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We study equilibrium as well as out-of-equilibrium properties of the strongly interacting QGP medium under extreme conditions of high temperature T and high baryon densities or baryon chemical potentials μB within a kinetic approach. We present the thermodynamic and transport properties of the QGP close to equilibrium in the framework of effective models with Nf=3 active quark flavours such as the Polyakov extended Nambu-Jona Lasinio (PNJL) and dynamical quasiparticle model with the CEP (DQPM-CP). Considering the transport coefficients and the EoS of the QGP phase, we compare our results with various results from the literature. Furthermore, out-of equilibrium properties of the QGP medium and in particular, the effect of a μB- dependence of thermodynamic and transport properties of the QGP are studied within the Parton-Hadron-String-Dynamics (PHSD) transport approach, which covers the full evolution of the system during HICs. We find that bulk observables and flow coefficients for strange hadrons as well as for antiprotons are more sensitive to the properties of the QGP, in particular to the μB - dependence of the QGP interactions.
Presolar grain isotopic ratios as constraints to nuclear physics inputs for s-process calculations
(2023)
The isotopic abundances in presolar SiC grains of AGB origin provide important and precise constraints to those star nucleosynthesis models. By comparing the values of the s-element abundances resulting from calculations with the ones measured in these dust grains, it turns out that new measurements of weak-interaction rates in ionized plasmas, as well as of neutron-capture cross sections, are needed, especially in the region near the neutron magic numbers 50 and 82.
Results on proton and Λ flow, calculated with the UrQMD model that incorporates different realistic density dependent equations of state, are presented. It is shown that the proton and hyperon flow shows sensitivity to the equation of state and especially to the appearance of a phase transition at densities below 4n0. Even though qualitatively hyperons and protons exhibit the same beam energy dependence of the flow, the quantitative results are different. In this context it is suggested that the hyperon measurements can be used to study the density dependence of the hyperon interaction in high density QCD matter.
We introduce a novel technique that utilizes a physics-driven deep learning method to reconstruct the dense matter equation of state from neutron star observables, particularly the masses and radii. The proposed framework involves two neural networks: one to optimize the EoS using Automatic Differentiation in the unsupervised learning scheme; and a pre-trained network to solve the Tolman–Oppenheimer–Volkoff (TOV) equations. The gradient-based optimization process incorporates a Bayesian picture into the proposed framework. The reconstructed EoS is proven to be consistent with the results from conventional methods. Furthermore, the resulting tidal deformation is in agreement with the limits obtained from the gravitational wave event, GW170817.
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.
The appearance of strangeness in the form of hyperons within the inner core of neutron stars is expected to affect its detectable properties, such as its global structure or gravitational wave emission. This work explores the parameter space of hyperonic stars within the framework of the Relativistic Mean Field model allowed by the present uncertainties in the state-of-the-art nuclear and hypernuclear experimental data. We impose multi-physics constraints at different density regimes to restrict the parameter space: Chiral effective field theory, heavy-ion collision data, and multi-messenger astrophysical observations of neutron stars. We investigate possible correlations between empirical nuclear and hypernuclear parameters, particularly the symmetry energy and its slope, with observable properties of neutron stars. We do not find a correlation for the hyperon parameters and the astrophysical data. However, the inclusion of hyperons generates a tension between the astrophysical and heavy-ion data constraining considerably the available parameter space.
Determining the sound speed cs in compact stars is an important open question with numerous implications on the behavior of matter at large densities and hence on gravitational-wave emission from neutron stars. To this scope, we construct more than 107 equations of state (EOSs) with continuous sound speed and build more than 108 nonrotating stellar models consistent not only with nuclear theory and perturbative QCD, but also with astronomical observations. In this way, we find that EOSs with subconformal sound speeds, i.e., with cs 1 3 2 < within the stars, are possible in principle but very unlikely in practice, being only 0.03% of our sample. Hence, it is natural to expect that cs 1 3 2 > somewhere in the stellar interior. Using our large sample, we obtain estimates at 95% credibility of neutron-star radii for representative stars with 1.4 and 2.0 solar masses, R1.4 12.42 km 0.99 0.52 = - + , R2.0 12.12 km 1.23 1.11 = - + , and for the binary tidal deformability of the GW170817 event, 1.186 485 211 225 L = - ˜ + . Interestingly, our lower bounds on the radii are in very good agreement with the prediction derived from very different arguments, namely, the threshold mass. Finally, we provide simple analytic expressions to determine the minimum and maximum values of L˜ as a function of the chirp mass.
Using more than a million randomly generated equations of state that satisfy theoretical and observational constraints, we construct a novel, scale-independent description of the sound speed in neutron stars, where the latter is expressed in a unit cube spanning the normalized radius, r/R, and the mass normalized to the maximum one, M/MTOV. From this generic representation, a number of interesting and surprising results can be deduced. In particular, we find that light (heavy) stars have stiff (soft) cores and soft (stiff) outer layers, or that the maximum of the sound speed is located at the center of light stars but moves to the outer layers for stars with M/MTOV ≳ 0.7, reaching a constant value of cs = 1 2 2 as M → MTOV. We also show that the sound speed decreases below the conformal limit cs = 1 3 2 at the center of stars with M = MTOV. Finally, we construct an analytic expression that accurately describes the radial dependence of the sound speed as a function of the neutron-star mass, thus providing an estimate of the maximum sound speed expected in a neutron star.
We have investigated the systematic differences introduced when performing a Bayesian-inference analysis of the equation of state (EOS) of neutron stars employing either variable- or constant-likelihood functions. The former has the advantage of retaining the full information on the distributions of the measurements, making exhaustive usage of the data. The latter, on the other hand, has the advantage of a much simpler implementation and reduced computational costs. In both approaches, the EOSs have identical priors and have been built using the sound speed parameterization method so as to satisfy the constraints from X-ray and gravitational waves observations, as well as those from chiral effective theory and perturbative quantum chromodynamics. In all cases, the two approaches lead to very similar results and the 90% confidence levels essentially overlap. Some differences do appear, but in regions where the probability density is extremely small and are mostly due to the sharp cutoff on the binary tidal deformability L˜ 720 set in the constant-likelihood approach. Our analysis has also produced two additional results. First, an inverse correlation between the normalized central number density, nc,TOV/ns, and the radius of a maximally massive star, RTOV. Second, and most importantly, it has confirmed the relation between the chirp mass and the binary tidal deformability. The importance of this result is that it relates chirp, which is measured very accurately, and L˜ , which contains important information on the EOS. Hence, when chirp is measured in future detections, our relation can be used to set tight constraints on L˜ .
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 assess 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 modeling of the X-ray emission from the surface of rotating stars.
The amplification of magnetic fields plays an important role in explaining numerous astrophysical phenomena associated with binary neutron star mergers, such as mass ejection and the powering of short gamma-ray bursts. Magnetic fields in isolated neutron stars are often assumed to be confined to a small region near the stellar surface, while they are normally taken to fill the whole star in numerical modeling of mergers. By performing high-resolution, global, and high-order general-relativistic magnetohydrodynamic simulations, we investigate the impact of a purely crustal magnetic field and contrast it with the standard configuration consisting of a dipolar magnetic field with the same magnetic energy but filling the whole star. While the crust configurations are very effective in generating strong magnetic fields during the Kelvin–Helmholtz-instability stage, they fail to achieve the same level of magnetic-field amplification of the full-star configurations. This is due to the lack of magnetized material in the neutron-star interiors to be used for further turbulent amplification and to the surface losses of highly magnetized matter in the crust configurations. Hence, the final magnetic energies in the two configurations differ by more than 1 order of magnitude. We briefly discuss the impact of these results on astrophysical observables and how they can be employed to deduce the magnetic topology in merging binaries.
Post-merger gravitational-wave signal from neutron-star binaries: a new look at an old problem
(2023)
The spectral properties of the post-merger gravitational-wave signal from a binary of neutron stars encodes a variety of information about the features of the system and of the equation of state describing matter around and above nuclear saturation density. Characterizing the properties of such a signal is an “old” problem, which first emerged when a number of frequencies were shown to be related to the properties of the binary through “quasiuniversal” relations. Here we take a new look at this old problem by computing the properties of the signal in terms of the Weyl scalar ψ4. In this way, and using a database of more than 100 simulations, we provide the first evidence for a new instantaneous frequency, y f0 4, associated with the instant of quasi-time-symmetry in the dynamics, and which also follows a quasi-universal relation. We also derive a new quasi-universal relation for the merger frequency f h mer, which provides a description of the data that is 4 times more accurate than previous expressions while requiring fewer fitting coefficients. Finally, consistent with the findings of numerous studies before ours, and using an enlarged ensemble of binary systems, we point out that the ℓ = 2, m = 1 gravitational-wave mode could become comparable with the traditional ℓ = 2, m = 2 mode on sufficiently long timescales, with strain amplitudes in a ratio |h21|/|h22| ∼ 0.1–1 under generic orientations of the binary, which could be measured by present detectors for signals with a large signal-to-noise ratio or by third-generation detectors for generic signals should no collapse occur.
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.
We use the quantum null energy condition in strongly coupled two-dimensional field theories (QNEC2) as diagnostic tool to study a variety of phase structures, including crossover, second and first order phase transitions. We find a universal QNEC2 constraint for first order phase transitions with kinked entanglement entropy and discuss in general the relation between the QNEC2-inequality and monotonicity of the Casini-Huerta c-function. We then focus on a specific example, the holographic dual of which is modelled by three-dimensional Einstein gravity plus a massive scalar field with one free parameter in the self-interaction potential. We study translation invariant stationary states dual to domain walls and black branes. Depending on the value of the free parameter we find crossover, second and first order phase transitions between such states, and the c-function either flows to zero or to a finite value in the infrared. We present evidence that evaluating QNEC2 for ground state solutions allows to predict the existence of phase transitions at finite temperature.
Holography has provided valuable insights into the time evolution of strongly coupled gauge theories in a fixed spacetime. However, this framework is insufficient if this spacetime is dynamical. We present a scheme to evolve a four-dimensional, strongly interacting gauge theory coupled to four-dimensional dynamical gravity in the semiclassical regime. As in previous work, we use holography to evolve the quantum gauge theory stress tensor, whereas the four-dimensional metric evolves according to Einstein’s equations coupled to the expectation value of the stress tensor. The novelty of our approach is that both the boundary and the bulk spacetimes are constructed dynamically, one time step at a time. We focus on Friedmann-Lemaître-Robertson-Walker geometries and evolve far-from-equilibrium initial states that lead to asymptotically expanding, flat or collapsing Universes.
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.
Using full 3+1 dimensional general-relativistic hydrodynamic simulations of equal- and unequal-mass neutron-star binaries with properties that are consistent with those inferred from the inspiral of GW170817, we perform a detailed study of the quark-formation processes that could take place after merger. We use three equations of state consistent with current pulsar observations derived from a novel finite-temperature framework based on V-QCD, a non-perturbative gauge/gravity model for Quantum Chromodynamics. In this way, we identify three different post-merger stages at which mixed baryonic and quark matter, as well as pure quark matter, are generated. A phase transition triggered collapse already ≲ 10 ms after the merger reveals that the softest version of our equations of state is actually inconsistent with the expected second-long post-merger lifetime of GW170817. Our results underline the impact that gravitational wave observations of binary neutron-star mergers can have in constraining the equation of state of nuclear matter, especially in its most extreme regimes.
We present a novel framework for the equation of state of dense and hot quantum chromodynamics (QCD), which focuses on the region of the phase diagram relevant for neutron star mergers and core-collapse supernovae. The model combines predictions from the gauge/gravity duality with input from lattice field theory, QCD perturbation theory, chiral effective theory, and statistical modeling. It is therefore, by construction, in good agreement with theoretical constraints both at low and high densities and temperatures. The main ingredients of our setup are the nonperturbative V-QCD model based on the gauge/gravity duality, a van der Waals model for nucleon liquid, and the DD2 version of the Hempel-Schaffner-Bielich statistical model of nuclear matter. By consistently combining these models, we also obtain a description for the nuclear to quark matter phase transition and its critical end point. The parameter dependence of the model is represented by three (soft, intermediate, and stiff) variants of the equation of state, all of which agree with observational constraints from neutron stars and their mergers. We discuss resulting constraints for the equation of state, predictions for neutron stars, and the location of the critical point.
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.
We analyzed a eukaryotically encoded rubredoxin from the cryptomonad Guillardia theta and identified additional domains at the N- and C-termini in comparison to known prokaryotic paralogous molecules. The cryptophytic N-terminal extension was shown to be a transit peptide for intracellular targeting of the protein to the plastid, whereas a C-terminal domain represents a membrane anchor. Rubredoxin was identified in all tested phototrophic eukaryotes. Presumably facilitated by its C-terminal extension, nucleomorph-encoded rubredoxin (nmRub) is associated with the thylakoid membrane. Association with photosystem II (PSII) was demonstrated by co-localization of nmRub and PSII membrane particles and PSII core complexes and confirmed by comparative electron paramagnetic resonance measurements. The midpoint potential of nmRub was determined as +125 mV, which is the highest redox potential of all known rubredoxins. Therefore, nmRub provides a striking example of the ability of the protein environment to tune the redox potentials of metal sites, allowing for evolutionary adaption in specific electron transport systems, as for example that coupled to the PSII pathway.
IHMCIF: an extension of the PDBx/mmCIF data standard for integrative structure determination methods
(2024)
IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.
Highlights
• Sampling the large conformational space of disordered proteins requires extensive molecular dynamics (MD) simulations.
• Fragment assembly complements MD simulations to produce extensive ensembles of disordered proteins with atomic detail.
• Hierarchical chain growth (HCG) ensembles capture key experimental descriptors “out of the box”.
• HCG has revealed local structural characteristics associated with protein dysfunction in neurodegeneration.
Abstract
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here, we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. While atomistic molecular dynamics (MD) simulation has seen a lot of improvement in recent years, large-scale computing resources and careful validation are required to simulate full-length disordered biopolymers in solution. As a computationally efficient alternative, hierarchical chain growth (HCG) combines pre-sampled chain fragments in a statistically reproducible manner into ensembles of full-length atomically detailed biomolecular structures. Experimental data can be integrated during and after chain assembly. Applications to the neurodegeneration-linked proteins α-synuclein, tau, and TDP-43, including as condensate, illustrate the use of HCG. We conclude by highlighting the emerging connections to AI-based structural modeling including AlphaFold2.
Substantial progress in the field of neuroscience has been made from anaesthetized preparations. Ketamine is one of the most used drugs in electrophysiology studies, but how ketamine affects neuronal responses is poorly understood. Here, we used in vivo electrophysiology and computational modelling to study how the auditory cortex of bats responds to vocalisations under anaesthesia and in wakefulness. In wakefulness, acoustic context increases neuronal discrimination of natural sounds. Neuron models predicted that ketamine affects the contextual discrimination of sounds regardless of the type of context heard by the animals (echolocation or communication sounds). However, empirical evidence showed that the predicted effect of ketamine occurs only if the acoustic context consists of low-pitched sounds (e.g., communication calls in bats). Using the empirical data, we updated the naïve models to show that differential effects of ketamine on cortical responses can be mediated by unbalanced changes in the firing rate of feedforward inputs to cortex, and changes in the depression of thalamo-cortical synaptic receptors. Combined, our findings obtained in vivo and in silico reveal the effects and mechanisms by which ketamine affects cortical responses to vocalisations.
Recent lattice QCD results, comparing to a hadron resonance gas model, have shown the need for hundreds of particles in hadronic models. These extra particles influence both the equation of state and hadronic interactions within hadron transport models. Here, we introduce the PDG21+ particle list, which contains the most up-to-date database of particles and their properties. We then convert all particles decays into 2 body decays so that they are compatible with SMASH in order to produce a more consistent description of a heavy-ion collision.
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.
The effect of a single site mutation of Arg-54 to methionine in Paracoccus denitrificans cytochrome c oxidase was studied using a combination of optical spectroscopy, electrochemical and rapid kinetics techniques, and time-resolved measurements of electrical membrane potential. The mutation resulted in a blue-shift of the heme a alpha-band by 15 nm and partial occupation of the low-spin heme site by heme O. Additionally, there was a marked decrease in the midpoint potential of the low-spin heme, resulting in slow reduction of this heme species. A stopped-flow investigation of the reaction with ferrocytochrome c yielded a kinetic difference spectrum resembling that of heme a(3). This observation, and the absence of transient absorbance changes at the corresponding wavelength of the low-spin heme, suggests that, in the mutant enzyme, electron transfer from Cu(A) to the binuclear center may not occur via heme a but that instead direct electron transfer to the high-spin heme is the dominating process. This was supported by charge translocation measurements where Deltapsi generation was completely inhibited in the presence of KCN. Our results thus provide an example for how the interplay between protein and cofactors can modulate the functional properties of the enzyme complex.
Subensemble is a type of statistical ensemble which is the generalization of grand canonical and canonical ensembles. The subensemble acceptance method (SAM) provides general formulas to correct the cumulants of distributions in heavy-ion collisions for the global conservation of all QCD charges. The method is applicable for an arbitrary equation of state and sufficiently large systems, such as those created in central collisions of heavy ions. The new fluctuation measures insensitive to global conservation effects are presented. The main results are illustrated in the hadron resonance gas and van der Waals fluid frameworks.
We show the absence of an instability of homogeneous (chiral) condensates against spatially inhomogeneous perturbations for various (2+1)-dimensional four-fermion and Yukawa models. All models are studied at nonzero baryon chemical potential, while some of them are also subjected to chiral and isospin chemical potential. The considered theories contain up to 16 Lorentz-(pseudo)scalar fermionic interaction channels. We prove the stability of homogeneous condensates by analyzing the bosonic two-point function, which can be expressed in a purely analytical form at zero temperature. Our analysis is presented in a general manner for all of the different discussed models. We argue that the absence of an inhomogeneous chiral phase (where the chiral condensate is spatially nonuniform) follows from this lack of instability. Furthermore, the existence of a moat regime, where the bosonic wave-function renormalization is negative, in these models is ruled out.
Inhomogeneous condensation in the Gross-Neveu model in noninteger spatial dimensions 1 ≤ d < 3
(2023)
The Gross-Neveu model in the N→∞ limit in d=1 spatial dimensions exhibits a chiral inhomogeneous phase (IP), where the chiral condensate has a spatial dependence that spontaneously breaks translational invariance and the Z2 chiral symmetry. This phase is absent in d=2, while in d=3 its existence and extent strongly depends on the regularization and the value of the finite regulator. This work connects these three results smoothly by extending the analysis to noninteger spatial dimensions 1≤d<3, where the model is fully renormalizable. To this end, we adapt the stability analysis, which probes the stability of the homogeneous ground state under inhomogeneous perturbations, to noninteger spatial dimensions. We find that the IP is present for all d<2 and vanishes exactly at d=2. Moreover, we find no instability toward an IP for 2≤d<3, which suggests that the IP in d=3 is solely generated by the presence of a regulator.
Inhomogeneous phases in the Gross-Neveu model in 1 + 1 dimensions at finite number of flavors
(2020)
We explore the thermodynamics of the 1+1-dimensional Gross-Neveu (GN) model at a finite number of fermion flavors Nf, finite temperature, and finite chemical potential using lattice field theory. In the limit Nf→∞ the model has been solved analytically in the continuum. In this limit three phases exist: a massive phase, in which a homogeneous chiral condensate breaks chiral symmetry spontaneously; a massless symmetric phase with vanishing condensate; and most interestingly an inhomogeneous phase with a condensate, which oscillates in the spatial direction. In the present work we use chiral lattice fermions (naive fermions and SLAC fermions) to simulate the GN model with 2, 8, and 16 flavors. The results obtained with both discretizations are in agreement. Similarly as for Nf→∞ we find three distinct regimes in the phase diagram, characterized by a qualitatively different behavior of the two-point function of the condensate field. For Nf=8 we map out the phase diagram in detail and obtain an inhomogeneous region smaller as in the limit Nf→∞, where quantum fluctuations are suppressed. We also comment on the existence or absence of Goldstone bosons related to the breaking of translation invariance in 1+1 dimensions.
The traffic AAA-ATPase PilF is essential for pilus biogenesis and natural transformation of Thermus thermophilus HB27. Recently, we showed that PilF forms hexameric complexes containing six zinc atoms coordinated by conserved tetracysteine motifs. Here we report that zinc binding is essential for complex stability. However, zinc binding is neither required for pilus biogenesis nor natural transformation. A number of the mutants did not exhibit any pili during growth at 64 °C but still were transformable. This leads to the conclusion that type 4 pili and the DNA translocator are distinct systems. At lower growth temperatures (55 °C) the zinc-depleted multiple cysteine mutants were hyperpiliated but defective in pilus-mediated twitching motility. This provides evidence that zinc binding is essential for the role of PilF in pilus dynamics. Moreover, we found that zinc binding is essential for complex stability but dispensable for ATPase activity. In contrast to many polymerization ATPases from mesophilic bacteria, ATP binding is not required for PilF complex formation; however, it significantly increases complex stability. These data suggest that zinc and ATP binding increase complex stability that is important for functionality of PilF under extreme environmental conditions.
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.
Formation of Hubbard-like bands as a fingerprint of strong electron-electron interactions in FeSe
(2017)
We use angle-resolved photo-emission spectroscopy (ARPES) to explore the electronic structure of single crystals of FeSe over a wide range of binding energies and study the effects of strong electron-electron correlations. We provide evidence for the existence of "Hubbard-like bands" at high binding energies consisting of incoherent many-body excitations originating from Fe 3d states in addition to the renormalized quasiparticle bands near the Fermi level. Many high energy features of the observed ARPES data can be accounted for when incorporating effects of strong local Coulomb interactions in calculations of the spectral function via dynamical mean-field theory, including the formation of a Hubbard-like band. This shows that over the energy scale of several eV, local correlations arising from the on-site Coulomb repulsion and Hund's coupling are essential for a proper understanding of the electronic structure of FeSe and other related iron based superconductors.
Type-II multiferroic materials, in which ferroelectric polarization is induced by inversion non-symmetric magnetic order, promise new and highly efficient multifunctional applications based on mutual control of magnetic and electric properties. However, to date this phenomenon is limited to low temperatures. Here we report giant pressure-dependence of the multiferroic critical temperature in CuBr2: at 4.5 GPa it is enhanced from 73.5 to 162 K, to our knowledge the highest TC ever reported for non-oxide type-II multiferroics. This growth shows no sign of saturating and the dielectric loss remains small under these high pressures. We establish the structure under pressure and demonstrate a 60\% increase in the two-magnon Raman energy scale up to 3.6 GPa. First-principles structural and magnetic energy calculations provide a quantitative explanation in terms of dramatically pressure-enhanced interactions between CuBr2 chains. These large, pressure-tuned magnetic interactions motivate structural control in cuprous halides as a route to applied high-temperature multiferroicity.
In the search for novel organic charge transfer salts with variable degrees of charge transfer we have studied the effects of two modifications of the recently synthesized donor–acceptor system [tetramethoxypyrene (TMP)]–[tetracyanoquinodimethane (TCNQ)]. One is of chemical nature by substituting the acceptor TCNQ molecules by F4TCNQ molecules. The second consists in simulating the application of uniaxial pressure along the stacking axis of the system. In order to test the chemical substitution, we have grown single crystals of the TMP–F4TCNQ complex and analyzed its electronic structure via electronic transport measurements, ab initio density functional theory (DFT) calculations and UV/VIS/IR absorption spectroscopy. This system shows an almost ideal geometrical overlap of nearly planar molecules stacked alternately (mixed stack) and this arrangement is echoed by a semiconductor-like transport behavior with an increased conductivity along the stacking direction. This is in contrast to TMP–TCNQ which shows a less pronounced anisotropy and a smaller conductivity response. Our band structure calculations confirm the one-dimensional behavior of TMP–F4TCNQ with pronounced dispersion only along the stacking axis. Infrared measurements illustrating the C[triple bond, length as m-dash]N vibration frequency shift in F4TCNQ suggest however no improvement in the degree of charge transfer in TMP–F4TCNQ with respect to TMP–TCNQ. In both complexes about 0.1e is transferred from TMP to the acceptor. Concerning the pressure effect, our DFT calculations on the designed TMP–TCNQ and TMP–F4TCNQ structures under different pressure conditions show that application of uniaxial pressure along the stacking axis of TMP–TCNQ may be the route to follow in order to obtain a much more pronounced charge transfer.
The rich functionalities of transition-metal oxides and their interfaces bear an enormous technological potential. Its realization in practical devices requires, however, a significant improvement of yet relatively low electron mobility in oxide materials. Recently, a mobility boost of about 2 orders of magnitude has been demonstrated at the spinel–perovskite γ-Al2O3/SrTiO3 interface compared to the paradigm perovskite–perovskite LaAlO3/SrTiO3 interface. We explore the fundamental physics behind this phenomenon from direct measurements of the momentum-resolved electronic structure of this interface using resonant soft-X-ray angle-resolved photoemission. We find an anomaly in orbital ordering of the mobile electrons in γ-Al2O3/SrTiO3 which depopulates electron states in the top SrTiO3 layer. This rearrangement of the mobile electron system pushes the electron density away from the interface, which reduces its overlap with the interfacial defects and weakens the electron–phonon interaction, both effects contributing to the mobility boost. A crystal-field analysis shows that the band order alters owing to the symmetry breaking between the spinel γ-Al2O3 and perovskite SrTiO3. Band-order engineering, exploiting the fundamental symmetry properties, emerges as another route to boost the performance of oxide devices.
In recent years, the notion of 'Quantum Materials' has emerged as a powerful unifying concept across diverse fields of science and engineering, from condensed-matter and coldatom physics to materials science and quantum computing. Beyond traditional quantum materials such as unconventional superconductors, heavy fermions, and multiferroics, the field has significantly expanded to encompass topological quantum matter, two-dimensional materials and their van der Waals heterostructures, Moiré materials, Floquet time crystals, as well as materials and devices for quantum computation with Majorana fermions. In this Roadmap collection we aim to capture a snapshot of the most recent developments in the field, and to identify outstanding challenges and emerging opportunities. The format of the Roadmap, whereby experts in each discipline share their viewpoint and articulate their vision for quantum materials, reflects the dynamic and multifaceted nature of this research area, and is meant to encourage exchanges and discussions across traditional disciplinary boundaries. It is our hope that this collective vision will contribute to sparking new fascinating questions and activities at the intersection of materials science, condensed matter physics, device engineering, and quantum information, and to shaping a clearer landscape of quantum materials science as a new frontier of interdisciplinary scientific inquiry. We stress that this article is not meant to be a fully comprehensive review but rather an up-to-date snapshot of different areas of research on quantum materials with a minimal number of references focusing on the latest developments.
Controlling and understanding electron correlations in quantum matter is one of the most challenging tasks in materials engineering. In the past years a plethora of new puzzling correlated states have been found by carefully stacking and twisting two-dimensional van der Waals materials of different kind. Unique to these stacked structures is the emergence of correlated phases not foreseeable from the single layers alone. In Ta-dichalcogenide heterostructures made of a good metallic “1H”- and a Mott insulating “1T”-layer, recent reports have evidenced a cross-breed itinerant and localized nature of the electronic excitations, similar to what is typically found in heavy fermion systems. Here, we put forward a new interpretation based on first-principles calculations which indicates a sizeable charge transfer of electrons (0.4-0.6 e) from 1T to 1H layers at an elevated interlayer distance. We accurately quantify the strength of the interlayer hybridization which allows us to unambiguously determine that the system is much closer to a doped Mott insulator than to a heavy fermion scenario. Ta-based heterolayers provide therefore a new ground for quantum-materials engineering in the regime of heavily doped Mott insulators hybridized with metallic states at a van der Waals distance.
Deconfinement of Mott localized electrons into topological and spin–orbit-coupled Dirac fermions
(2020)
The interplay of electronic correlations, spin–orbit coupling and topology holds promise for the realization of exotic states of quantum matter. Models of strongly interacting electrons on honeycomb lattices have revealed rich phase diagrams featuring unconventional quantum states including chiral superconductivity and correlated quantum spin Hall insulators intertwining with complex magnetic order. Material realizations of these electronic states are, however, scarce or inexistent. In this work, we propose and show that stacking 1T-TaSe2 into bilayers can deconfine electrons from a deep Mott insulating state in the monolayer to a system of correlated Dirac fermions subject to sizable spin–orbit coupling in the bilayer. 1T-TaSe2 develops a Star-of-David charge density wave pattern in each layer. When the Star-of-David centers belonging to two adyacent layers are stacked in a honeycomb pattern, the system realizes a generalized Kane–Mele–Hubbard model in a regime where Dirac semimetallic states are subject to significant Mott–Hubbard interactions and spin–orbit coupling. At charge neutrality, the system is close to a quantum phase transition between a quantum spin Hall and an antiferromagnetic insulator. We identify a perpendicular electric field and the twisting angle as two knobs to control topology and spin–orbit coupling in the system. Their combination can drive it across hitherto unexplored grounds of correlated electron physics, including a quantum tricritical point and an exotic first-order topological phase transition.
The antiferromagnet and semimetal EuCd2As2 has recently attracted a lot of attention due to a wealth of topological phases arising from the interplay of topology and magnetism. In particular, the presence of a single pair of Weyl points is predicted for a ferromagnetic configuration of Eu spins along the c-axis in EuCd2As2. In the search for such phases, we investigate here the effects of hydrostatic pressure in EuCd2As2. For that, we present specific heat, transport and μSR measurements under hydrostatic pressure up to ∼2.5GPa, combined with {\it ab initio} density functional theory (DFT) calculations. Experimentally, we establish that the ground state of EuCd2As2 changes from in-plane antiferromagnetic (AFMab) to ferromagnetic at a critical pressure of ≈2\,GPa, which is likely characterized by the moments dominantly lying within the ab plane (FMab). The AFMab-FMab transition at such a relatively low pressure is supported by our DFT calculations. Furthermore, our experimental and theoretical results indicate that EuCd2As2 moves closer to the sought-for FMc state (moments ∥ c) with increasing pressure further. We predict that a pressure of ≈\,23\,GPa will stabilize the FMc state, if Eu remains in a 2+ valence state. Thus, our work establishes hydrostatic pressure as a key tuning parameter that (i) allows for a continuous tuning between magnetic ground states in a single sample of EuCd2As2 and (ii) enables the exploration of the interplay between magnetism and topology and thereby motivates a series of future experiments on this magnetic Weyl semimetal.
Electronic systems living on Archimedean lattices such as kagome and square–octagon networks are presently being intensively discussed for the possible realization of topological insulating phases. Coining the most interesting electronic topological states in an unbiased way is however not straightforward due to the large parameter space of possible Hamiltonians. A possible approach to tackle this problem is provided by a recently developed statistical learning method (Mertz and Valentí in Phys Rev Res 3:013132, 2021. https://doi.org/10.1103/PhysRevResearch.3.013132), based on the analysis of a large data sets of randomized tight-binding Hamiltonians labeled with a topological index. In this work, we complement this technique by introducing a feature engineering approach which helps identifying polynomial combinations of Hamiltonian parameters that are associated with non-trivial topological states. As a showcase, we employ this method to investigate the possible topological phases that can manifest on the square–octagon lattice, focusing on the case in which the Fermi level of the system lies at a high-order van Hove singularity, in analogy to recent studies of topological phases on the kagome lattice at the van Hove filling.
Critical spin liquid versus valence-bond glass in a triangular-lattice organic antiferromagnet
(2019)
In the quest for materials with unconventional quantum phases, the organic triangular-lattice antiferromagnet κ-(ET)2Cu2(CN)3 has been extensively discussed as a quantum spin liquid (QSL) candidate. The description of its low temperature properties has become, however, a particularly challenging task. Recently, an intriguing quantum critical behaviour was suggested from low-temperature magnetic torque experiments. Here we highlight significant deviations of the experimental observations from a quantum critical scenario by performing a microscopic analysis of all anisotropic contributions, including Dzyaloshinskii–Moriya and multi-spin scalar chiral interactions. Instead, we show that disorder-induced spin defects provide a comprehensive explanation of the low-temperature properties. These spins are attributed to valence bond defects that emerge spontaneously as the QSL enters a valence-bond glass phase at low temperature. This theoretical treatment is applicable to a general class of frustrated magnetic systems and has important implications for the interpretation of magnetic torque, nuclear magnetic resonance, thermal transport and thermodynamic experiments.
The aim of the present overview article is to raise awareness of an essential aspect that is usually not accounted for in the modelling of electron transport for focused-electron-beam-induced deposition (FEBID) of nanostructures: Surface excitations are on the one hand responsible for a sizeable fraction of the intensity in reflection-electron-energy-loss spectra for primary electron energies of up to a few kiloelectronvolts and, on the other hand, they play a key role in the emission of secondary electrons from solids, regardless of the primary energy. In this overview work we present a general perspective of recent works on the subject of surface excitations and on low-energy electron transport, highlighting the most relevant aspects for the modelling of electron transport in FEBID simulations.
The phase diagram of the square lattice bilayer Hubbard model: a variational Monte Carlo study
(2014)
We investigate the phase diagram of the square lattice bilayer Hubbard model at half-filling with the variational Monte Carlo method for both the magnetic and the paramagnetic case as a function of the interlayer hopping and on-site Coulomb repulsion U. With this study we resolve some discrepancies in previous calculations based on the dynamical mean-field theory, and we are able to determine the nature of the phase transitions between metal, Mott insulator and band insulator. In the magnetic case we find only two phases: an antiferromagnetic Mott insulator at small for any value of U and a band insulator at large . At large U values we approach the Heisenberg limit. The paramagnetic phase diagram shows at small a metal to Mott insulator transition at moderate U values and a Mott to band insulator transition at larger U values. We also observe a re-entrant Mott insulator to metal transition and metal to band insulator transition for increasing in the range of . Finally, we discuss the phase diagrams obtained in relation to findings from previous studies based on different many-body approaches.
The interaction of trimethyl(methylcyclopentadienyl)platinum(IV) ((C5H4CH3)Pt(CH3)3) molecules on fully and partially hydroxylated SiO2 surfaces, as well as the dynamics of this interaction were investigated using density functional theory (DFT) and finite temperature DFT-based molecular dynamics simulations. Fully and partially hydroxylated surfaces represent substrates before and after electron beam treatment and this study examines the role of electron beam pretreatment on the substrates in the initial stages of precursor dissociation and formation of Pt deposits. Our simulations show that on fully hydroxylated surfaces or untreated surfaces, the precursor molecules remain inactivated while we observe fragmentation of (C5H4CH3)Pt(CH3)3 on partially hydroxylated surfaces. The behavior of precursor molecules on the partially hydroxylated surfaces has been found to depend on the initial orientation of the molecule and the distribution of surface active sites. Based on the observations from the simulations and available experiments, we discuss possible dissociation channels of the precursor.
We investigate the magnetism of a previously unexplored distorted spin-1/2 kagome model consisting of three symmetry-inequivalent nearest-neighbor antiferromagnetic Heisenberg couplings Jhexagon, J and J', and uncover a rich ground state phase diagram even at the classical level. Using analytical arguments and numerical techniques we identify a collinear Q = 0 magnetic phase, two unusual non-collinear coplanar Q = (1/3,1/3) phases and a classical spin liquid phase with a degenerate manifold of non-coplanar ground states, resembling the jammed spin liquid phase found in the context of a bond-disordered kagome antiferromagnet. We further show with density functional theory calculations that the recently synthesized Y-kapellasite Y3Cu9(OH)19Cl8 is a realization of this model and predict its ground state to lie in the region of Q = (1/3,1/3) order, which remains stable even after inclusion of quantum fluctuation effects within variational Monte Carlo and pseudofermion functional renormalization group. The presented model opens a new direction in the study of kagome antiferromagnets.
Recent density functional theory (DFT) calculations for KFe2As2 have been shown to be insufficient to satisfactorily describe angle-resolved photoemission (ARPES) measurements as well as observed de Haas–van Alphen (dHvA) frequencies. In the present work, we extend DFT calculations based on the full-potential linear augmented plane-wave method by dynamical mean field theory (DFT+DMFT) to include correlation effects beyond the local density approximation. We present results for two sets of reported crystal structures. Our calculations indicate that KFe2As2 is a moderately correlated metal with a mass renormalization factor of the Fe $3{\rm d}$ orbitals between 1.6 and 2.7. Furthermore, the obtained shape and size of the Fermi surface are in good agreement with ARPES measurements and we observe some topological changes with respect to DFT calculations such as the opening of an inner hole cylinder at the Z point. As a result, our calculated dHvA frequencies differ greatly from existing DFT results and qualitatively agree with experimental data. On this basis, we argue that correlation effects are important to understand the -presently under debate- nature of the superconducting state in KFe2As2.