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Relative fractions and phases of the intermediate decays are determined. With the detection efficiency estimated by the results of the amplitude analysis, the branching fraction of Dþ s → K−Kþπþπ0 decay is measured to be ð5.42 0.10stat 0.17systÞ%.
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.
In quantum scattering processes between two particles, aspects characterizing the strong and Coulomb forces can be observed in kinematic distributions of the particle pairs. The sensitivity to the interaction potential reaches a maximum at low relative momentum and vanishing distance between the two particles. Ultrarelativistic heavy-ion collisions at the LHC provide an abundant source of many hadron species and can be employed as a measurement method of scattering parameters that is complementary to scattering experiments. This study confirms that momentum correlations of particles produced in Pb–Pb collisions at the LHC provide an accurate measurement of kaon–proton scattering parameters at low relative momentum, allowing precise access to the K−p→K−p process. This work also validates the femtoscopic measurement in ultrarelativistic heavy-ion collisions as an alternative to scattering experiments and a complementary tool to the study of exotic atoms with comparable precision. In this work, the first femtoscopic measurement of momentum correlations of K−p(K+p‾) and K+p(K−p‾) pairs in Pb–Pb collisions at centre-of-mass energy per nucleon pair of sNN=5.02 TeV registered by the ALICE experiment is reported. The components of the K−p complex scattering length are extracted and found to be ℜf0=−0.91±0.03(stat)−0.03+0.17(syst) and ℑf0=0.92±0.05(stat)−0.33+0.12(syst). The results are compared with chiral effective field theory predictions as well as with existing data from dedicated scattering and exotic kaonic atom experiments.
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.
Abstract
The endoplasmic reticulum (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 crosslinking 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.
Summary
The endoplasmic reticulum (ER) is a hotspot of lipid biosynthesis and crucial for the folding of membrane and secretory proteins. The unfolded protein response (UPR) controls the size and folding capacity of the ER. The conserved UPR transducer Ire1 senses both unfolded proteins and aberrant lipid compositions to mount adaptive responses. Using a biochemical assay to study Ire1 in signaling-active clusters, Väth et al. provide evidence that the neighboring transmembrane helices of clustered Ire1 form an ‘X’ irrespectively of the primary cause of ER stress. Hence, different forms of ER stress converge in a common, signaling-active transmembrane architecture of Ire1.
Very-long-baseline interferometry (VLBI) observations of active galactic nuclei at millimetre wavelengths have the power to reveal the launching and initial collimation region of extragalactic radio jets, down to 10–100 gravitational radii (rg ≡ GM/c2) scales in nearby sources. Centaurus A is the closest radio-loud source to Earth. It bridges the gap in mass and accretion rate between the supermassive black holes (SMBHs) in Messier 87 and our Galactic Centre. A large southern declination of −43° has, however, prevented VLBI imaging of Centaurus A below a wavelength of 1 cm thus far. Here we show the millimetre VLBI image of the source, which we obtained with the Event Horizon Telescope at 228 GHz. Compared with previous observations, we image the jet of Centaurus A at a tenfold higher frequency and sixteen times sharper resolution and thereby probe sub-lightday structures. We reveal a highly collimated, asymmetrically edge-brightened jet as well as the fainter counterjet. We find that the source structure of Centaurus A resembles the jet in Messier 87 on ~500 rg scales remarkably well. Furthermore, we identify the location of Centaurus A’s SMBH with respect to its resolved jet core at a wavelength of 1.3 mm and conclude that the source’s event horizon shadow should be visible at terahertz frequencies. This location further supports the universal scale invariance of black holes over a wide range of masses.
Based on an e+e− collision data sample corresponding to an integrated luminosity of 2.93 fb−1 collected with the BESIII detector at √s=3.773 GeV, the first amplitude analysis of the singly Cabibbo-suppressed decay D+→K+K0Sπ0 is performed. From the amplitude analysis, the K∗(892)+K0S component is found to be dominant with a fraction of (57.1±2.6±4.2)%, where the first uncertainty is statistical and the second systematic. In combination with the absolute branching fraction B(D+→K+K0Sπ0) measured by BESIII, we obtain B(D+→K∗(892)+K0S)=(8.69±0.40±0.64±0.51)×10−3, where the third uncertainty is due to the branching fraction B(D+→K+K0Sπ0). The precision of this result is significantly improved compared to the previous measurement. This result also differs from most of theoretical predictions by about 4σ, which may help to improve the understanding of the dynamics behind.
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.
Using 10.1 × 109 J/ψ events produced by the Beijing Electron Positron Collider (BEPCII) at a center-of-mass energy √s = 3.097 GeV and collected with the BESIII detector, we present a search for the rare semi-leptonic decay J/ψ → D−e+νe + c.c. No excess of signal above background is observed, and an upper limit on the branching fraction ℬ(J/ψ → D−e+νe + c. c.) < 7.1 × 10−8 is obtained at 90% confidence level. This is an improvement of more than two orders of magnitude over the previous best limit.
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.