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We study the μ-μ45-T phase diagram of the 2+1-dimensional Gross-Neveu model, where μ denotes the ordinary chemical potential, μ45 the chiral chemical potential and T the temperature. We use the mean-field approximation and two different lattice regularizations with naive chiral fermions. An inhomogeneous phase at finite lattice spacing is found for one of the two regularizations. Our results suggest that there is no inhomogeneous phase in the continuum limit. We show that a chiral chemical potential is equivalent to an isospin chemical potential. Thus, all results presented in this work can also be interpreted in the context of isospin imbalance.
We explore the phase structure of the 1+1 dimensional Gross-Neveu model at finite number of fermion flavors using lattice field theory. Besides a chirally symmetric phase and a homogeneously broken phase we find evidence for the existence of an inhomogeneous phase, where the condensate is a spatially oscillating function. Our numerical results include a crude μ-T phase diagram.
Inhomogeneous condensation in the Gross-Neveu model in noninteger spatial dimensions 1 ≤ d < 3
(2023)
The Gross-Neveu model in the N→∞ approximation 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 non-integer 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 non-integer spatial dimensions. We find that the IP is present for all d<2 and vanishes exactly at d=2. Moreover, we find no instability towards an IP for 2≤d<3, which suggests that the IP in d=3 is solely generated by the presence of a regulator.
Inhomogeneous condensation in the Gross-Neveu model in non-integer spatial dimensions 1 ≤ d < 3
(2023)
he Gross-Neveu model in the N→∞ approximation 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 non-integer 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 non-integer spatial dimensions. We find that the IP is present for all d<2 and vanishes exactly at d=2. Moreover, we find no instability towards an IP for 2≤d<3, which suggests that the IP in d=3 is solely generated by the presence of a regulator.
Strontium ruthenate Sr2RuO4 is an unconventional superconductor whose pairing symmetry has not been fully clarified, despite more than two decades of intensive research. Recent NMR Knight shift experiments have rekindled the Sr2RuO4 pairing debate by giving strong evidence against all odd-parity pairing states, including chiral p-wave pairing that was for a long time the leading pairing candidate. Here, we exclude additional pairing states by analyzing recent elastocaloric measurements [YS. Li et al., Nature 607, 276--280 (2022)]. To be able to explain the elastocaloric experiment, we find that unconventional even-parity pairings must include either large dx2−y2-wave or large {dxz∣dyz}-wave admixtures, where the latter possibility arises because of the body-centered point group symmetry. These {dxz∣dyz}-wave admixtures take the form of distinctively body-centered-periodic harmonics that have horizontal line nodes. Hence gxy(x2−y2)-wave and dxy-wave pairings are excluded as possible dominant even pairing states.
Strontium ruthenate Sr2RuO4 is an unconventional superconductor whose pairing symmetry has not been fully clarified, despite more than two decades of intensive research. Recent NMR Knight shift experiments have rekindled the Sr2RuO4 pairing debate by giving strong evidence against all odd-parity pairing states, including chiral p-wave pairing that was for a long time the leading pairing candidate. Here, we exclude additional pairing states by analyzing recent elastocaloric measurements [YS. Li et al., Nature 607, 276--280 (2022)]. To be able to explain the elastocaloric experiment, we find that unconventional even-parity pairings must include either large dx2−y2-wave or large {dxz∣dyz}-wave admixtures, where the latter possibility arises because of the body-centered point group symmetry. These {dxz∣dyz}-wave admixtures take the form of distinctively body-centered-periodic harmonics that have horizontal line nodes. Hence gxy(x2−y2)-wave and dxy-wave pairings are excluded as possible dominant even pairing states.
The effects of internal quark structure of baryons on the composition and structure of neutron star matter with hyperons are investigated in the quark- meson coupling (QMC) model. The QMC model is based on mean-field description of nonoverlapping spherical bags bound by self-consistent exchange of scalar and vector mesons. The predictions of this model are compared with quantum hadrodynamic (QHD) model calibrated to reproduce identical nuclear matter saturation properties. By employing a density dependent bag constant through direct coupling to the scalar field, the QMC model is found to exhibit identical properties as QHD near saturation density. Furthermore, this modified QMC model provides well-behaved and continuous solutions at high densities relevant to the core of neutron stars. Two additional strange mesons are introduced which couple only to the strange quark in the QMC model and to the hyperons in the QHD model. The constitution and structure of stars with hyperons in the QMC and QHD models reveal interesting di erences. This suggests the importance of quark structure e ects in the baryons at high densities. PACS number(s): 26.60.+c, 21.65.+f, 12.39.Ba, 24.85.+p
We investigate in stable strange hadronic matter (SHM) the modifica- tion of the masses of the scalar (sigma,sigma') and the vector (omega,phi) mesons. The baryon ground state is treated in the relativistic Hartree approximation in the nonlinear sigma-omega and linear sigma'- phi model. In stable SHM, the masses of all the mesons reveal considerable reduction due to large vacuum polarization contribution from the hyperons and small density dependent effects caused by larger binding. PACS: 21.65+f, 24.10Jv
We introduce a model for the real-time evolution of a relativistic fluid of quarks coupled to non-equilibrium dynamics of the long wavelength (classical) modes of the chiral condensate. We solve the equations of motion numerically in 3+1 spacetime dimensions. Starting the evolution at high temperature in the symmetric phase, we study dynamical trajectories that either cross the line of first-order phase transitions or evolve through its critical endpoint. For those cases, we predict the behavior of the azimuthal momentum asymmetry for highenergy heavy-ion collisions at nonzero impact parameter.
We investigate the excitation function of directed flow, which can provide a clear signature of the creation of the QGP and demonstrate that the minimum of the directed flow does not correspond to the softest point of the EoS for isentropic expansion. A novel technique measuring the compactness is introduced to determine the QGP transition in relativistic-heavy ion collisions: The QGP transition will lead to higher compression and therefore to higher compactness of the source in coordinate space. This e ect can be observed by pion interferometry. We propose to measure the compactness of the source in the appropriate principal axis frame of the compactness tensor in coordinate space.
Compactness is introduced as a new method to search for the onset of the quark matter transition in relativistic heavy ion collisions. That transition supposedly leads to stronger compression and higher compactness of the source in coordinate space. That effect could be observed via pion interferometry. We propose to measure the compactness of the source in the appropriate principal axis frame of the compactness tensor in coordinate space.
Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments
(2023)
The release of inorganic phosphate (Pi) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. However, the molecular mechanisms underlying Pi release from both the core and barbed end of actin filaments remain unclear. Here, we combine cryo-EM with molecular dynamics simulations and in vitro reconstitution to demonstrate how actin releases Pi through a ‘molecular backdoor’. While constantly open at the barbed end, the backdoor is predominantly closed in filament-core subunits and only opens transiently through concerted backbone movements and rotameric rearrangements of residues close to the nucleotide binding pocket. This mechanism explains why Pi escapes rapidly from the filament end and yet slowly from internal actin subunits. In an actin variant associated with nemaline myopathy, the backdoor is predominantly open in filament-core subunits, resulting in greatly accelerated Pi release after polymerization and filaments with drastically shortened ADP-Pi caps. This demonstrates that the Pi release rate from F-actin is controlled by steric hindrance through the backdoor rather than by the disruption of the ionic bond between Pi and Mg2+ at the nucleotide-binding site. Our results provide the molecular basis for Pi release from actin and exemplify how a single, disease-linked point mutation distorts the nucleotide state distribution and atomic structure of the actin filament.
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.
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport. Their intricate 120 MDa architecture remains incompletely understood. Here, we report a near-complete structural model of the human NPC scaffold with explicit membrane and in multiple conformational states. We combined AI-based structure prediction with in situ and in cellulo cryo-electron tomography and integrative modeling. We show that linker Nups spatially organize the scaffold within and across subcomplexes to establish the higher-order structure. Microsecond-long molecular dynamics simulations suggest that the scaffold is not required to stabilize the inner and outer nuclear membrane fusion, but rather widens the central pore. Our work exemplifies how AI-based modeling can be integrated with in situ structural biology to understand subcellular architecture across spatial organization levels.
Using a microscopic transport model together with a coalescence after-burner, we study the formation of deuterons in Au + Au central collisions at s = 200 AGeV . It is found that the deuteron transverse momentum distributions are strongly a ected by the nucleon space-momentum correlations, at the moment of freeze-out, which are mostly determined by the number of rescatterings. This feature is useful for studying collision dynamics at ultrarelativistic energies.
A non-monotonic energy dependence of the K + / pi + ratio with a sharp maximum close to 30 A GeV is observed in central Pb+Pb collisions. Within a statistical model of the early stage, this is interpreted as a sign of the phase transition to a QGP, which causes a sharp change in the energy dependence of the strangeness to entropy ratio. This observation naturally motivates us to study the production of multistrange hyperons (Xi, Omega) as a function of the beam energy. Furthermore it was suggested that the kinematic freeze-out of Omega takes place directly at QGP hadronization. If this is indeed the case, the transverse momentum spectra of the Omega directly reflect the transverse expansion velocity of a hadronizing QGP. In this report we show preliminary NA49 results on Omega - and Omega + production in central Pb+Pb collisions at 40 and 158 A GeV and compare them to measurements of Xi - and Xi + production in central Pb+Pb collisions at 30, 40, 80 and 158 A GeV.
We compare different models for hadronic and quark phases of cold baryon rich matter in an attempt to find a deconfinement phase transition between them. For the hadronic phase we consider Walecka type mean field models which describe well the nuclear saturation properties. We also use the variational chain model which takes into account correlation effects. For the quark phase we consider the MIT bag model, the Nambu Jona-Lasinio and the massive quasiparticle models. By comparing pressure as a function of baryon chemical potential we find that crossings of hadronic and quark branches are possible only in some exceptional cases while for most realistic parameter sets these branches do not cross at all. Moreover, the chiral phase transition, often discussed within the framework of QCD motivated models, lies in the region where the quark phases are unstable with respect to the hadronic phase. We discuss possible physical consequences of these findings.
Chemically non equilibrated quark antiquark matter is studied within the Nambu Jona-Lasinio model. The equations of state of non strange (q = u, d) and strange (q = s) qq systems are calculated in the mean field approximation. The existence of metastable bound states with zero pressure is predicted at finite densities and temperatures T 50 MeV. It is shown that the minimum energy per particle occurs for symmetric systems, with equal densities of quarks and antiquarks. At T = 0 these metastable states have quark number densities of about 0.5 fm 3 for q = u, d and of 1 fm 3 for q = s. A first order chiral phase transition is found at finite densities and temperatures. The critical temperature for this phase transition is approximately 75 MeV (90 MeV) for the non strange (strange) baryon free quark antiquark matter. For realistic choices of parameters, the model does not predict a phase transition in chemically equilibrated systems. Possible decay channels of the metastable qq droplets and their signatures in relativistic heavy ion collisions are discussed.
Properties of dense quark matter in and out of chemical equilibrium are studied within the SU(3) Nambu Jona-Lasinio model. In addition to the 4 fermion scalar and vector terms the model includes also the 6 fermion flavour mixing interaction. First we study a novel form of deconfined matter, meso-matter, which is composed of equal number of quarks and antiquarks. It can be thought of as a strongly compressed meson gas where mesons are melted into their elementary constituents, quarks and antiquarks. Strongly bound states in this quark antiquark matter are predicted for all flavour combinations of qq pairs. The maximum binding energy reaches up to 180 MeV per qq pair for mixtures with about 70% of strange (s¯s) pairs. Equilibrated baryon rich quark matter with various flavour compositions is also studied. In this case only shallow bound states appear in systems with a significant admixture(about 40%) of strange quarks (strangelets). Their binding energies are quite sensitive to the relative strengths of scalar and vector interactions. The common property of all these bound states is that they appear at high particle densities when the chiral symmetry is nearly restored. Thermal properties of meso-matter as well as chemically equilibrated strange quark matter are also investigated. Possible decay modes of these bound states are discussed.
We study the bremsstrahlung of virtual omega mesons due to the collective deceleration of nuclei at the initial stage of an ultrarelativistic heavy ion collision. It is shown that electromagnetic decays of these mesons may give an important contribution to the observed yields of dileptons. Mass spectra of e+e and µ+µ pairs produced in central Au+Au collisions are calculated under some simplifying assumptions on the space time variation of the baryonic current in a nuclear collision process. Comparison with the CERES data for 160 AGev Pb+Au collisions shows that the proposed mechanism gives a noticeable fraction of the observed e+e pairs in the intermediate region of invariant masses. Sensi tivity of the dilepton yield to the in medium modification of masses and widths of vector mesons is demonstrated.
According to the Walecka mean field theory of nuclear interaction the collective mutual deceleration of the colliding nuclei gives rise to the bremsstrahlung of real and virtual ! mesons. It is shown that decays of these mesons may give a noticeable contribution to the observed yields of the baryon antibaryon pairs, dileptons and pions. Excitation functions and rapidity distributions of particles produced by this mechanism are calculated under some simplifying assumptions about the space time variation of meson fields in nuclear collisions. The calculated multiplicities of coherently produced particles grow fast with the bombarding energy, reaching a saturation above the RHIC bombarding energy. In the case of central Au+Au collisions the bremsstrahlung mechanism becomes comparable with particle production in incoherent hadron hadron collisions above the AGS energies. The rapidity spectra of antibaryons and pions exhibit a characteristic two hump structure which is a consequence of incomplete projectile target stopping at the initial stage of the reaction. The predicted distribution of e+e pairs has a strong peak at invariant masses Me+e < 0.5 GeV.
Collective bremsstrahlung of vector meson fields in relativistic nuclear collisions is studied within the time dependent Walecka model. Mutual deceleration of the colliding nuclei is described by introducing the e ective stopping time and average rapidity loss of baryons. It is shown that electromagnetic decays of virtual ω mesons produced by bremsstrahlung mechanism can provide a substantial contribution to the soft dilepton yield at the SPS bombarding energies. In particular, it may be responsible for the dilepton enhancement observed in 160 AGev central Pb+Au collisions. Suggestions for future experiments to estimate the relative contribution of the collective mechanism are given.
Equation of state of baryon rich quark matter is studied within the SU(3) Nambu Jona-Lasinio model with flavour mixing interaction. Possible bound states (strangelets) and chiral phase transitions in this matter are investigated at various values of strangeness fraction rs. The model predictions are very sensitive to the ratio of vector and scalar coupling constants, ¾ = GV /GS. At ¾ = 0.5 and zero temperature the maximum binding energy (about 15 MeV per baryon) takes place at rs C 0.4. Such strangelets are negatively charged and have typical life times < 10 7 s. The calculations are carried out also at finite temperatures. They show that bound states exist up to temperatures of about 15 MeV. The model predicts a first order chiral phase transition at finite baryon densities. The parameters of this phase transition are calculated as a function of rs.
Antibaryons bound in nuclei
(2004)
We study the possibility of producing a new kind of nuclear systems which in addition to ordinary nucleons contain a few antibaryons (B = p, , etc.). The properties of such systems are described within the relativistic mean field model by employing G parity transformed interactions for antibaryons. Calculations are first done for infinite systems and then for finite nuclei from 4He to 208Pb. It is demonstrated that the presence of a real antibaryon leads to a strong rearrangement of a target nucleus resulting in a significant increase of its binding energy and local compression. Noticeable e ects remain even after the antibaryon coupling constants are reduced by factor 3 4 compared to G parity motivated values. We have performed detailed calculations of the antibaryon annihilation rates in the nuclear environment by applying a kinetic approach. It is shown that due to significant reduction of the reaction Q values, the in medium annihilation rates should be strongly suppressed leading to relatively long lived antibaryon nucleus systems. Multi nucleon annihilation channels are analyzed too. We have also estimated formation probabilities of bound B + A systems in pA reactions and have found that their observation will be feasible at the future GSI antiproton facility. Several observable signatures are proposed. The possibility of producing multi quark antiquark clusters is discussed. PACS numbers: 25.43.+t, 21.10.-k, 21.30.Fe, 21.80.+a
We study properties of compact stars with the deconfinement phase transition in their interiors. The equation of state of cold baryon-rich matter is constructed by combining a relativistic mean-field model for the hadronic phase and the MIT Bag model for the deconfined phase. In a narrow parameter range two sequences of compact stars (twin stars), which differ by the size of the quark core, have been found. We demonstrate the possibility of a rapid transition between the twin stars with the energy release of about 10 ^52 ergs. This transition should be accompanied by the prompt neutrino burst and the delayed gamma-ray burst.
The in-medium properties of the vector mesons are known to be modified significantly in hot and dense hadronic matter due to vacuum polarisation e ects from the baryon sector in the Walecka model. The vector meson mass drops significantly in the medium due to the e ects of the Dirac sea. In the variational approach adopted in the present paper, these e ects are taken into account through a realignment of the ground state with baryon condensates. Such a realignment of the ground state becomes equivalent to summing of the baryonic tadpole diagrams in the relativistic Hartree approximation (RHA). The approximation scheme adopted here goes beyond RHA to include quantum e ects from the scalar meson and is nonperturbative and self consistent. It includes multiloop e ects, thus corresponding to a di erent approximation as compared to the one loop approximation of including scalar field quantum corrections. In the present work, we study the properties of the vector mesons in the hot and dense matter as modified due to such quantum correction e ects from the baryon as well as scalar meson sectors. These medium modifications of the properties of the vector mesons are reflected, through the shifting and broadening of the respective peaks, in the low mass dilepton spectra. There is broadening of the peaks due to corrections from scalar meson quantum e ects as compared to the relativistic Hartree approximation. It is seen to be rather prominent for the ! meson in the invariant mass plot. PACS number: 21.65.+f,12.40.Yx
We evaluate the in-medium D and -meson masses in hot hadronic matter induced by interactions with the light hadron sector described in a chiral SU(3) model. The e ective Lagrangian approach is generalized to SU(4) to include charmed mesons. We find that the D-mass drops substantially at finite temperatures and densities, which open the channels of the decay of the charmonium states ( 2, c, J/ ) to D pairs in the thermal medium. The e ects of vacuum polarisations from the baryon sector on the medium modification of the D-meson mass relative to those obtained in the mean field approximation are investigated. The results of the present work are compared to calculations based on the QCD sum-rule approach, the quark-meson coupling model, chiral perturbation theory, as well as to studies of quarkonium dissociation using heavy quark potential from lattice QCD.
Abstract: The medium modification of kaon and antikaon masses, compatible with low energy KN scattering data, are studied in a chiral SU(3) model. The mutual interactions with baryons in hot hadronic matter and the e ects from the baryonic Dirac sea on the K( ¯K ) masses are examined. The in-medium masses from the chiral SU(3) e ective model are compared to those from chiral perturbation theory. Furthermore, the influence of these in-medium e ects on kaon rapidity distributions and transverse energy spectra as well as the K, ¯K flow pattern in heavy-ion collision experiments at 1.5 to 2 A·GeV are investigated within the HSD transport approach. Detailed predictions on the transverse momentum and rapidity dependence of directed flow v1 and the elliptic flow v2 are provided for Ni+Ni at 1.93 A·GeV within the various models, that can be used to determine the in-medium K± properties from the experimental side in the near future.
Abstract: The e ect of vacuum fluctuations on the in-medium hadronic properties is investigated using a chiral SU(3) model in the nonlinear realization. The e ect of the baryon Dirac sea is seen to modify hadronic properties and in contrast to a calculation in mean field approximation it is seen to give rise to a significant drop of the vector meson masses in hot and dense matter. This e ect is taken into account through the summation of baryonic tadpole diagrams in the relativistic Hartree approximation (RHA), where the baryon self energy is modified due to interactions with both the non-strange ( ) and the strange ( ) scalar fields.
In this paper we present recent results from the NA49 experiment for Lambda and Lambda hyperons produced in central Pb+Pb collisions at 40, 80 and 158 A GeV. Transverse mass spectra and rapidity distributions for Lambda are shown for all three energies. The shape of the rapidity distribution becomes flatter with increasing beam energy. The multiplicities at mid-rapidity as well as the total yields are studied as a function of collision energy including AGS measurements. The ratio Lambda/pi at mid-rapidity and in 4 pi has a maximum around 40 A GeV. In addition, Lambda rapidity distributions have been measured at 40 and 80 A GeV, which allows to study the Lambda Lambda ratio.
Rapidity distributions for $\Lambda$ and $\bar{\Lambda}$ hyperons in central Pb-Pb collisions at 40, 80 and 158 A$\cdot$GeV and for ${\rm K}_{s}^{0}$ mesons at 158 A$\cdot$GeV are presented. The lambda multiplicities are studied as a function of collision energy together with AGS and RHIC measurements and compared to model predictions. A different energy dependence of the $\Lambda/\pi$ and $\bar{\Lambda}/\pi$ is observed. The $\bar{\Lambda}/\Lambda$ ratio shows a steep increase with collision energy. Evidence for a $\bar{\Lambda}/\bar{\rm p}$ ratio greater than 1 is found at 40 A$\cdot$GeV.
Rapidity distributions for Lambda and anti-Lambda hyperons in central Pb-Pb collisions at 40, 80 and 158 AGeV and for K 0 s mesons at 158 AGeV are presented. The lambda multiplicities are studied as a function of collision energy together with AGS and RHIC measurements and compared to model predictions. A different energy dependence of the Lambda/pi and anti-Lambda/pi is observed. The anti-Lambda/Lambda ratio shows a steep increase with collision energy. Evidence for a anti-Lambda/anti-p ratio greater than 1 is found at 40 AGeV.
The existence of bound states induced by local impurities coupled to an insulating host depends decisively on the global topological properties of the host's electronic structure. In this context, we consider magnetic impurities modelled as classical unit-length spins that are exchange-coupled to the spinful Haldane model on the honeycomb lattice. We investigate the spectral flow of bound states with the coupling strength J in both the topologically trivial and Chern-insulating phases. In addition to conventional k-space topology, an additional, spatially local topological feature is available, based on the space of impurity-spin configurations forming, in case of R impurities, an R-fold direct product of two-dimensional spheres. Global k-space and local S-space topology are represented by different topological invariants, the first (k-space) Chern number and the R-th (S-space) spin-Chern number. We demonstrate that there is a local S-space topological transition as a function of J associated with a change in the spin Chern number and work out the implications of this for the J-dependent local electronic structure close to the impurities and, in particular, for in-gap bound states. The critical exchange couplings' dependence on the parameters of the Haldane model, and thus on the k-space topological state, is obtained numerically to construct local topological phase diagrams for systems with R=1 and R=2 impurity spins.
Using CORSIKA for simulating extensive air showers, we study the relation between the shower characteristics and features of hadronic multiparticle production at low energies. We report about investigations of typical energies and phase space regions of secondary particles which are important for muon production in extensive air showers. Possibilities to measure relevant quantities of hadron production in existing and planned accelerator experiments are discussed.
Binding of the spike protein of SARS-CoV-2 to the human angiotensin converting enzyme 2 (ACE2) receptor triggers translocation of the virus into cells. Both the ACE2 receptor and the spike protein are heavily glycosylated, including at sites near their binding interface. We built fully glycosylated models of the ACE2 receptor bound to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Using atomistic molecular dynamics (MD) simulations, we found that the glycosylation of the human ACE2 receptor contributes substantially to the binding of the virus. Interestingly, the glycans at two glycosylation sites, N90 and N322, have opposite effects on spike protein binding. The glycan at the N90 site partly covers the binding interface of the spike RBD. Therefore, this glycan can interfere with the binding of the spike protein and protect against docking of the virus to the cell. By contrast, the glycan at the N322 site interacts tightly with the RBD of the ACE2-bound spike protein and strengthens the complex. Remarkably, the N322 glycan binds into a conserved region of the spike protein identified previously as a cryptic epitope for a neutralizing antibody. By mapping the glycan binding sites, our MD simulations aid in the targeted development of neutralizing antibodies and SARS-CoV-2 fusion inhibitors.
Nuclear clusters as a probe for expansion flow in heavy ion reactions at 10-A/GeV - 15-A/GeV.
(1996)
A phase space coalescence description based on the Wigner-function method for cluster formation in relativistic nucleus-nucleus collisions is presented. The momentum distributions of nuclear clusters d,t and He are predicted for central Au(11.6AGeV)Au and Si(14.6AGeV)Si reactions in the framework of the RQMD transport approach. Transverse expansion leads to a strong shoulderarm shape and di erent inverse slope parameters in the transverse spectra of nuclear clusters deviating markedly from thermal distributions. A clear bounce-o event shape is seen: the averaged transverse flow velocities in the reaction plane are for clusters larger than for protons. The cluster yields particularly at low pt at midrapidities and the in-plane (anti)flow of clusters and pions change if suitably strong baryon potential interactions are included. This allows to study the transient pressure at high density via the event shape analysis of nucleons, nucleon clusters and other hadrons.
The spike protein of SARS-CoV-2 is a highly flexible membrane receptor that triggers the translocation of the virus into cells by attaching to the human receptors. Like other type I membrane receptors, this protein has several extracellular domains connected by flexible hinges. The presence of these hinges results in high flexibility, which consequently results in challenges in defining the conformation of the protein. Here, We developed a new method to define the conformational space based on a few variables inspired by the robotic field’s methods to determine a robotic arm’s forward kinematics. Using newly performed atomistic molecular dynamics (MD) simulations and publicly available data, we found that the Denavit-Hartenberg (DH) parameters can reliably show the changes in the local conformation. Furthermore, the rotational and translational components of the homogenous transformation matrix constructed based on the DH parameters can identify the changes in the global conformation of the spike and also differentiate between the conformation with a similar position of the spike head, which other types of parameters, such as spherical coordinates, fail to distinguish between such conformations. Finally, the new method will be beneficial for looking at the conformational heterogeneity in all other type I membrane receptors.
We develop a relativistic model to describe the bound states of positive energy and negative energy in finite nuclei at the same time. Instead of searching for the negative-energy solution of the nucleon s Dirac equation, we solve the Dirac equations for the nucleon and the anti-nucleon simultaneously. The single-particle energies of negative-energy nucleons are obtained through changing the sign of the single-particle energies of positive-energy anti-nucleons. The contributions of the Dirac sea to the source terms of the meson fields are evaluated by means of the derivative expansion up to the leading derivative order for the one-meson loop and one-nucleon loop. After refitting the parameters of the model to the properties of spherical nuclei, the results of positive-energy sector are similar to that calculated within the commonly used relativistic mean field theory under the no-sea approximation. However, the bound levels of negative-energy nucleons vary drastically when the vacuum contributions are taken into account. It implies that the negative-energy spectra deserve a sensitive probe to the e ective interactions in addition to the positive-energy spectra.
We develop a relativistic model to describe the bound states of positive energy and negative energy in finite nuclei at the same time. Instead of searching for the negative-energy solution of the nucleon's Dirac equation, we solve the Dirac equations for the nucleon and the anti-nucleon simultaneously. The single-particle energies of negative-energy nucleons are obtained through changing the sign of the single-particle energies of positive-energy anti-nucleons. The contributions of the Dirac sea to the source terms of the meson fields are evaluated by means of the derivative expansion up to the leading derivative order for the one-meson loop and one-nucleon loop. After refitting the parameters of the model to the properties of spherical nuclei, the results of positive-energy sector are similar to that calculated within the commonly used relativistic mean field theory under the no-sea approximation. However, the bound levels of negative-energy nucleons vary drastically when the vacuum contributions are taken into account. It implies that the negative-energy spectra deserve a sensitive probe to the effective interactions in addition to the positive-energy spectra.
A new chiral SU(3) Lagrangian is proposed to describe the properties of kaons and anti-kaons in the nuclear medium. The saturation properties of nuclear matter are reproduced as well as the results of the Dirac-Brückner theory. After introducing the coupling between the omega meson and the kaon, our results for e ective kaon and anti-kaon energy are quite similar as calculated in the one-boson-exchange model.
A new chiral SU(3) Lagrangian is proposed to describe the properties of kaons and antikaons in the nuclear medium, the ground state of dense matter and the kaon-nuclear interactions consistently. The saturation properties of nuclear matter are reproduced as well as the results of the Dirac-Brückner theory. After taking into account the coupling between the omega meson and the kaon, we obtain similar results for the e ective kaon and antikaon energies as calculated in the one-boson-exchange model while in our model the parameters of the kaon-nuclear interactions are constrained by the SU(3) chiral symmetry. PACS number(s): 14.40.Aq, 12.39.Fe, 21.30.Fe
A self-consistent relativistic integral-di erential equation of the Boltzmann- Uehling-Uhlenbeck-type for the N*(1440) resonance is developed based on an effective Lagrangian of baryons interacting through mesons. The closed time-path Green s function technique and semi-classical, quasi-particle and Born approxima- tions are employed in the derivation. The non-equilibrium RBUU-type equation for the N*(1440) is consistent with that of nucleon s and delta s which we derived before. Thus, we obtain a set of coupled equations for the N,Delta and N*(1440) distribution functions. All the N (1440)-relevant in-medium two-body scattering cross sections within the N,Delta and N*(1440) system are derived from the same effective Lagrangian in addition to the mean field and presented analytically, which can be directly used in the study of relativistic heavy-ion collisions. The theoreticalprediction of the free pp - pp* (1440) cross section is in good agreement with the experimental data. We calculate the in-medium N+N - N+N* , N* +N - N+N and N*+N - N* +N cross sections in cold nuclear matter up to twice the nuclear matter density. The influence of different choices of the N* N* coupling strengths, which can not be obtained through fitting certain experimental data, are discussed. The results show that the density dependence of predicted in-medium cross sections are sensitive to the N* N* coupling strengths used. An evident density dependence will appear when a large scalar coupling strength of g^(sigma) N*N* is assumed. PACS number(s): 24.10.Cn; 25.70.-z; 21.65.+f
A self-consistent relativistic Boltzmann-Uehling-Uhlenbeck equation for the N (1440) resonance is developed based on an effective Lagrangian of baryons interacting through mesons. The equation is consistent with that of nucleon s and delta s which we derived before. Thus, we obtain a set of coupled equations for the N, Delta and N (1440) distribution functions. All the N (1440)-relevant in-medium two-body scattering cross sections within the N, Delta and N (1440) system are derived from the same effective Lagrangian in addition to the mean field and presented analytically. Medium effects on the cross sections are discussed.
We derive the self-consistent relativistic quantum transport equation for the pion distribution function based on an effective Lagrangian of the QHD-II model. The closed time-path Green's function technique, the semi-classical, quasi-particle and Born approximation are employed in the derivation. Both the mean field and collision term are derived from the same Lagrangian and presented analytically. The dynamical equation for the pions is consistent with that for the nucleons and deltas which we developed before. Thus, we obtain a self-consistent relativistic transport model which describes the hadronic matter with N, Delta and pi degrees of freedom simultaneously. Within this approach, we investigate the medium effects on the pion dispersion relation as well as the pion absorption and pion production channels in cold nuclear matter. In contrast to the results of the non-relativistic model, the pion dispersion relation becomes harder at low momenta and softer at high momenta as compared to the free one. The theoretically predicted free pi N to Delta cross section is in agreement with the experimental data. Medium effects on the pi N to Delta cross section and momentum-dependent Delta-decay width are shown to be substantial.
Relativistic quantum transport theory of hadronic matter: the coupled nucleon, delta and pion system
(1998)
We derive the relativistic quantum transport equation for the pion distribution function based on an effective Lagrangian of the QHD-II model. The closed time-path Green s function technique, the semi-classical, quasiparticle and Born approximation are employed in the derivation. Both the mean field and collision term are derived from the same Lagrangian and presented analytically. The dynamical equation for the pions is consistent with that for the nucleons and deltas which we developed before. Thus, we obtain a relativistic transport model which describes the hadronic matter with N,Delta and pi degrees of freedom simultaneously. Within this approach, we investigate the medium e ects on the pion dispersion relation as well as the pion absorption and pion production channels in cold nuclear matter. In contrast to the results of the non-relativistic model, the pion dispersion relation becomes harder at low momenta and softer at high momenta as compared to the free one, which is mainly caused by the relativistic kinetics. The theoretically predicted free pi*N -> Delta cross section is in agreement with the experimental data. Medium e ects on the pi*N -> Delta cross section and momentum-dependent Delta-decay width are shown to be substantial. PACS number(s): 24.10.Cn; 13.75.Cs; 21.65.+f; 25.70.-z
The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of this fundamental interaction are still elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarsegrained and atomistic models with co-evolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted into a novel structural model that rationalizes previous experimental observations. We identify an evolutionary-conserved interaction surface formed by helix II of the DnaJ J-domain and a groove on lobe IIA of the DnaK nucleotide binding domain, involving the inter-domain linker.
Freeze out of particles across three dimensional space-time hypersurface is discussed in a simple kinetic model. The final momentum distribution of emitted particles, for freeze out surfaces with space-like normal, shows a non-exponential transverse momentum spectrum. The slope parameter of the pt distribution increases with increasing pt, in agreement with recently measured SPS pion and h spectra.
In continuum and fluid dynamical models, particles, which leave the system and reach the detectors, can be taken into account via freeze-out (FO) or final break-up schemes, where the frozen out particles are formed on a 3-dimensional hypersurface in space-time. Such FO descriptions are important ingredients of evaluations of two-particle correlation data, transverse-, longitudinal-, radial- and cylindrical- flow analyses, transverse momentum and transverse mass spectra and many other observables. The FO on a hypersurface is a discontinuity, where the pre FO equilibrated and interacting matter abruptly changes to non-interacting particles, showing an ideal gas type of behavior.
Kinetic freeze out models
(1999)
Freeze out of particles across a space-time hypersurface is discussed in kinetic models. The calculation of final momentum distribution of emitted particles is described for freeze out surfaces, with spacelike normals. The resulting non-equilibrium distribution does not resemble, the previously proposed, cut Jüttner distribution, and shows non-exponential pt-spectra similar to the ones observed in experiments. PACS: 24.10.Nz, 25.75.-q
We introduce a smooth mapping of some discrete space-time symmetries into quasi-continuous ones. Such transformations are related with q-deformations of the dilations of the Euclidean space and with the non-commutative space. We work out two examples of Hamiltonian invariance under such symmetries. The Schrodinger equation for a free particle is investigated in such a non-commutative plane and a connection with anyonic statistics is found. PACS: 03.65.Fd, 11.30.Er