The resulting x-ray spectrum with a critical energy of 5 keV reveals an ultrahigh photon number of 7 × 1011 in the 1–30 keV photon energy range at the focused laser energy of 20 J. Numerical simulations of betatron x-ray phase contrast imaging based on the DLA process for the parameters of a PHELIX laser are presented. The results are of interest for applications in HED experiments, which require a ps x-ray pulse and a high photon flux.
Binding of the spike protein of SARS-CoV-2 to the human angiotensin-converting enzyme 2 (ACE2) receptor triggers translocation of the virus into cells. Both the ACE2 receptor and the spike protein are heavily glycosylated, including at sites near their binding interface. We built fully glycosylated models of the ACE2 receptor bound to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Using atomistic molecular dynamics (MD) simulations, we found that the glycosylation of the human ACE2 receptor contributes substantially to the binding of the virus. Interestingly, the glycans at two glycosylation sites, N90 and N322, have opposite effects on spike protein binding. The glycan at the N90 site partly covers the binding interface of the spike RBD. Therefore, this glycan can interfere with the binding of the spike protein and protect against docking of the virus to the cell. By contrast, the glycan at the N322 site interacts tightly with the RBD of the ACE2-bound spike protein and strengthens the complex. Remarkably, the N322 glycan binds to a conserved region of the spike protein identified previously as a cryptic epitope for a neutralizing antibody. By mapping the glycan binding sites, our MD simulations aid in the targeted development of neutralizing antibodies and SARS-CoV-2 fusion inhibitors.
By using 6.32 fb−1 of data collected with the BESIII detector at center-of-mass energies between 4.178 and 4.226 GeV, we perform an amplitude analysis of the decay D+s ! K0S + 0 and determine the relative fractions and phase differences of different intermediate processes, which include K0S (770)+, K0S (1450)+, K (892)0 +, K (892)+ 0, and K (1410)0 +. With the detection efficiency based on the amplitude analysis results, the absolute branching fraction is measured to be B(D+s ! K0S + 0) = (5.43 ± 0.30stat ± 0.15syst) × 10−3.
Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1
(2021)
The ER is a key organelle of membrane biogenesis and crucial for the folding of both membrane and secretory proteins. Sensors of the unfolded protein response (UPR) monitor the unfolded protein load in the ER and convey effector functions for maintaining ER homeostasis. Aberrant compositions of the ER membrane, referred to as lipid bilayer stress, are equally potent activators of the UPR. How the distinct signals from lipid bilayer stress and unfolded proteins are processed by the conserved UPR transducer Ire1 remains unknown. Here, we have generated a functional, cysteine-less variant of Ire1 and performed systematic cysteine cross-linking experiments in native membranes to establish its transmembrane architecture in signaling-active clusters. We show that the transmembrane helices of two neighboring Ire1 molecules adopt an X-shaped configuration independent of the primary cause for ER stress. This suggests that different forms of stress converge in a common, signaling-active transmembrane architecture of Ire1.
Background: Organoids are morphologically heterogeneous three-dimensional cell culture systems and serve as an ideal model for understanding the principles of collective cell behaviour in mammalian organs during development, homeostasis, regeneration, and pathogenesis. To investigate the underlying cell organisation principles of organoids, we imaged hundreds of pancreas and cholangiocarcinoma organoids in parallel using light sheet and bright-field microscopy for up to 7 days.
Results: We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation, and degeneration and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation, and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright-field microscopy analysis of entire cultures.
Conclusion: Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying the core regulatory principles of organoid morphogenesis.
The search for short-lived particles is usually the final stage in the chain of event reconstruction and precedes event selection when operating in online mode or physics analysis when operating in offline mode. Most often such short-lived particles are neutral and their search and reconstruction is carried out using their daughter charged particles resulting from their decay.
The use of the missing mass method makes it possible to find and analyze also decays of charged short-lived particles, when one of the daughter particles is neutral and is not registered in the detector system. One of the most known examples of such decays is the decay Σ− → nπ−.
In this paper, we discuss in detail the missing mass method, which was implemented as part of the KF Particle Finder package for the search and analysis of short-lived particles, and describe the use of the method in the STAR experiment (BNL, USA).
The method was used to search for pion (π± → μ±ν) and kaon (K± → μ±ν and K± → π±π0) decays online on the HLT farm in the express production chain. An important feature of the express production chain in the STAR experiment is that it allows one to start calibration, production, and analysis of the data immediately after receiving them.
Here, the particular features and results of the real-time application of the method within the express processing of data obtained in the BES-II program at a beam energy of 3.85 GeV/n when working with a fixed target are presented and discussed.
Lattice constraints on the QCD chiral phase transition at finite temperature and baryon density
(2021)
The thermal restoration of chiral symmetry in QCD is known to proceed by an analytic crossover, which is widely expected to turn into a phase transition with a critical endpoint as the baryon density is increased. In the absence of a genuine solution to the sign problem of lattice QCD, simulations at zero and imaginary baryon chemical potential in a parameter space enlarged by a variable number of quark flavours and quark masses constitute a viable way to constrain the location of a possible non-analytic phase transition and its critical endpoint. In this article I review recent progress towards an understanding of the nature of the transition in the massless limit, and its critical temperature at zero density. Combined with increasingly detailed studies of the physical crossover region, current data bound a possible critical point to μB ≳ 3T.
In dieser Bachelorarbeit werden verschiedene Methoden zur Bestimmung der Betriebsfrequenz von CH-Kavitäten untersucht. Aufgrund der geometrisch komplexen Form der Beschleunigungsstruktur, können die Eigenfrequenzen nicht mithilfe von analytischen Methoden bestimmt werden. Üblicherweise werden die Eigenfrequenzen, ihre Ladungsund Stromdichten, sowie die elektromagnetischen Felder über numerische Methoden der Computational Electromagnetics (CEM) ermittelt. Die CEM ist eine junge Disziplin, deren Performanz und Anwendungsgebiete in den letzten 20 Jahren rapide gewachsen sind. Hauptverantwortlich hierfür ist zum einen das exponentielle Wachstum der Rechenleitung bei gleichbleibenden Kosten, zum anderen die Entwicklung und Verbesserung der Algorithmen. Bis zum Ende des letzten Jahrhunderts wurden elektronische Komponenten hauptsächlich dadurch entwickelt, indem Prototypen angefertigt und analysiert wurden. Diese zeitaufwendige und kostspielige Herangehensweise ist heutzutage nahezu vollständig durch CEM-Simulationen ersetzt worden. Die Hauptmethoden der CEM sind die Finite-Differenzen-Methode (FDM), die Momenten-Methode (MoM) und die Finite-Elemente-Methode (FEM). Für die Bestimmung der Eigenwerte und Eigenvektoren der Beschleunigungsstrukturen eignet sich aufgrund der Stabilität von diesen Dreien am besten die Methode der finiten Elemente. Da die FEM ein rechen- und speicherintensives Verfahren ist, wurde in dieser Arbeit nach einer schnelleren Methode gesucht, um die Betriebsfrequenz von CH-Kavitäten zu bestimmen. Hierfür wurden 84 CH-Kavitäten mithilfe von CST Studio Suite erstellt und simuliert. Es handelt sich hierbei um vier Grundtypen, drei wurden bei einer fixierten Sollfrequenz von 300 MHz konstruiert; die Sollfrequenz des vierten Grundtyps betrug 175 MHz. Die Teilchengeschwindigkeit wurde jeweils in 0,01er-Schrtitten von 0,05 c bis 0,25 c variiert. Aus den Untersuchungen der EM-Felder wurde anschließend ein semi-analytisches Modell entwickelt, das aufgrund der Geometrie der CH-Kavität die Betriebsfrequenz liefern soll.
The magnetic fields generated in non-central heavy-ion collisions are among the strongest fields produced in the Universe, reaching magnitudes comparable to the scale of the strong interactions. Backed by model simulations, the resulting field is expected to be spatially modulated, deviating significantly from the commonly considered uniform profile. To improve our understanding of the physics of quarks and gluons under such extreme conditions, we use lattice QCD simulations with 2+1 staggered fermion flavors with physical quark masses and an inhomogeneous magnetic background for a range of temperatures covering the QCD phase transition. We assume a 1/cosh2 function to model the field profile and vary its strength to analyze the impact on the computed observables and on the transition. We calculate local chiral condensates, local Polyakov loops and estimate the size of lattice artifacts. We find that both observables show non-trivial spatial features due to the interplay between the sea and the valence effects.
We consider a dual representation of an effective three-dimensional Polyakov loop model for the SU(3) theory at nonzero real chemical potential. This representation is free of the sign problem and can be used for numeric Monte-Carlo simulations. These simulations allow us to locate the line of second order phase transitions, that separates the region of first order phase transition from the crossover one. The behavior of local observables in different phases of the model is studied numerically and compared with predictions of the mean-field analysis. Our dual formulation allows us to study also Polyakov loop correlation functions. From these results, we extract the screening masses and compare them with large-N predictions.
The broad class of U(N) and SU(N) Polyakov loop models on the lattice are solved exactly in the combined large N, Nf limit, where N is a number of colors and Nf is a number of quark flavors, and in any dimension. In this ’t Hooft-Veneziano limit the ratio N/Nf is kept fixed. We calculate both the free energy and various correlation functions. The critical behavior of the models is described in details at finite temperatures and non-zero baryon chemical potential. Furthermore, we prove that the calculation of the N-point (baryon) correlation function reduces to the geometric median problem in the confinement phase. In the deconfinement phase we establish an existence of the complex masses and an oscillating decay of correlations in a certain region of parameters.
According to perturbation theory predictions, QCD matter in the zero-temperature, high-density limits of QCD at nonzero isospin chemical potential is expected to be in a superfluid Bardeen-Cooper-Schrieffer (BCS) phase of u and d¯ Cooper pairs. It is also expected, on symmetry grounds, that such phase connects via an analytical crossover to the phase with Bose-Einstein condensation (BEC) of charged pions at μI≥mπ/2. With lattice results, showing some indications that the deconfinement crossover also smoothly penetrates the BEC phase, the conjecture was made that the former connects continuously to the BEC-BCS crossover. We compute the spectrum of the Dirac operator, and use generalized Banks-Casher relations, to test this conjecture and identify signatures of the superfluid BCS phase.
The production of prompt Λ+c baryons at midrapidity (|y|<0.5) was measured in central (0-10%) and mid-central (30-50%) Pb-Pb collisions at the center-of-mass energy per nucleon-nucleon pair sNN−−−√=5.02 TeV with the ALICE detector. The Λ+c production yield, the Λ+c/D0 production ratio, and the Λ+c nuclear modification factor RAA are reported. The results are more precise and more differential in transverse momentum (pT) and centrality with respect to previous measurements. The Λ+c/D0 ratio, which is enhanced with respect to the pp measurement for 4<pT<8 GeV/c, is described by theoretical calculations that model the charm-quark transport in the quark-gluon plasma and include hadronization via both coalescence and fragmentation mechanisms.
The order of the chiral phase transition of lattice QCD with unimproved staggered fermions is known to depend on the number of quark flavours, their masses and the lattice spacing. Previous studies in the literature for Nf∈{3,4} show first-order transitions, which weaken with decreasing lattice spacing. Here we investigate what happens when lattices are made coarser to establish contact to the strong coupling region. For Nf∈{4,8} we find a drastic weakening of the transition when going from Nτ=4 to Nτ=2, which is consistent with a second-order chiral transition reported in the literature for Nf=4 in the strong coupling limit. This implies a non-monotonic behaviour of the critical quark or pseudo-scalar meson mass, which separates first-order transitions from crossover behaviour, as a function of lattice spacing.