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DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2
(2023)
More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.
Neutron stars are unique laboratories for the investigation of the high density properties of bulk matter. In this work, the astrophysical constraints for a phase transition from hadronic matter to deconfined quark matter are examined thoroughly. A scheme for relating known astrophysical observables such as mass, radius and tidal deformability to the parameter space of such a transition is devised and applied to the set of data currently available.
In order to span a wide parameter space, a highly parameterizable relativistic mean field equation in compliance with chiral effective field theory results is used, where the stiffness of the equation of state can be varied via the effective mass at saturation density. The phase transitions are modelled using a Maxwell construction and assumed to be of first order, with a constant speed of sound quark matter model. The resulting equations of state are analyzed and divided into four categories, which can be used to constrain the parameter space that allows phase transition. It is highlighted, that a subset of this parameter space would even be detectable without the need of higher precision measurements. A phase transition at high densities is shown to be particularly promising in this regard. Finally, the groundwork is laid to apply the equation of state used in this work for supernova or merger simulations, by extending it to non-zero temperatures.
Asymptotic giant branch (AGB) stars are responsible for the production of the main component of the solar s-process distribution. Despite enormous progress in the theoretical modeling of these objects over the last few decades, many uncertainties remain. The still-unknown mechanism leading to the production of 13C neutron source is one example. The nucleosynthetic signature of AGB stars can be examined in a number of stellar sources, from spectroscopic observations of intrinsic and extrinsic stars to the heavy-element isotopic composition of presolar grains found in meteorites. The wealth of available observational data allows for constraining the processes occurring in AGB interiors. In this view, we discuss recent results from new AGB models including the effects of mixing triggered by magnetic fields, and show comparisons of the related s-process nucleosynthesis with available observations.
We investigate the development of the directed, v1, and elliptic flow, v2, in heavy ion collisions in mid-central Au+Au reactions at Elab=1.23A GeV. We demonstrate that the elliptic flow of hot and dense matter is initially positive (v2>0) due to the early pressure gradient. This positive v2 transfers its momentum to the spectators, which leads to the creation of the directed flow v1. In turn, the spectator shadowing of the in-plane expansion leads to a preferred decoupling of hadrons in the out-of-plane direction and results in a negative v2 for the observable final state hadrons. We propose a measurement of v1−v2 flow correlations and of the elliptic flow of dileptons as methods to pin down this evolution pattern. The elliptic flow of the dileptons allows then to determine the early-state EoS more precisely, because it avoids the strong modifications of the momentum distribution due to shadowing seen in the protons. This opens the unique opportunity for the HADES and CBM collaborations to measure the Equation-of-State directly at 2-3 times nuclear saturation density.
Transient receptor potential (TRP) ion channels are among the most well-studied classes of temperature-sensing molecules. Yet, the molecular mechanism and thermodynamic basis for the temperature sensitivity of TRP channels remains to this day poorly understood. One hypothesis is that the temperature-sensing mechanism can simply be described by a difference in heat capacity between the closed and open channel states. While such a two-state model may be simplistic it nonetheless has descriptive value, in the sense that it can be used to to compare overall temperature sensitivity between different channels and mutants. Here, we introduce a mathematical framework based on the two-state model to reliably extract temperature-dependent thermodynamic potentials and heat capacities from measurements of equilibrium constants at different temperatures. Our framework is implemented in an open-source data analysis package that provides a straightforward way to fit both linear and nonlinear van ‘t Hoff plots, thus avoiding some of the previous, potentially erroneous, assumptions when extracting thermodynamic variables from TRP channel electrophysiology data.
In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis1–3. Studies of human and mouse GSDM pores reveal the functions and architectures of 24–33 protomers assemblies4–9, but the mechanism and evolutionary origin of membrane targeting and GSDM pore formation remain unknown. Here we determine a structure of a bacterial GSDM (bGSDM) pore and define a conserved mechanism of pore assembly. Engineering a panel of bGSDMs for site-specific proteolytic activation, we demonstrate that diverse bGSDMs form distinct pore sizes that range from smaller mammalian-like assemblies to exceptionally large pores containing >50 protomers. We determine a 3.3 Å cryo-EM structure of a Vitiosangium bGSDM in an active slinky-like oligomeric conformation and analyze bGSDM pores in a native lipid environment to create an atomic-level model of a full 52-mer bGSDM pore. Combining our structural analysis with molecular dynamics simulations and cellular assays, our results support a stepwise model of GSDM pore assembly and suggest that a covalently bound palmitoyl can leave a hydrophobic sheath and insert into the membrane before formation of the membrane-spanning β-strand regions. These results reveal the diversity of GSDM pores found in nature and explain the function of an ancient post-translational modification in enabling programmed host cell death.
The Heidelberg Ion-Beam Therapy Centre (HIT) provides proton, helium, and carbon-ion beams with different energies and intensities for cancer treatment and oxygen-ion beams for experiments. For several experiments and possible future applications, such as helium ion beam radiography, a low-intensity ion beam monitor integrated into the dose delivery feedback system for the accelerator control is a necessary pre-requisite. The updated 2D prototype for this purpose consists of scintillating fibres with enhanced radiation hardness, silicon photomultipliers (SiPMs) to amplify the emitted light, and a dedicated front-end readout system (FERS) to process and record the generated signals. This setup was tested successfully on monitoring ion-beam position and profile horizontally and vertically, as well as the beam intensity, for all four ion types with energies from 50 to 430 MeV/u and intensities from 1E2 to 1E7 ions/s. Additionally, time-of-arrival (ToA) measurements on single ions have been successfully performed for a limited intensity range, allowing for ion tracking in a further update. This will reduce noise, and will also improve the accuracy and usability of ion radiography.
According to the inflationary theory of cosmology, most elementary particles in the current Universe were created during a period of reheating after inflation. In this Letter, we self-consistently couple the Einstein-inflaton equations to a strongly coupled quantum field theory as described by holography. We show that this leads to an inflating universe, a reheating phase, and finally a universe dominated by the quantum field theory in thermal equilibrium.
A considerable effort has been dedicated recently to the construction of generic equations of state (EOSs) for matter in neutron stars. The advantage of these approaches is that they can provide model-independent information on the interior structure and global properties of neutron stars. Making use of more than 106 generic EOSs, we asses the validity of quasi-universal relations of neutron star properties for a broad range of rotation rates, from slow-rotation up to the mass-shedding limit. In this way, we are able to determine with unprecedented accuracy the quasi-universal maximum-mass ratio between rotating and nonrotating stars and reveal the existence of a new relation for the surface oblateness, i.e., the ratio between the polar and equatorial proper radii. We discuss the impact that our findings have on the imminent detection of new binary neutron-star mergers and how they can be used to set new and more stringent limits on the maximum mass of nonrotating neutron stars, as well as to improve the modelling of the X-ray emission from the surface of rotating stars.
In the framework of the LHC Injectors Upgrade Project (LIU), the CERN Proton Synchrotron Booster (PSB) went through major upgrades resulting in new effects to study, challenges to overcome and new parameter regimes to explore. To assess the achievable beam brightness limit of the machine, a series of experimental and computational studies in the transverse planes were performed. In particular, the new injection scheme induces optics perturbations that are strongly enhanced near the half-integer resonance. In this thesis, methods for dynamically measuring and correcting these perturbations and their impact on the beam performance will be presented. Additionally, the quality of the transverse beam distributions and strategies for improvement will be addressed. Finally, the space charge effects when dynamically crossing the half-integer resonance will be characterized. The results of these studies and their broader significance beyond the PSB will be discussed.
Vertebrate life depends on renal function to filter excess fluid and remove low-molecular-weight waste products. An essential component of the kidney filtration barrier is the slit diaphragm (SD), a specialized cell-cell junction between podocytes. Although the constituents of the SD are largely known, its molecular organization remains elusive. Here, we use super-resolution correlative light and electron microscopy to quantify a linear rate of reduction in albumin concentration across the filtration barrier. Next, we use cryo-electron tomography of vitreous lamellae from high-pressure frozen native glomeruli to analyze the molecular architecture of the SD. The resulting densities resemble a fishnet pattern. Fitting of Nephrin and Neph1, the main constituents of the SD, results in a complex interaction pattern with multiple contact sites between the molecules. Using molecular dynamics flexible fitting, we construct a blueprint of the SD, where we describe all interactions. Our architectural understanding of the SD reconciles previous findings and provides a mechanistic framework for the development of novel therapies to treat kidney dysfunction.
Vertebrate life depends on renal function to filter excess fluid and remove low-molecular-weight waste products. An essential component of the kidney filtration barrier is the slit diaphragm (SD), a specialized cell-cell junction between podocytes. Although the constituents of the SD are largely known, its molecular organization remains elusive. Here, we use super-resolution correlative light and electron microscopy to quantify a linear rate of reduction in albumin concentration across the filtration barrier under no-flow conditions. Next, we use cryo-electron tomography of vitreous lamellae from high-pressure frozen native glomeruli to analyze the molecular architecture of the SD. The resulting densities resemble a fishnet pattern. Fitting of Nephrin and Neph1, the main constituents of the SD, results in a complex interaction pattern with multiple contact sites between the molecules. Using molecular dynamics simulations, we construct a blueprint of the SD that explains its molecular architecture. Our architectural understanding of the SD reconciles previous findings and provides a mechanistic framework for the development of novel therapies to treat kidney dysfunction.
The ALICE Collaboration reports a differential measurement of inclusive jet suppression using pp and Pb−Pb collision data at a center-of-mass energy per nucleon-nucleon collision sNN−−−√=5.02 TeV. Charged-particle jets are reconstructed using the anti-kT algorithm with resolution parameters R= 0.2, 0.3, 0.4, 0.5, and 0.6 in pp collisions and R= 0.2, 0.4, 0.6 in central (0−10%), semi-central (30−50%), and peripheral (60−80%) Pb−Pb collisions. A novel approach based on machine learning is employed to mitigate the influence of jet background. This enables measurements of inclusive jet suppression in new regions of phase space, including down to the lowest jet pT≥40 GeV/c at R=0.6 in central Pb−Pb collisions. This is an important step for discriminating different models of jet quenching in the quark-gluon plasma. The transverse momentum spectra, nuclear modification factors, derived cross section, and nuclear modification factor ratios for different jet resolution parameters of charged-particle jets are presented and compared to model predictions. A mild dependence of the nuclear modification factor ratios on collision centrality and resolution parameter is observed. The results are compared to a variety of jet-quenching models with varying levels of agreement.
Supermassive black hole binaries (SMBHBs) are among the most powerful known sources of gravitational waves (GWs). Accordingly, these systems could dominate the stochastic gravitational wave background (GWB) in the micro- and millihertz frequency range. The time until the merger of two SMBHs in the nucleus of a galaxy can be shortened through dynamical friction due to the presence of dark matter (DM) spikes around the SMBHs. To calculate the orbital evolution of individual SMBHBs within the Newtonian approximation, the SMBHBpy code is developed. This work confirms that the GW signals from SMBHBs with DM spikes can be clearly distinguished from those without any matter. Making use of the upper limit on the characteristic strain of the GWB derived from the data of the Cassini spacecraft mission in 2001/2002, a lower limit on the matter density around SMBHBs is derived in this study. The result is subsequently compared with the theoretical density profiles for cold dark matter and self-interacting dark matter spikes.
The production yields of the Σ(1385)± and Ξ(1530)0 resonances are measured in pp collisions at s√=13 TeV with ALICE. The measurements are performed as a function of the charged particle multiplicity ⟨dNch/dη⟩, which is related to the energy density produced in the collision. The results include transverse momentum (pT) distributions, pT-integrated yields, mean transverse momenta of Σ(1385)± and Ξ(1530)0, as well as ratios of the pT-integrated resonance yields relative to yields of other hadron species. The Σ(1385)±/π± and Ξ(1530)0/π± yield ratios are consistent with the trend of the enhancement of strangeness production from low to high multiplicity pp collisions, which was previously observed for strange and multi-strange baryons. The yield ratio between the measured resonances and the long-lived baryons with the same strangeness content exhibits a hint of a mild increasing trend at low multiplicity, despite too large uncertainties to exclude the flat behaviour. The results are compared to predictions from models such as EPOS-LHC and PYTHIA 8 with Rope shoving. The latter provides the best description of the multiplicity dependence of the Σ(1385)± and Ξ(1530)0 production in pp collisions at s√=13 TeV.
Measurements of the production cross sections of prompt D0, D+, D∗+, D+s, Λ+c, and Ξ+c charm hadrons at midrapidity in proton−proton collisions at s√=13 TeV with the ALICE detector are presented. The D-meson cross sections as a function of transverse momentum (pT) are provided with improved precision and granularity. The ratios of pT-differential meson production cross sections based on this publication and on measurements at different rapidity and collision energy provide a constraint on gluon parton distribution functions at low values of Bjorken-x (10−5−10−4). The measurements of Λ+c (Ξ+c) baryon production extend the measured pT intervals down to pT=0(3)~GeV/c. These measurements are used to determine the charm-quark fragmentation fractions and the cc¯¯ production cross section at midrapidity (|y|<0.5) based on the sum of the cross sections of the weakly-decaying ground-state charm hadrons D0, D+, D+s, Λ+c, Ξ0c and, for the first time, Ξ+c, and of the strongly-decaying J/psi mesons. The first measurements of Ξ+c and Σ0,++c fragmentation fractions at midrapidity are also reported. A significantly larger fraction of charm quarks hadronising to baryons is found compared to e+e− and ep collisions. The cc¯¯ production cross section at midrapidity is found to be at the upper bound of state-of-the-art perturbative QCD calculations.
Measurements of the production cross sections of prompt D0, D+, D∗+, D+s, Λ+c, and Ξ+c charm hadrons at midrapidity in proton−proton collisions at s√=13 TeV with the ALICE detector are presented. The D-meson cross sections as a function of transverse momentum (pT) are provided with improved precision and granularity. The ratios of pT-differential meson production cross sections based on this publication and on measurements at different rapidity and collision energy provide a constraint on gluon parton distribution functions at low values of Bjorken-x (10−5−10−4). The measurements of Λ+c (Ξ+c) baryon production extend the measured pT intervals down to pT=0(3)~GeV/c. These measurements are used to determine the charm-quark fragmentation fractions and the cc¯¯ production cross section at midrapidity (|y|<0.5) based on the sum of the cross sections of the weakly-decaying ground-state charm hadrons D0, D+, D+s, Λ+c, Ξ0c and, for the first time, Ξ+c, and of the strongly-decaying J/psi mesons. The first measurements of Ξ+c and Σ0,++c fragmentation fractions at midrapidity are also reported. A significantly larger fraction of charm quarks hadronising to baryons is found compared to e+e− and ep collisions. The cc¯¯ production cross section at midrapidity is found to be at the upper bound of state-of-the-art perturbative QCD calculations.
Binary neutron star mergers represent unique observational phenomena because all four fundamental interactions play an important role at various stages of their evolution by leaving imprints in astronomical observables. This makes their accurate numerical modeling a challenging multiphysics problem that promises to increase our understanding of the high-energy astrophysics at play, thereby providing constraints for the underlying fundamental theories such as the gravitational interaction or the strong interaction of dense matter. For example, the first and so far only multi-messenger observation of the binary neutron star merger GW170817 resulted in numerous bounds on the parameters of isolated non-rotating neutron stars, e.g., their maximum mass or their distribution in radii, which can be directly used to constrain the equation of state of cold nuclear matter. While many of these results stem from the observation of the inspiral gravitational-wave signal, the postmerger phase of binary neutron star mergers encodes even more details about the extreme physics of hot and dense neutron star matter. In this Thesis we focus on the exploration of dissipative and shearing effects in binary neutron star mergers in order to identify novel approaches to constrain hot and dense neutron star matter.
The first effect is the well-motivated dissipation of energy due to the bulk viscosity which arises from violations of weak chemical equilibrium. We start by exploring the impact of bulk viscosity on black-hole accretion. This simplified problem gives us the opportunity to develop a test case for future codes taking into account the effects of dissipation in a fully general-relativistic setup and build intuition in the physics of relativistic dissipation. Next, we move on to isolated neutron stars and binary neutron star mergers by developing a robust implementation of bulk-viscous dissipation for numerical relativity simulations. We test our implementation by calculating the damping of eigenmodes of isolated neutron stars and the violent migration scenario. Finally, we present the first results on the impact of bulk viscosity on binary neutron star mergers. We identify a number of ways how bulk viscosity impacts the postmerger phase, out of which the suppression of gravitational-wave emission and dynamical mass ejection are the most notable ones.
In the last part of this Thesis we investigate how the shearing dynamics at the beginning of the merger affects the amplification of different initial magnetic-field topologies. We explore the hypothesis that magnetic fields which are located only in a small region near the stellar surface prior to merger lead to a weaker magnetic-field amplification. We show first evidence which confirms this hypothesis and discuss possible implications for constraining the physics of superconduction in cold neutron stars.
Study of flavor dependence of the baryon-to-meson ratio in proton–proton collisions at √s= 13 TeV
(2023)
The production cross sections of D0 and Λ+c hadrons originating from beauty-hadron decays (i.e. non-prompt) were measured for the first time at midrapidity (|y|<0.5) by the ALICE Collaboration in proton-proton collisions at a center-of-mass energy s√=13 TeV. They are described within uncertainties by perturbative QCD calculations employing the fragmentation fractions of beauty quarks to baryons measured at forward rapidity by the LHCb Collaboration. The bb¯¯¯ production cross section per unit of rapidity at midrapidity, estimated from these measurements, is dσbb¯¯¯/dy||y|<0.5=83.1±3.5(stat.)±5.4(syst.)+12.3−3.2(extrap.)μb. The baryon-to-meson ratios are computed to investigate the hadronization mechanism of beauty quarks. The non-prompt Λ+c/D0 production ratio has a similar trend to the one measured for the promptly produced charmed particles and to the p/π+ and Λ/K0S ratios, suggesting a similar baryon-formation mechanism among light, strange, charm, and beauty hadrons. The pT-integrated non-prompt Λc/D0 ratio is found to be significantly higher than the one measured in e+e− collisions.
We continue previous investigations of the (inhomogeneous) phase structure of the Gross-Neveu model in a noninteger number of spatial dimensions (1≤d<3) in the limit of an infinite number of fermion species (N→∞) at (non)zero chemical potential μ. In this work, we extend the analysis from zero to nonzero temperature T.
The phase diagram of the Gross-Neveu model in 1≤d<3 spatial dimensions is well known under the assumption of spatially homogeneous condensation with both a symmetry broken and a symmetric phase present for all spatial dimensions. In d=1 one additionally finds an inhomogeneous phase, where the order parameter, the condensate, is varying in space. Similarly, phases of spatially varying condensates are also found in the Gross-Neveu model in d=2 and d=3, as long as the theory is not fully renormalized, i.e., in the presence of a regulator. For d=2, one observes that the inhomogeneous phase vanishes, when the regulator is properly removed (which is not possible for d=3 without introducing additional parameters).
In the present work, we use the stability analysis of the symmetric phase to study the presence (for 1≤d<2) and absence (for 2≤d<3) of these inhomogeneous phases and the related moat regimes in the fully renormalized Gross-Neveu model in the μ,T-plane. We also discuss the relation between "the number of spatial dimensions" and "studying the model with a finite regulator" as well as the possible consequences for the limit d→3.