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A single wavelength heterodyne interferometer has been set up to investigate the free electron density integrated axially along the line of sight (line density) in a theta-pinch plasma to determine its applicability as a plasma target for ion beam stripping. The maximal line density reached in this experiment was (3.57 ± 0.28) × 1018 cm−2 at 80 Pa and 20 kV. The findings demonstrate the pulsed character of the line density and its increase by raising the load voltage and the working gas pressure. Additionally, the results were compared with spectroscopic free electron density estimations, which were carried out by Hβ -line broadening and peak separation. The time behavior of the line density indicates that its peak value is delayed by about 10 μs compared to the spectroscopic results. This effect is due to the formation of an extended, magnetically compressed plasma column in the vicinity of the current maximum, although the highest volumetric free electron density is reached near the current zero crossing. Since the line density is an essential parameter in describing the stripping capabilities of the plasma target, the interferometric diagnostic is superior to a spectroscopic diagnostic, because it directly provides integrated values along the line of sight. Furthermore, the measurements of the line density in this experiment partially show nonphysical negative values, which is due to gaseous effects and residual shot vibrations.
We use holography to study the dynamics of a strongly-coupled gauge theory in four-dimensional de Sitter space with Hubble rate H. The gauge theory is non-conformal with a characteristic mass scale M. We solve Einstein’s equations numerically and determine the time evolution of homogeneous gauge theory states. If their initial energy density is high compared with H4 then the early-time evolution is well described by viscous hydrodynamics with a non-zero bulk viscosity. At late times the dynamics is always far from equilibrium. The asymptotic late-time state preserves the full de Sitter symmetry group and its dual geometry is a domain-wall in AdS5. The approach to this state is characterised by an emergent relation of the form P = w ℰ that is different from the equilibrium equation of state in flat space. The constant w does not depend on the initial conditions but only on H/M and is negative if the ratio H/M is close to unity. The event and the apparent horizons of the late-time solution do not coincide with one another, reflecting its non-equilibrium nature. In between them lies an “entanglement horizon” that cannot be penetrated by extremal surfaces anchored at the boundary, which we use to compute the entanglement entropy of boundary regions. If the entangling region equals the observable universe then the extremal surface coincides with a bulk cosmological horizon that just touches the event horizon, while for larger regions the extremal surface probes behind the event horizon.
Biological as well as advanced artificial intelligences (AIs) need to decide which goals to pursue. We review nature's solution to the time allocation problem, which is based on a continuously readjusted categorical weighting mechanism we experience introspectively as emotions. One observes phylogenetically that the available number of emotional states increases hand in hand with the cognitive capabilities of animals and that raising levels of intelligence entail ever larger sets of behavioral options. Our ability to experience a multitude of potentially conflicting feelings is in this view not a leftover of a more primitive heritage, but a generic mechanism for attributing values to behavioral options that can not be specified at birth. In this view, emotions are essential for understanding the mind. For concreteness, we propose and discuss a framework which mimics emotions on a functional level. Based on time allocation via emotional stationarity (TAES), emotions are implemented as abstract criteria, such as satisfaction, challenge and boredom, which serve to evaluate activities that have been carried out. The resulting timeline of experienced emotions is compared with the “character” of the agent, which is defined in terms of a preferred distribution of emotional states. The long-term goal of the agent, to align experience with character, is achieved by optimizing the frequency for selecting individual tasks. Upon optimization, the statistics of emotion experience becomes stationary.
This paper reports on Monte Carlo simulation results for future measurements of the moduli of time-like proton electromagnetic form factors, |GE | and |GM|, using the ¯pp → μ+μ− reaction at PANDA (FAIR). The electromagnetic form factors are fundamental quantities parameterizing the electric and magnetic structure of hadrons. This work estimates the statistical and total accuracy with which the form factors can be measured at PANDA, using an analysis of simulated data within the PandaRoot software framework. The most crucial background channel is ¯pp → π+π−,due to the very similar behavior of muons and pions in the detector. The suppression factors are evaluated for this and all other relevant background channels at different values of antiproton beam momentum. The signal/background separation is based on a multivariate analysis, using the Boosted Decision Trees method. An expected background subtraction is included in this study, based on realistic angular distribuations of the background contribution. Systematic uncertainties are considered and the relative total uncertainties of the form factor measurements are presented.
How long does it take to emit an electron from an atom? This question has intrigued scientists for decades. As such emission times are in the attosecond regime, the advent of attosecond metrology using ultrashort and intense lasers has re-triggered strong interest on the topic from an experimental standpoint. Here, we present an approach to measure such emission delays, which does not require attosecond light pulses, and works without the presence of superimposed infrared laser fields. We instead extract the emission delay from the interference pattern generated as the emitted photoelectron is diffracted by the parent ion’s potential. Targeting core electrons in CO, we measured a 2d map of photoelectron emission delays in the molecular frame over a wide range of electron energies. The emission times depend drastically on the photoelectrons’ emission directions in the molecular frame and exhibit characteristic changes along the shape resonance of the molecule.
Upon antibiotic stress Gram-negative pathogens deploy resistance-nodulation-cell division-type tripartite efflux pumps. These include a H+/drug antiporter module that recognizes structurally diverse substances, including antibiotics. Here, we show the 3.5 Å structure of subunit AdeB from the Acinetobacter baumannii AdeABC efflux pump solved by single-particle cryo-electron microscopy. The AdeB trimer adopts mainly a resting state with all protomers in a conformation devoid of transport channels or antibiotic binding sites. However, 10% of the protomers adopt a state where three transport channels lead to the closed substrate (deep) binding pocket. A comparison between drug binding of AdeB and Escherichia coli AcrB is made via activity analysis of 20 AdeB variants, selected on basis of side chain interactions with antibiotics observed in the AcrB periplasmic domain X-ray co-structures with fusidic acid (2.3 Å), doxycycline (2.1 Å) and levofloxacin (2.7 Å). AdeABC, compared to AcrAB-TolC, confers higher resistance to E. coli towards polyaromatic compounds and lower resistance towards antibiotic compounds.
Many Polyakov loop models can be written in a dual formulation which is free of sign problem even when a non-vanishing baryon chemical potential is introduced in the action. Here, results of numerical simulations of a dual representation of one such effective Polyakov loop model at finite baryon density are presented. We compute various local observables such as energy density, baryon density, quark condensate and describe in details the phase diagram of the model. The regions of the first order phase transition and the crossover, as well as the line of the second order phase transition, are established. We also compute several correlation functions of the Polyakov loops.
We study the μ-μ45-T phase diagram of the 2+1-dimensional Gross-Neveu model, where μ denotes the ordinary chemical potential, μ45 the chiral chemical potential and T the temperature. We use the mean-field approximation and two different lattice regularizations with naive chiral fermions. An inhomogeneous phase at finite lattice spacing is found for one of the two regularizations. Our results suggest that there is no inhomogeneous phase in the continuum limit. We show that a chiral chemical potential is equivalent to an isospin chemical potential. Thus, all results presented in this work can also be interpreted in the context of isospin imbalance.
The phase diagram of the (1+1)-dimensional Gross-Neveu model is reanalyzed for (non-)zero chemical potential and (non-)zero temperature within the mean-field approximation. By investigating the momentum dependence of the bosonic two-point function, the well-known second-order phase transition from the Z2 symmetric phase to the so-called inhomogeneous phase is detected. In the latter phase the chiral condensate is periodically varying in space and translational invariance is broken. This work is a proof of concept study that confirms that it is possible to correctly localize second-order phase transition lines between phases without condensation and phases of spatially inhomogeneous condensation via a stability analysis of the homogeneous phase. To complement other works relying on this technique, the stability analysis is explained in detail and its limitations and successes are discussed in context of the Gross-Neveu model. Additionally, we present explicit results for the bosonic wave-function renormalization in the mean-field approximation, which is extracted analytically from the bosonic two-point function. We find regions -- a so-called moat regime -- where the wave function renormalization is negative accompanying the inhomogeneous phase as expected.
In this work, the phase diagram of the 2+1-dimensional Gross-Neveu model is investigated with baryon chemical potential as well as chiral chemical potential in the mean-field approximation. We study the theory using two lattice discretizations, which are both based on naive fermions. An inhomogeneous chiral phase is observed only for one of the two discretizations. Our results suggest that this phase disappears in the continuum limit.
Understanding the physics of strongly correlated electronic systems has been a central issue in condensed matter physics for decades. In transition metal oxides, strong correlations characteristic of narrow d bands are at the origin of remarkable properties such as the opening of Mott gap, enhanced effective mass, and anomalous vibronic coupling, to mention a few. SrVO3 with V4+ in a 3d1 electronic configuration is the simplest example of a 3D correlated metallic electronic system. Here, the authors' focus on the observation of a (roughly) quadratic temperature dependence of the inverse electron mobility of this seemingly simple system, which is an intriguing property shared by other metallic oxides. The systematic analysis of electronic transport in SrVO3 thin films discloses the limitations of the simplest picture of e–e correlations in a Fermi liquid (FL); instead, it is shown show that the quasi-2D topology of the Fermi surface (FS) and a strong electron–phonon coupling, contributing to dress carriers with a phonon cloud, play a pivotal role on the reported electron spectroscopic, optical, thermodynamic, and transport data. The picture that emerges is not restricted to SrVO3 but can be shared with other 3d and 4d metallic oxides.
The upcoming commissioning of the superconducting (SC) continuous wave Helmholtz linear accelerators first of series cryomodule is going to demand precise alignment of the four internal SC cavities and two SC solenoids. For optimal results, a beam-based alignment method is used to reduce the misalignment of the whole cryomodule, as well as its individual components. A symmetric beam of low transverse emittance is required for this method, which is to be formed by a collimation system. It consists of two separate plates with milled slits, aligned in the horizontal and vertical direction. The collimation system and alignment measurements are proposed, investigated, and realized. The complete setup of this system and its integration into the existing environment at the GSI High Charge State Injector are presented, as well as the results of the recent reference measurements.
Anti-inflammatory effects of low-dose irradiation often follow a non-linear dose–effect relationship. These characteristics were also described for the modulation of leukocyte adhesion to endothelial cells. Previous results further revealed a contribution of reactive oxygen species (ROS) and anti-oxidative factors to a reduced leukocyte adhesion. Here, we evaluated the expression of anti-oxidative enzymes and the transcription factor Nrf2 (Nuclear factor-erythroid-2-related factor 2), intracellular ROS content, and leukocyte adhesion in primary human microvascular endothelial cells (HMVEC) upon low-dose irradiation under physiological laminar shear stress or static conditions after irradiation with X-ray or Carbon (C)-ions (0–2 Gy). Laminar conditions contributed to increased mRNA expression of anti-oxidative factors and reduced ROS in HMVEC following a 0.1 Gy X-ray and 0.5 Gy C-ion exposure, corresponding to reduced leukocyte adhesion and expression of adhesion molecules. By contrast, mRNA expression of anti-oxidative markers and adhesion molecules, ROS, and leukocyte adhesion were not altered by irradiation under static conditions. In conclusion, irradiation of endothelial cells with low doses under physiological laminar conditions modulates the mRNA expression of key factors of the anti-oxidative system, the intracellular ROS contents of which contribute at least in part to leucocyte adhesion, dependent on the radiation source.
Some terms identify enigmata of today’s cosmology: “Inflation” is expected to explain the homogeneity and isotropy of the cosmic background. The repulsive force of a “dark energy” shall prevent a re-collapse of the cosmos. The additional gravitational effect of a “dark matter” was originally supposed to explain the deviations of the rotation curves of the galaxies from Kepler’s laws. Adopting a theory founded on the core notion of absolute quantum information–Protyposis–being a cosmological concept from the outset, the observed phenomena can be explained without postulating further unknown specific “particles” or “fields”. Moreover, this theory allows for a rationalization of the fact that huge black holes with their enormous jet structures, acting as “seeds” of the galaxies, are detected ever closer to the big bang. The problem of the rotation curves in the galaxies can be addressed outside of General Relativity within a Newtonian approximation: by an attenuation of the gravitational acceleration as in the modified Newtonian dynamics, or by the effect of additional invisible “particles of dark matter”, yet unknown and not yet established in natural sciences. Within the Protyposis theory, these problems are solved without having to invent a lot of parameters. The cosmology of the Protyposis causes the change of the gravitational acceleration in the vicinity of large (black hole) masses and, at the same time, avoids a recollapse of the cosmos for which a cosmological constant or “dark energy” was invented.
The RFQ direct injection project (RFQ-DIP) for the neutrino physics experiment IsoDAR aims at an efficient injection of a high-current H²⁺ beam into the dedicated 60 MeV driver cyclotron. Therefore, it is intended to use a compact 32.8 MHz RFQ structure of the split-coaxial type as a pre-buncher. To determine the thermal elongation of the 1.4 m long electrode rods as well as the thermal frequency detuning of the RF structure at a maximum nominal power load of 3.6 kW, an extensive thermal and structural mechanical analysis using COMSOL Multiphysics was conducted. The water heating along the cooling channels as well as the properties of heat transfer from the copper structure to the cooling water were taken into account, which required CFD simulations of the cooling water flow in the turbulent regime. Here we present the methods and results of the sophisticated thermal and structural mechanical simulations using COMSOL and provide a comparison to more simplistic simulations conducted with CST Studio Suite.
We show that the implementation of the 1/c2 transverse current–current interaction between electrons resulting from the non-relativistic QED into the standard self-consistent electron BCS model in bulk under thermal equilibrium in the stable superconductive phase ensures the full compensation of a constant external magnetic field by the internal magnetic field created by the electrons, i.e. one has an ideal diamagnet.
Mixing and magnetic fields in asymptotic giant branch stars in the framework of FRUITY models
(2021)
In the last few years, the modeling of asymptotic giant branch (AGB) stars has been much investigated, both focusing on nucleosynthesis and stellar evolution aspects. Recent advances in the input physics required for stellar computations made it possible to construct more accurate evolutionary models, which are an essential tool to interpret the wealth of available observational and nucleosynthetic data. Motivated by such improvements, the FUNS stellar evolutionary code has been updated. Nonetheless, mixing processes occurring in AGB stars’ interiors are currently not well-understood. This is especially true for the physical mechanism leading to the formation of the 13C pocket, the major neutron source in low-mass AGB stars. In this regard, post-processing s-process models assuming that partial mixing of protons is induced by magneto-hydrodynamics processes were shown to reproduce many observations. Such mixing prescriptions have now been implemented in the FUNS code to compute stellar models with fully coupled nucleosynthesis. Here, we review the new generation of FRUITY models that include the effects of mixing triggered by magnetic fields by comparing theoretical findings with observational constraints available either from the isotopic analysis of trace-heavy elements in presolar grains or from carbon AGB stars and Galactic open clusters.
Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.
Experimental and theoretical studies of fluctuations in nucleus-nucleus interactions at high energies have started to play a major role in understanding of the concept of strong interactions. The elaborated procedures have been developed to disentangle different processes happening during nucleus-nucleus collisions. The fluctuations caused by a variation of the number of nucleons which participated in a collision are frequently considered the unwanted one. The methods to reduce the impact of these fluctuations in fixed-target experiments are reviewed and tested. They can be of key importance in the following ongoing fixed-target heavy-ion experiments: NA61/SHINE at the CERN SPS, STAR-FXT at the BNL RHIC, BMN at JINR Nuclotron, HADES at the GSI SIS18 and in future experiments such as NA60+ at the CERN SPS, CBM at the FAIR SIS100, JHITS at J-PARC-HI MR.
We review the properties of the strongly interacting quark-gluon plasma (QGP) at finite temperature T and baryon chemical potential µB as created in heavy-ion collisions at ultrarelativistic energies. The description of the strongly interacting (non-perturbative) QGP in equilibrium is based on the effective propagators and couplings from the Dynamical QuasiParticle Model (DQPM) that is matched to reproduce the equation-of-state of the partonic system above the deconfinement temperature Tc from lattice QCD. Based on a microscopic transport description of heavy-ion collisions, we discuss which observables are sensitive to the QGP creation and its properties.
A deep convolutional neural network (CNN) is developed to study symmetry energy (Esym(ρ)) effects by learning the mapping between the symmetry energy and the two-dimensional (transverse momentum and rapidity) distributions of protons and neutrons in heavy-ion collisions. Supervised training is performed with labeled data-set from the ultrarelativistic quantum molecular dynamics (UrQMD) model simulation. It is found that, by using proton spectra on event-by-event basis as input, the accuracy for classifying the soft and stiff Esym(ρ) is about 60% due to large event-by-event fluctuations, while by setting event-summed proton spectra as input, the classification accuracy increases to 98%. The accuracies for 5-label (5 different Esym(ρ)) classification task are about 58% and 72% by using proton and neutron spectra, respectively. For the regression task, the mean absolute errors (MAE) which measure the average magnitude of the absolute differences between the predicted and actual L (the slope parameter of Esym(ρ)) are about 20.4 and 14.8 MeV by using proton and neutron spectra, respectively. Fingerprints of the density-dependent nuclear symmetry energy on the transverse momentum and rapidity distributions of protons and neutrons can be identified by convolutional neural network algorithm.
The deuteron coalescence parameter 𝐵2 in proton+proton and nucleus+nucleus collisions in the energy range of √s N N = 900–7000 GeV for proton + proton and √s N N = 2–2760 GeV for nucleus + nucleus collisions is analyzed with the Ultrarelativistic Quantum Molecular Dynamics (UrQMD) transport model, supplemented by an event-by-event phase space coalescence model for deuteron and anti-deuteron production. The results are compared to data by the E866, E877, PHENIX, STAR and ALICE experiments. The 𝐵2 values are calculated from the final spectra of protons and deuterons. At lower energies, √s N N ≤ 20 GeV, B2 drops drastically with increasing energy. The calculations confirm that this is due to the increasing freeze-out volume reflected in B2 ∼ 1/V . At higher energies, √s N N ≥ 20 GeV, B2 saturates at a constant level. This qualitative change and the vanishing of the volume suppression is shown to be due to the development of strong radial flow with increasing energy. The flow leads to strong space-momentum correlations which counteract the volume effect.
The β-barrel assembly machinery (BAM) consisting of the central β-barrel BamA and four other lipoproteins mediates the folding of the majority of the outer membrane proteins. BamA is placed in an asymmetric bilayer and its lateral gate is suggested to be the functional hotspot. Here we used in situ pulsed electron-electron double resonance spectroscopy to characterize BamA in the native outer membrane. In the detergent micelles, the data is consistent with mainly an inward-open conformation of BamA. The native membrane considerably enhanced the conformational heterogeneity. The lateral gate and the extracellular loop 3 exist in an equilibrium between different conformations. The outer membrane provides a favorable environment for occupying multiple conformational states independent of the lipoproteins. Our results reveal a highly dynamic behavior of the lateral gate and other key structural elements and provide direct evidence for the conformational modulation of a membrane protein in situ.
Geometrical frustration among interacting spins combined with strong quantum fluctuations destabilize long-range magnetic order in favor of more exotic states such as spin liquids. By following this guiding principle, a number of spin liquid candidate systems were identified in quasi-two-dimensional (quasi-2D) systems. For 3D, however, the situation is less favorable as quantum fluctuations are reduced and competing states become more relevant. Here we report a comprehensive study of thermodynamic, magnetic and dielectric properties on single crystalline and pressed-powder samples of PbCuTe2O6, a candidate material for a 3D frustrated quantum spin liquid featuring a hyperkagome lattice. Whereas the low-temperature properties of the powder samples are consistent with the recently proposed quantum spin liquid state, an even more exotic behavior is revealed for the single crystals. These crystals show ferroelectric order at TFE ≈ 1 K, accompanied by strong lattice distortions, and a modified magnetic response—still consistent with a quantum spin liquid—but with clear indications for quantum critical behavior.
Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments
(2021)
Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting trajectories, it is common practice to perform a linear fit on mean-squared-displacement curves. However, this strategy is suboptimal and prone to errors. Recently, it was shown that the increments between the observed positions provide a good estimate for the diffusion coefficient, and their statistics are well-suited for likelihood-based analysis methods. Here, we revisit the problem of extracting diffusion coefficients from single-particle tracking experiments subject to static noise and dynamic motion blur using the principle of maximum likelihood. Taking advantage of an efficient real-space formulation, we extend the model to mixtures of subpopulations differing in their diffusion coefficients, which we estimate with the help of the expectation–maximization algorithm. This formulation naturally leads to a probabilistic assignment of trajectories to subpopulations. We employ the theory to analyze experimental tracking data that cannot be explained with a single diffusion coefficient. We test how well a dataset conforms to the assumptions of a diffusion model and determine the optimal number of subpopulations with the help of a quality factor of known analytical distribution. To facilitate use by practitioners, we provide a fast open-source implementation of the theory for the efficient analysis of multiple trajectories in arbitrary dimensions simultaneously.
Abstract
The primary immunological target of COVID-19 vaccines is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface and mediates viral entry into the host cell. To identify possible antibody binding sites, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation, and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for structure-based vaccine design. We find that the extensive and inherently flexible glycan coat shields a surface area larger than expected from static structures, highlighting the importance of structural dynamics. The protective glycan shield and the high flexibility of its hinges give the stalk overall low epitope scores. Our computational epitope-mapping procedure is general and should thus prove useful for other viral envelope proteins whose structures have been characterized.
Author summary
The SARS-CoV-2 virus has caused a global health crisis. The spike protein exposed at its surface is key for infection and the primary antibody target. However, spike is covered by highly mobile glycan molecules that could impair antibody binding. To identify accessible epitopes, we performed molecular dynamics simulations of an atomistic model of glycosylated spike embedded in a membrane. By combining extensive simulations with bioinformatics analyses, we recovered known antibody binding sites and identified several epitope candidates as targets for further vaccine development.
As part of the research for this thesis, a momentum spectrometer was set up and initial measurements on accelerated ions were performed. For this purpose, the necessary hardware for the operation of the spectrometer and for high-precision measurements was were assembled. A control system for remote operation was developed and the spectrometer was installed at the used beamline.
There, measurements of low-energy ion beams in superposition with electrons confined in a Gabor lens can be carried out.
Investigations were made on both the Gabor lens-generated ions and the beam ions, leading to first results regarding the charge changes of beam ions during propagation through an electron atmosphere.
Using combined data from the Relativistic Heavy Ion and Large Hadron Colliders, we constrain the shear and bulk viscosities of quark-gluon plasma (QGP) at temperatures of ∼150–350 MeV. We use Bayesian inference to translate experimental and theoretical uncertainties into probabilistic constraints for the viscosities. With Bayesian model averaging we propagate an estimate of the model uncertainty generated by the transition from hydrodynamics to hadron transport in the plasma’s final evolution stage, providing the most reliable phenomenological constraints to date on the QGP viscosities.
During infection the SARS-CoV-2 virus fuses its viral envelope with cellular membranes of its human host. Initial contact with the host cell and membrane fusion are both mediated by the viral spike (S) protein. Proteolytic cleavage of S at the S2′ site exposes its 40 amino acid long fusion peptide (FP). Binding of the FP to the host membrane anchors the S2 domain of S in both the viral and the host membrane. The reorganization of S2 then pulls the two membranes together. Here we use molecular dynamics (MD) simulations to study the two core functions of the SARS-CoV-2 FP: to attach quickly to cellular membranes and to form an anchor strong enough to withstand the mechanical force during membrane fusion. In eight 10 μs-long MD simulations of FP in proximity to endosomal and plasma membranes, we find that FP binds spontaneously to the membranes and that binding proceeds predominantly by insertion of two short amphipathic helices into the membrane interface. Connected via a flexible linker, the two helices can bind the membrane independently, yet binding of one promotes the binding of the other by tethering it close to the target membrane. By simulating mechanical pulling forces acting on the C-terminus of the FP we then show that the bound FP can bear forces up to 250 pN before detaching from the membrane. This detachment force is more than ten-fold higher than an estimate of the force required to pull host and viral membranes together for fusion. We identify a fully conserved disulfide bridge in the FP as a major factor for the high mechanical stability of the FP membrane anchor. We conclude, first, that the sequential binding of two short amphipathic helices allows the SARS-CoV-2 FP to insert quickly into the target membrane, before the virion is swept away after shedding the S1 domain connecting it to the host cell receptor. Second, we conclude that the double attachment and the conserved disulfide bridge establish the strong anchoring required for subsequent membrane fusion. Multiple distinct membrane-anchoring elements ensure high avidity and high mechanical strength of FP-membrane binding.
Transport of lipids across membranes is fundamental for diverse biological pathways in cells. Multiple ion-coupled transporters participate 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 acids 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.
We extend the standard solid-state quantum mechanical Hamiltonian containing only Coulomb interactions between the charged particles by inclusion of the (transverse) current-current diamagnetic interaction starting from the non-relativistic QED restricted to the states without photons and neglecting the retardation in the photon propagator. This derivation is supplemented with a derivation of an analogous result along the non-rigorous old classical Darwin-Landau-Lifshitz argumentation within the physical Coulomb gauge.
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.
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.
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.
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 direct study of transcription or DNA–protein-binding events, requires imaging of individual genes at molecular resolution. Electron microscopy (EM) can show local detail of the genome. However, direct visualization and analysis of specific individual genes is currently not feasible as they cannot be unambiguously localized in the crowded, landmark-free environment of the nucleus. Here, we present a method for the genomic insertion of gene clusters that can be localized and imaged together with their associated protein complexes in the EM. The method uses CRISPR/Cas9 technology to incorporate several genes of interest near the 35S rRNA gene, which is a frequently occurring, easy-to-identify genomic locus within the nucleolus that can be used as a landmark in micrographs. As a proof of principle, we demonstrate the incorporation of the locus-native gene RDN5 and the locus-foreign gene HSX1. This led to a greater than 7-fold enrichment of RNA polymerase III (Pol III) complexes associated with the genes within the field of view, allowing for a significant increase in the analysis yield. This method thereby allows for the insertion and direct visualization of gene clusters for a range of analyses, such as changes in gene activity upon alteration of cellular or external factors.
Die vorliegende Arbeit präsentiert Forschungsarbeiten basierend auf nanoskopischen Oberflächenmessungen an plasmonischen Metaoberflächen und zweidimensionalen Materialien, insbesondere dem halbleitenden Übergangsmetal-Dichalcogenid (TMDC) WS_2. Die Thesis ist in sieben Kapitel untergegliedert. Die Einleitung vermittelt einen Überblick über die treibenden Kräfte hinter der Forschung im Bereich der Nanophotonik an zweidimensionalen Materialsystemen. Die Untersuchung der Licht-Materie-Wechselwirkung an dünnen Materialgrenzflächen zieht sich als roter Faden durch die gesamte Arbeit.
Das zweite Kapitel beschreibt den experimentellen Aufbau, der für die Durchführung der nanoskopischen Messungen in dieser Arbeit implementiert wurde. Es werden theoretische Grundlagen, das Messprinzip und die Implementierung des optischen Rasternahfeldmikroskops (s-SNOM) skizziert. Außerdem wird ein Strom-Spannungs-Rasterkraftmikroskop (c-AFM) im Kontaktmodus genutzt, um elektrische Ströme auf mikroskopischen zweidimensionalen TMDC-Terrassen zu messen. In den darauffolgenden vier Kapiteln werden die Beiträge dieser Arbeit zur Untersuchung der Licht-Materie-Wechselwirkung auf der Nanoskala aus verschiedenen Perspektiven vorgestellt. Jedes Kapitel enthält eine kurze Einleitung, einen Theorieteil, Messdaten oder Simulationsergebnisse sowie eine Analyse; vervollständigt durch einen Schlussteil.
Die zentrale Arbeit an einer metallischen Metaoberfläche aus elliptischen Goldscheiben wird in Kapitel 3 vorgestellt. Der zugehörige Theorieteil führt in das Konzept von Oberflächen-Plasmon-Polaritonen (SPP) ein, das für den Forschungsbereich der Plasmonik im Allgemeinen wesentlich ist. Verschiedene Methoden zur Berechnung der Dispersionsrelation dieser Oberflächenmoden an ein- und mehrschichtigen Grenzflächen werden auf die untersuchte Metaoberflächenprobe angewendet. Das Modell sagt drei verschiedene Moden voraus, die sich an der Grenzfläche ausbreiten. Eine teil-gebundene ins Substrat abstrahlende Oberflächenmode sowie zwei vergrabene stark gebundene anisotrope Moden. Eine auf der Probe platzierte Nanokugel aus Silizium wird als radiale Anregungsquelle verwendet.
Der Vergleich mit s-SNOM-Nahfeldbildern zeigt, dass nur die schwach gebundene geführte Modenresonanz ausreichend angeregt wurde, um durch s-SNOM-Bildgebung nachgewiesen werden zu können. Die schwache Oberflächenbindung erklärt die scheinbar isotrope Ausbreitung auf der anisotropen Oberfläche. Die Beobachtung der verbleibenden stark eingegrenzten anisotropen vergrabenen Moden würde eine verbesserte tiefenempfindliche Auflösung des Systems erfordern, die im Prinzip für Schichtdicken von 20 nm möglich sein sollte. Darüber hinaus wirft die Beobachtung die Frage auf, ob die durch Impuls- und Modenvolumenanpassung der Nanokugel gegebene Anregungseffizienz einen ausreichenden Anregungsquerschnitt erzeugt, um nachweisbare vergrabene SPP-Moden zu erzeugen.
In Kapitel 4 wird die Idee der Visualisierung vergrabener elektrischer Felder mit s-SNOM fortgesetzt. Hier wird es auf die Untersuchung von WS_2 angewendet, einem zweidimensionalen TMDC-Material, welches Photolumineszenz zeigt. Durch die Strukturierung des Galliumphosphid-Substrats unter der hängenden Monolage, die von einer dünnen Schicht aus hBN getragen wird, wird die Photolumineszenzausbeute um den Faktor 10 erhöht. Dies wird durch den Entwurf einer lateralen DBR-Mikrokavität mit zusätzlich optimierter vertikaler Tiefe erreicht, die in das Substrat geätzt wurde.
Die hochauflösende Abbildung der elektrischen Feldverteilung im Resonator wird durch den Einsatz von s-SNOM ermöglicht, um die Verbesserung der Einkopplung durch diese beiden Ansätze zu bewerten. Es konnte festgestellt werden, dass die laterale Struktur überwiegend zur verstärkten Photolumineszenzausbeute beiträgt, während für die Einkopplung keine offensichtliche Verstärkung auf die vertikale Strukturoptimierung zurückgeführt werden konnte.
Das zweidimensionale Material WS_2 wird in Kapitel 5 erneut mit Hilfe von c-AFM untersucht. Unterschiedlich dicke Multilagen auf Graphen und Gold dienen als Tunnelbarrieren für vertikale Ströme zwischen Substrat und leitender c-AFM-Messpitze. Die Daten können mit einem Fowler-Nordheim-Modell mit Parametern für die Tunnelbreite und Schottky-Barrierenhöhen der beiden Grenzflächen erklärt werden. Die Messungen zeigen jedoch eine schwache Reproduzierbarkeit, was eine detailliertere Zusammenfassung der relevanten Fehlerquellen erfordert. In der Schlussfolgerung des Kapitels werden mehrere Schlüsselaspekte vorgeschlagen, die bei künftigen Messungen berücksichtigt werden sollten. Entscheidend ist, dass c-AFM sehr empfindlich auf die Adsorption von Wasserfilmen an der Probenoberfläche reagiert, worunter WS_2-Oberflächen unter Umgebungsbedingungen leiden...
NeuLAND (New Large-Area Neutron Detector) is the next-generation neutron detector for the R3B (Reactions with Relativistic Radioactive Beams) experiment at FAIR (Facility for Antiproton and Ion Research). NeuLAND detects neutrons with energies from 100 to 1000 MeV, featuring a high detection efficiency, a high spatial and time resolution, and a large multi-neutron reconstruction efficiency. This is achieved by a highly granular design of organic scintillators: 3000 individual submodules with a size of 5 × 5 × 250 cm3 are arranged in 30 double planes with 100 submodules each, providing an active area of 250 × 250 cm2 and a total depth of 3 m. The spatial resolution due to the granularity together with a time resolution of 150 ps ensures high-resolution capabilities. In conjunction with calorimetric properties, a multi-neutron reconstruction efficiency of 50% to 70% for four-neutron events will be achieved, depending on both the emission scenario and the boundary conditions allowed for the reconstruction method. We present in this paper the final design of the detector as well as results from test measurements and simulations on which this design is based.
Quasi-universal behavior of the threshold mass in unequal-mass, spinning binary neutron star mergers
(2021)
The lifetime of the remnant produced by the merger of two neutron stars can provide a wealth of information on the equation of state of nuclear matter and on the processes leading to the electromagnetic counterpart. Hence, it is essential to determine when this lifetime is the shortest, corresponding to when the remnant has a mass equal to the threshold mass, Mth, to prompt collapse to a black hole. We report on the results of more than 360 simulations of merging neutron-star binaries covering 40 different configurations differing in mass ratio and spin of the primary. Using this data, we have derived a quasi-universal relation for Mth and expressed its dependence on the mass ratio and spin of the binary. The new expression recovers the results of Koeppel et al. for equal-mass, irrotational binaries and reveals that Mth can increase (decrease) by 5% (10%) for binaries that have spins aligned (antialigned) with the orbital angular momentum and provides evidence for a nonmonotonic dependence of Mth on the mass asymmetry in the system. Finally, we extend to unequal masses and spinning binaries the lower limits that can be set on the stellar radii once a neutron star binary is detected, illustrating how the merger of an unequal-mass, rapidly spinning binary can significantly constrain the allowed values of the stellar radii.
Neutron-induced cross sections of short-lived nuclei are highly relevant in many domains such as fundamental nuclear physics, astrophysics and applications in nuclear technology. In particular, these cross sections are essential for understanding the synthesis of elements via the s- and r stellar processes. However, the measurement of such cross sections with current techniques is very difficult or even impossible, because of the difficulties to produce and handle the necessary amounts of radioactive nuclei. Reaching the nuclei of interest is only possible by inverting the reaction kinematics with radioactive beams.
In this contribution we present a project for indirectly determining neutron cross sections via the surrogate-reaction method. This project is based on the measurement of transfer- or inelastic-scattering-induced decay probabilities in inverse kinematics at storage rings. The measured probabilities are then used to tune nuclear-reaction models that will provide much more accurate predictions of the desired neutron cross sections. We also discuss a very ambitious, long-term project to directly measure neutron cross sections in inverse kinematics. It consists in the combination of a radioactive beam facility, an ion storage ring and a spallation neutron source.
When a very strong light field is applied to a molecule an electron can be ejected by tunneling. In order to quantify the time-resolved dynamics of this ionization process, the concept of the Wigner time delay can be used. The properties of this process can depend on the tunneling direction relative to the molecular axis. Here, we show experimental and theoretical data on the Wigner time delay for tunnel ionization of H2 molecules and demonstrate its dependence on the emission direction of the electron with respect to the molecular axis. We find, that the observed changes in the Wigner time delay can be quantitatively explained by elongated/shortened travel paths of the emitted electrons, which occur due to spatial shifts of the electrons’ birth positions after tunneling. Our work provides therefore an intuitive perspective towards the Wigner time delay in strong-field ionization.
Classical light microscopy is one of the main tools for science to study small things. Microscopes and their technology and optics have been developed and improved over centuries, however their resolution is ultimately restricted physically by the diffraction of light based on its wave nature described by Maxwell’s equations. Hence, the nanoworld – often characterized by sub-100-nm structural sizes – is not accessible with classical far-field optics (apart from special x-ray laser concepts) since its lateral resolution scales with the wavelength.
It was not until the 20th century that various technologies emerged to circumvent the diffraction limit, including so-called near-field microscopy. Although conceptually based on Maxwell’s long known equations, it took a long time for the scientific community to recognize its powerful opportunities and the first embodiments of near-field microscopes were developed. One representative of them is the scattering-type Scanning Near-field Optical Microscope (s-SNOM). It is a Scanning Probe Microscope (SPM) that enables imaging and spectroscopy at visible light frequencies down to even radio waves with a sub-100-nm resolution regardless of the wavelength used. This work also reflects this wide spectral range as it contains applications from near-infrared light down to deep THz/GHz radiation.
This thesis is subdivided into two parts. First, new experimental capabilities for the s-SNOM are demonstrated and evaluated in a more technical manner. Second, among other things, these capabilities are used to study various transport phenomena in solids, as already indicated in the title.
On the technical side, preliminary studies on the suitability of the qPlus sensor – a novel scanning probe technology – for near-field microscopy are presented.
The scanning head incorporating the qPlus sensor–named TRIBUS – is originally intended and built for ultra-high vacuum, low temperature, and high resolution applications. These are desirable environments and properties for sensitive nearfield measurements as well. However, since its design was not planned for near-field measurements, several special technical and optical aspects have to be taken into account, among others the scanning tip design and a spring suspended measurement head.
In addition, in this thesis field-effect transistors are used as THz detectors in an s-SNOM for the first time. Although THz s-SNOM is already an emerging technology, it still suffers from the requirements of sophisticated and specialized infrastructure on both the detector and laser side. Field-effect transistors offer an alternative that is flexible, cost-efficient, room-temperature operating, and easy to handle. Here, their suitability for s-SNOM measurements, which in general require very sensitive and fast detectors, is evaluated.
In the scientific part of this thesis, electromagnetic surface waves on silver nanowires and the conductivity/charge carrier density in silicon are investigated. Both are completely different concepts of transport phenomena, but this already shows the general versatility of the s-SNOM as it can enter both fields. Silver nanowires are analysed by means of near-infrared radiation. Their plasmonic behaviour in this spectral region is studied complementing other simulations and studies in literature performed on them using for example far-field optics.
Furthermore, the surface wave imaging ability of the s-SNOM in the near-infrared regime is thoroughly investigated in this thesis. Mapping surface waves in the mid-infrared regime is widespread in the community, however for much smaller wavelengths there are several important aspects to be considered additionally, such as the smaller focal spot size.
After that, doped and photo-excited silicon substrates are investigated. As the characteristic frequencies of charge carriers in semiconductors – described by the plasma frequency and the Drude model – are within the THz range, the THz s-SNOM is very well suited to probe their behaviour and to reveal contrasts, which has already been shown qualitatively by numerous literature reports. Here, the photo-excitation enables to set and tune the charge carrier density continuously.
Furthermore, the analysis of all silicon samples focuses on a quantitative extraction of the charge carrier densities and doping levels ...
We investigate general properties of the eigenvalue spectrum for improved staggered quarks. We introduce a new chirality operator [y5⊗1] and a new shift operator [1⊗ξ5], which respect the same recursion relation as the γ5 operator in the continuum. Then we show that matrix elements of the chirality operator sandwiched between two eigenstates of the staggered Dirac operator are related to those of the shift operator by the Ward identity of the conserved U (1)A symmetry of staggered fermion actions. We perform a numerical study in quenched QCD using HYP staggered quarks to demonstrate the Ward identity. We introduce a new concept of leakage patterns which collectively represent the matrix elements of the chirality operator and the shift operator sandwiched between two eigenstates of the staggered Dirac operator. The leakage pattern provides a new method to identify zero modes and nonzero modes in the Dirac eigenvalue spectrum. This method is as robust as the spectral flow method but requires much less computing power. Analysis using a machine learning technique confirms that the leakage pattern is universal, since the staggered Dirac eigenmodes on normal gauge configurations respect it. In addition, the leakage pattern can be used to determine a ratio of renormalization factors as a by-product. We conclude that it might be possible and realistic to measure the topological charge Q using the Atiya-Singer index theorem and the leakage pattern of the chirality operator in the staggered fermion formalism.
We derive the collision term in the Boltzmann equation using the equation of motion for the Wigner function of massive spin-1/2 particles. To next-to-lowest order in h, it contains a nonlocal contribution, which is responsible for the conversion of orbital into spin angular momentum. In a proper choice of pseudogauge, the antisymmetric part of the energy-momentum tensor arises solely from this nonlocal contribution. We show that the collision term vanishes in global equilibrium and that the spin potential is, then, equal to the thermal vorticity. In the nonrelativistic limit, the equations of motion for the energy-momentum and spin tensors reduce to the well-known form for hydrodynamics for micropolar fluids.
During infection the SARS-CoV-2 virus fuses its viral envelope with cellular membranes of its human host. The viral spike (S) protein mediates both the initial contact with the host cell and the subsequent membrane fusion. Proteolytic cleavage of S at the S2′ site exposes its fusion peptide (FP) as the new N-terminus. By binding to the host membrane, the FP anchors the virus to the host cell. The reorganization of S2 between virus and host then pulls the two membranes together. Here we use molecular dynamics (MD) simulations to study the two core functions of the SARS-CoV-2 FP: to attach quickly to cellular membranes and to form an anchor strong enough to withstand the mechanical force during membrane fusion. In eight 10 μs long MD simulations of FP in proximity to endosomal and plasma membranes, we find that FP binds spontaneously to the membranes and that binding proceeds predominantly by insertion of two short amphipathic helices into the membrane interface. Connected via a flexible linker, the two helices can bind the membrane independently, yet binding of one promotes the binding of the other by tethering it close to the target membrane. By simulating mechanical pulling forces acting on the C-terminus of the FP, we then show that the bound FP can bear forces up to 250 pN before detaching from the membrane. This detachment force is more than 10-fold higher than an estimate of the force required to pull host and viral membranes together for fusion. We identify a fully conserved disulfide bridge in the FP as a major factor for the high mechanical stability of the FP membrane anchor. We conclude, first, that the sequential binding of two short amphipathic helices allows the SARS-CoV-2 FP to insert quickly into the target membrane, before the virion is swept away after shedding the S1 domain connecting it to the host cell receptor. Second, we conclude that the double attachment and the conserved disulfide bridge establish the strong anchoring required for subsequent membrane fusion. Multiple distinct membrane-anchoring elements ensure high avidity and high mechanical strength of FP–membrane binding.
Famotidine inhibits toll-like receptor 3-mediated inflammatory signaling in SARS-CoV-2 infection
(2021)
Apart from prevention using vaccinations, the management options for COVID-19 remain limited. In retrospective cohort studies, use of famotidine, a specific oral H2 receptor antagonist (antihistamine), has been associated with reduced risk of intubation and death in patients hospitalized with COVID-19. In a case series, nonhospitalized patients with COVID-19 experienced rapid symptom resolution after taking famotidine, but the molecular basis of these observations remains elusive. Here we show using biochemical, cellular, and functional assays that famotidine has no effect on viral replication or viral protease activity. However, famotidine can affect histamine-induced signaling processes in infected Caco2 cells. Specifically, famotidine treatment inhibits histamine-induced expression of Toll-like receptor 3 (TLR3) in SARS-CoV-2 infected cells and can reduce TLR3-dependent signaling processes that culminate in activation of IRF3 and the NF-κB pathway, subsequently controlling antiviral and inflammatory responses. SARS-CoV-2-infected cells treated with famotidine demonstrate reduced expression levels of the inflammatory mediators CCL-2 and IL6, drivers of the cytokine release syndrome that precipitates poor outcome for patients with COVID-19. Given that pharmacokinetic studies indicate that famotidine can reach concentrations in blood that suffice to antagonize histamine H2 receptors expressed in mast cells, neutrophils, and eosinophils, these observations explain how famotidine may contribute to the reduced histamine-induced inflammation and cytokine release, thereby improving the outcome for patients with COVID-19.