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Cellular informational and metabolic processes are propagated with specific membrane fusions governed by soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNARE). SNARE protein Ykt6 is highly expressed in brain neurons and plays a critical role in the membrane-trafficking process. Studies suggested that Ykt6 undergoes a conformational change at the interface between its longin domain and the SNARE core. In this work, we study the conformational state distributions and dynamics of rat Ykt6 by means of single-molecule Förster Resonance Energy Transfer (smFRET) and Fluorescence Cross-Correlation Spectroscopy (FCCS). We observed that intramolecular conformational dynamics between longin domain and SNARE core occurred at the timescale ~200 μs. Furthermore, this dynamics can be regulated and even eliminated by the presence of lipid dodecylphoshpocholine (DPC). Our molecular dynamic (MD) simulations have shown that, the SNARE core exhibits a flexible structure while the longin domain retains relatively stable in apo state. Combining single molecule experiments and theoretical MD simulations, we are the first to provide a quantitative dynamics of Ykt6 and explain the functional conformational change from a qualitative point of view.
The pathological skin phenotype caused by hyperglycemia is an important indicator for the progress of diabetes mellitus. An early detection of diabetes assures an early intervention to regulate the carbohydrate metabolism. In this publication a non-invasive detection principle based on the measurement of complex scattering parameters in the millimeter-wave frequency range is presented. The measurement principle provides evidence of the applicability for the identification of different glycemic states in animal models. The method proposed here can be used to predict diabetes status in animal models and is interesting for application on humans in view of safeness of millimeter-wave radiation. Furthermore the complex scattering parameters give important information about the anatomic varieties between the analyzed skin samples of the different mice strains. In contrast to other methods, our approach is less sensitive to skin variations between animals.
A primordial state of matter consisting of free quarks and gluons that existed in the early universe a few microseconds after the Big Bang is also expected to form in high-energy heavy-ion collisions. Determining the equation of state (EoS) of such a primordial matter is the ultimate goal of high-energy heavy-ion experiments. Here we use supervised learning with a deep convolutional neural network to identify the EoS employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering the nature of the phase transition in quantum chromodynamics. Such EoS-meter is model-independent and insensitive to other simulation inputs including the initial conditions for hydrodynamic simulations.
The radiative capture cross section of 238U is very important for the developing of new reactor technologies and the safety of existing ones. Here the preliminary results of the 238U(n,γ) cross section measurement performed at n_TOF with C6D6 scintillation detectors are presented, paying particular attention to data reduction and background subtraction.
The toolbox for imaging molecules is well-equipped today. Some techniques visualize the geometrical structure, others the electron density or electron orbitals. Molecules are many-body systems for which the correlation between the constituents is decisive and the spatial and the momentum distribution of one electron depends on those of the other electrons and the nuclei. Such correlations have escaped direct observation by imaging techniques so far. Here, we implement an imaging scheme which visualizes correlations between electrons by coincident detection of the reaction fragments after high energy photofragmentation. With this technique, we examine the H2 two-electron wave function in which electron–electron correlation beyond the mean-field level is prominent. We visualize the dependence of the wave function on the internuclear distance. High energy photoelectrons are shown to be a powerful tool for molecular imaging. Our study paves the way for future time resolved correlation imaging at FELs and laser based X-ray sources.
Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of Thermus thermophilus is an oligomer of the 757-residue PilQ protein, essential for DNA uptake and pilus extrusion. Here, we present the cryo-EM structure of this bifunctional complex at a resolution of ~7 Å using a new reconstruction protocol. Thirteen protomers form a large periplasmic domain of six stacked rings and a secretin domain in the outer membrane. A homology model of the PilQ protein was fitted into the cryo-EM map. A crown-like structure outside the outer membrane capping the secretin was found not to be part of PilQ. Mutations in the secretin domain disrupted the crown and abolished DNA uptake, suggesting a central role of the crown in natural transformation.
Electromagnetic calorimeter (ECAL) is being developed to complement dilepton spectrometer HADES. ECAL will enable the HADES@FAIR experiment to measure data on neutral meson production in heavy ion collisions at the energy range of 2-10 AGeV on the beam of future accelerator SIS100@FAIR. We will report results of the last beam test with quasi-monoenergetic photons carried out in MAMI facility at Johannes Gutenberg Universität Mainz.
Ion channel gating is essential for cellular homeostasis and is tightly controlled. In some eukaryotic and most bacterial ligand-gated K+ channels, RCK domains regulate ion fluxes. Until now, a single regulatory mechanism has been proposed for all RCK-regulated channels, involving signal transduction from the RCK domain to the gating area. Here, we present an inactive ADP-bound structure of KtrAB from Vibrio alginolyticus, determined by cryo-electron microscopy, which, combined with EPR spectroscopy and molecular dynamics simulations, uncovers a novel regulatory mechanism for ligand-induced action at a distance. Exchange of activating ATP to inactivating ADP triggers short helical segments in the K+-translocating KtrB dimer to organize into two long helices that penetrate deeply into the regulatory RCK domains, thus connecting nucleotide-binding sites and ion gates. As KtrAB and its homolog TrkAH have been implicated as bacterial pathogenicity factors, the discovery of this functionally relevant inactive conformation may advance structure-guided drug development.
Recently the Universal Linear Accelerator (UNILAC) serves as a powerful high duty factor (25%) heavy ion beam accelerator for the ambitious experiment program at GSI. Beam time availability for SHE (Super Heavy Element)-research will be decreased due to the limitation of the UNILAC providing Uranium beams with an extremely high peak current for FAIR simultaneously. To keep the GSI-SHE program competitive on a high level and even beyond, a standalone superconducting continuous wave (100% duty factor) LINAC in combination with the upgraded GSI High Charge State injector is envisaged. In preparation for this, the first LINAC section (financed by HIM and GSI) will be tested with beam in 2017, demonstrating the future experimental capabilities. Further on the construction of an extended cryo module comprising two shorter Crossbar-H cavities is foreseen to test until end of 2017. As a final R&D step towards an entire LINAC three advanced cryo modules, each comprising two CH cavities, should be built until 2019, serving for first user experiments at the Coulomb barrier.
The quark gluon plasma produced in heavy ion collisions behaves like an almost ideal fluid described by viscous hydrodynamics with a number of transport coefficients. The second order coefficient κ is related to a Euclidean correlator of the energy-momentum tensor at vanishing frequency and low momentum. This allows for a lattice determination without maximum entropy methods or modelling, but the required lattice sizes represent a formidable challenge. We calculate κ in leading order lattice perturbation theory and simulations on 1203 × 6, 8 lattices with a < 0.1 fm. In the temperature range 2Tc − 10Tc we find κ = 0.36(15)T2. The error covers both a suitably rescaled AdS/CFT prediction as well as, remarkably, the result of leading order perturbation theory. This suggests that appropriate noise reduction methods on the lattice and NLO perturbative calculations could provide an accurate QCD prediction in the near future.
The study of lattice gauge theories with Monte Carlo simulations is hindered by the infamous sign problem that appears under certain circumstances, in particular at non-zero chemical potential. So far, there is no universal method to overcome this problem. However, recent years brought a new class of non-perturbative Hamiltonian techniques named tensor networks, where the sign problem is absent. In previous work, we have demonstrated that this approach, in particular matrix product states in 1+1 dimensions, can be used to perform precise calculations in a lattice gauge theory, the massless and massive Schwinger model. We have computed the mass spectrum of this theory, its thermal properties and real-time dynamics. In this work, we review these results and we extend our calculations to the case of two flavours and non-zero chemical potential. We are able to reliably reproduce known analytical results for this model, thus demonstrating that tensor networks can tackle the sign problem of a lattice gauge theory at finite density
The detailed biophysical mechanisms through which transcranial magnetic stimulation (TMS) activates cortical circuits are still not fully understood. Here we present a multi-scale computational model to describe and explain the activation of different pyramidal cell types in motor cortex due to TMS. Our model determines precise electric fields based on an individual head model derived from magnetic resonance imaging and calculates how these electric fields activate morphologically detailed models of different neuron types. We predict neural activation patterns for different coil orientations consistent with experimental findings. Beyond this, our model allows us to calculate activation thresholds for individual neurons and precise initiation sites of individual action potentials on the neurons’ complex morphologies. Specifically, our model predicts that cortical layer 3 pyramidal neurons are generally easier to stimulate than layer 5 pyramidal neurons, thereby explaining the lower stimulation thresholds observed for I-waves compared to D-waves. It also shows differences in the regions of activated cortical layer 5 and layer 3 pyramidal cells depending on coil orientation. Finally, it predicts that under standard stimulation conditions, action potentials are mostly generated at the axon initial segment of cortical pyramidal cells, with a much less important activation site being the part of a layer 5 pyramidal cell axon where it crosses the boundary between grey matter and white matter. In conclusion, our computational model offers a detailed account of the mechanisms through which TMS activates different cortical pyramidal cell types, paving the way for more targeted application of TMS based on individual brain morphology in clinical and basic research settings.
Motivated by the necessary replacement of the GSI UNILAC poststripper linac, a compact and efficient linac design based on IH-type cavities has been developed. Using KONUS beam dynamics, it was possible to design a linac consisting of only five cavities that can be operated by the existing UNILAC RF amplifier structure. The transversal focusing scheme is based on magnetic quadrupole triplet lenses. The optimized design provides full transmission and low emittance growth for the design current of 15 emA U28+, accelerating the beam from 1.4 MeV/u to 11.4 MeV/u. Extensive error studies were performed to define tolerances and verify the stability of the design with respect to misalignment and injection parameters. The design provides a compact and cost effective alternative to a new Alvarez linac. With a total length of just 22.8 meters it will leave room for future energy upgrades in the UNILAC tunnel.
Relativistic jets from active galactic nuclei (AGN) often display a non-uniform structure and are, under certain conditions, susceptible to a number of instabilities. An interesting example is the development of non-axisymmetric, Rayleigh-Taylor type instabilities in the case of differentially rotating two-component jets, with the toroidal component of the magnetic field playing a key role in the development or suppression of these instabilities. We have shown that higher magnetization leads to stability against these non-axisymmetric instabilities. Using ray-casting on data from relativistic MHD simulations of two-component jets, we now investigate the effect of these instabilities on the synchrotron emission pattern from the jets. We recover many well known trends from actual observations, e.g., regarding the polarization fraction and the distribution of the position angle of the electric field, in addition to a different emitting region, depending on the stability of the jet.
Autophagy is a physiological process for the recycling and degradation of cellular materials. Forming the autophagosome from the phagophore, a cup-shaped double-membrane vesicle, is a critical step in autophagy. The origin of the cup shape of the phagophore is poorly understood. In yeast, fusion of a small number of Atg9-containing vesicles is considered a key step in autophagosome biogenesis, aided by Atg1 complexes (ULK1 in mammals) localized at the preautophagosomal structure (PAS). In particular, the S-shaped Atg17-Atg31-Atg29 subcomplex of Atg1 is critical for phagophore nucleation at the PAS. To study this process, we simulated membrane remodeling processes in the presence and absence of membrane associated Atg17. We show that at least three vesicles need to fuse to induce the phagophore shape, consistent with experimental observations. However, fusion alone is not sufficient. Interactions with 34-nm long, S-shaped Atg17 complexes are required to overcome a substantial kinetic barrier in the transition to the cup-shaped phagophore. Our finding rationalizes the recruitment of Atg17 complexes to the yeast PAS, and their unusual shape. In control simulations without Atg17, with weakly binding Atg17, or with straight instead of S-shaped Atg17, the membrane shape transition did not occur. We confirm the critical role of Atg17-membrane interactions experimentally by showing that mutations of putative membrane interaction sites result in reduction or loss of autophagic activity in yeast. Fusion of a small number of vesicles followed by Atg17-guided membrane shape-remodeling thus emerges as a viable route to phagophore formation.
The phenomenon of jet quenching provides essential information about the properties of hot and dense matter created in ultra-relativistic heavy-ion collisions. Recent results from experiments at the Large Hadron Collider (LHC) show evidence for an unexpectedly similar suppression of both light and heavy flavor jets. Furthermore, the role of radiative energy loss of heavy quarks is still under active discussion within the theoretical community. By employing the parton cascade Boltzmann Approach to Multi-Parton Scatterings (BAMPS), which numerically solves the 3+1 D Boltzmann equation both for light and heavy flavor partons, we calculate the nuclear modification factor of inclusive and b-tagged reconstructed jets in 0–10% central sLHC=2.76ATeV Pb + Pb collisions. Based on perturbative QCD cross sections we find a suppression of both light and heavy flavor jets. While the inclusive jets are slightly too strong suppressed within Bamps in comparison with data, both elastic + radiative and only elastic interactions lead to a realistic b-tagged jet suppression. To further investigate light and heavy flavor energy loss we predict the R dependence of inclusive and b-tagged jet suppression. Furthermore, we propose the medium modification of b-tagged jet shapes as an observable for discriminating between different heavy quark energy loss scenarios.
In its weak field limit, Scalar-tensor-vector gravity theory introduces a Yukawa-correction to the gravitational potential. Such a correction depends on the two parameters, α which accounts for the modification of the gravitational constant, and μ∗−1 wwhich represents the scale length on which the scalar field propagates. These parameters were found to be universal when the modified gravitational potential was used to fit the galaxy rotation curves and the mass profiles of galaxy clusters, both without Dark Matter. We test the universality of these parameters using the temperature anisotropies due to the thermal Sunyaev–Zeldovich effect. In our model the intra-cluster gas is in hydrostatic equilibrium within the modified gravitational potential well and it is described by a polytropic equation of state. We predict the thermal Sunyaev–Zeldovich temperature anisotropies produced by Coma cluster, and we compare them with those obtained using the Planck 2013 Nominal maps. In our analysis, we find α and the scale length, respectively, to be consistent and to depart from their universal values. Our analysis points out that the assumption of the universality of the Yukawa-correction to the gravitational potential is ruled out at more than 3.5σ at galaxy clusters scale, while demonstrating that such a theory of gravity is capable to fit the cluster profile if the scale dependence of the gravitational potential is restored.
The goal of heavy ion reactions at low beam energies is to explore the QCD phase diagram at high net baryon chemical potential. To relate experimental observations with a first order phase transition or a critical endpoint, dynamical approaches for the theoretical description have to be developed. In this summary of the corresponding plenary talk, the status of the dynamical modeling including the most recent advances is presented. The remaining challenges are highlighted and promising experimental measurements are pointed out.