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Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting
(2019)
Na+/H+ antiporters exchange sodium ions and protons on opposite sides of lipid membranes. The electroneutral Na+/H+ antiporter NhaP from archaea Pyrococcus abyssi (PaNhaP) is a functional homolog of the human Na+/H+ exchanger NHE1, which is an important drug target. Here we resolve the Na+ and H+ transport cycle of PaNhaP by transition-path sampling. The resulting molecular dynamics trajectories of repeated ion transport events proceed without bias force, and overcome the enormous time-scale gap between seconds-scale ion exchange and microseconds simulations. The simulations reveal a hydrophobic gate to the extracellular side that opens and closes in response to the transporter domain motion. Weakening the gate by mutagenesis makes the transporter faster, suggesting that the gate balances competing demands of fidelity and efficiency. Transition-path sampling and a committor-based reaction coordinate optimization identify the essential motions and interactions that realize conformational alternation between the two access states in transporter function.
The beam energy dependence of v4 (the quadrupole moment of the transverse radial flow) is sensitive to the nuclear equation of state (EoS) in mid-central Au + Au collisions at the energy range of 3<sNN−−−−√<30 GeV, which is investigated within the hadronic transport model JAM. Different equations of state, namely, a free hadron gas, a first-order phase transition and a crossover are compared. An enhancement of v4 at sNN−−−−√≈6 GeV is predicted for an EoS with a first-order phase transition. This enhanced v4 flow is driven by both the enhancement of v2 as well as the positive contribution to v4 from the squeeze-out of spectator particles which turn into participants due to the admixture of the strong collective flow in the shocked, compressed nuclear matter.
From the colour glass condensate to filamentation: systematics of classical Yang–Mills theory
(2019)
The non-equilibrium early time evolution of an ultra-relativistic heavy ion collision is often described by classical lattice Yang–Mills theory, starting from the colour glass condensate (CGC) effective theory with an anisotropic energy momentum tensor as initial condition. In this work we investigate the systematics associated with such studies and their dependence on various model parameters (IR, UV cutoffs and the amplitude of quantum fluctuations) which are not yet fixed by experiment. We perform calculations for SU() and SU(), both in a static box and in an expanding geometry. Generally, the dependence on model parameters is found to be much larger than that on technical parameters like the number of colours, boundary conditions or the lattice spacing. In a static box, all setups lead to isotropisation through chromo-Weibel instabilities, which is illustrated by the accompanying filamentation of the energy density. However, the associated time scale depends strongly on the model parameters and in all cases is longer than the phenomenologically expected one. In the expanding system, no isotropisation is observed for any parameter choice. We show how investigations at fixed initial energy density can be used to better constrain some of the model parameters.
Chirality is omnipresent in living nature. On the single molecule level, the response of a chiral species to a chiral probe depends on their respective handedness. A prominent example is the difference in the interaction of a chiral molecule with left or right circularly polarized light. In the present study, we show by Coulomb explosion imaging that circularly polarized light can also induce a chiral fragmentation of a planar and thus achiral molecule. The observed enantiomer strongly depends on the orientation of the molecule with respect to the light propagation direction and the helicity of the ionizing light. This finding might trigger new approaches to improve laser-driven enantioselective chemical synthesis.
We study the well-known resonance ψ(4040), corresponding to a 33S1 charm–anticharm vector state ψ(3S), within a QFT approach, in which the decay channels into DD, D∗D, D∗D∗, DsDs and D∗s Ds are considered. The spectral function shows sizable deviations from a Breit–Wigner shape (an enhancement, mostly generated by DD∗loops, occurs); moreover, besides the c ¯ c pole of ψ(4040), a second dynamically generated broad pole at 4 GeV emerges. Naively, it is tempting to identify this new pole with the unconfirmed state Y (4008). Yet, this state was not seen inthe reaction e+e− → ψ(4040) → DD∗, but in processes with π+π−J/ψ in the final state. A detailed study shows a related but different mechanism: a broad peak at 4GeV in the process e+e− → ψ(4040) → DD∗ → π+π−J/ψ appears when DD∗ loops are considered. Its existence in this reaction is not necessarily connected to the existence of a dynamically generated pole, but the underlying mechanism – the strong coupling of c ¯ c to DD∗ loops – can generate both of them. Thus, the controversial state Y (4008) may not be a genuine resonance, but a peak generated by the ψ(4040) and D∗D loops with π+π−J/ψ in the final state.
We present a study of the elliptic flow and RAA of D and D¯ mesons in Au+Au collisions at FAIR energies. We propagate the charm quarks and the D mesons following a previously applied Langevin dynamics. The evolution of the background medium is modeled in two different ways: (I) we use the UrQMD hydrodynamics + Boltzmann transport hybrid approach including a phase transition to QGP and (II) with the coarse-graining approach employing also an equation of state with QGP. The latter approach has previously been used to describe di-lepton data at various energies very successfully. This comparison allows us to explore the effects of partial thermalization and viscous effects on the charm propagation. We explore the centrality dependencies of the collisions, the variation of the decoupling temperature and various hadronization parameters. We find that the initial partonic phase is responsible for the creation of most of the D/D¯ mesons elliptic flow and that the subsequent hadronic interactions seem to play only a minor role. This indicates that D/D¯ mesons elliptic flow is a smoking gun for a partonic phase at FAIR energies. However, the results suggest that the magnitude and the details of the elliptic flow strongly depend on the dynamics of the medium and on the hadronization procedure, which is related to the medium properties as well. Therefore, even at FAIR energies the charm quark might constitute a very useful tool to probe the quark–gluon plasma and investigate its physics.
Application of the Luttinger theorem to the Kondo lattice YbRh2Si2 suggests that its large 4f-derived Fermi surface (FS) in the paramagnetic (PM) regime should be similar in shape and volume to that of the divalent local-moment antiferromagnet (AFM) EuRh2Si2 in its PM regime. Here we show by angle-resolved photoemission spectroscopy that paramagnetic EuRh2Si2 has a large FS essentially similar to the one seen in YbRh2Si2 down to 1 K. In EuRh2Si2 the onset of AFM order below 24.5 K induces an extensive fragmentation of the FS due to Brillouin zone folding, intersection and resulting hybridization of the Fermi-surface sheets. Our results on EuRh2Si2 indicate that the formation of the AFM state in YbRh2Si2 is very likely also connected with similar changes in the FS, which have to be taken into account in the controversial analysis and discussion of anomalies observed at the quantum critical point in this system.
We report on the observation of coherent terahertz (THz) emission from the quasi-one-dimensional charge-density wave (CDW) system, blue bronze (K0.3MoO3), upon photo-excitation with ultrashort near-infrared optical pulses. The emission contains a broadband, low-frequency component due to the photo-Dember effect, which is present over the whole temperature range studied (30–300 K), as well as a narrow-band doublet centered at 1.5 THz, which is only observed in the CDW state and results from the generation of coherent transverse-optical phonons polarized perpendicular to the incommensurate CDW b-axis. As K0.3MoO3 is centrosymmetric, the lowest-order generation mechanism which can account for the polarization dependence of the phonon emission involves either a static surface field or quadrupolar terms due to the optical field gradients at the surface. This phonon signature is also present in the ground-state conductivity, and decays in strength with increasing temperature to vanish above $T\sim 100\,{\rm{K}}$, i.e. significantly below the CDW transition temperature. The temporal behavior of the phonon emission can be well described by a simple model with two coupled modes, which initially oscillate with opposite polarity.
We present the black hole accretion code (BHAC), a new multidimensional general-relativistic magnetohydrodynamics module for the MPI-AMRVAC framework. BHAC has been designed to solve the equations of ideal general-relativistic magnetohydrodynamics in arbitrary spacetimes and exploits adaptive mesh refinement techniques with an efficient block-based approach. Several spacetimes have already been implemented and tested. We demonstrate the validity of BHAC by means of various one-, two-, and three-dimensional test problems, as well as through a close comparison with the HARM3D code in the case of a torus accreting onto a black hole. The convergence of a turbulent accretion scenario is investigated with several diagnostics and we find accretion rates and horizon-penetrating fluxes to be convergent to within a few percent when the problem is run in three dimensions. Our analysis also involves the study of the corresponding thermal synchrotron emission, which is performed by means of a new general-relativistic radiative transfer code, BHOSS. The resulting synthetic intensity maps of accretion onto black holes are found to be convergent with increasing resolution and are anticipated to play a crucial role in the interpretation of horizon-scale images resulting from upcoming radio observations of the source at the Galactic Center.
We present entropy-limited hydrodynamics (ELH): a new approach for the computation of numerical fluxes arising in the discretization of hyperbolic equations in conservation form. ELH is based on the hybridisation of an unfiltered high-order scheme with the first-order Lax-Friedrichs method. The activation of the low-order part of the scheme is driven by a measure of the locally generated entropy inspired by the artificial-viscosity method proposed by Guermond et al. (J. Comput. Phys. 230(11):4248-4267, 2011, doi:10.1016/j.jcp.2010.11.043). Here, we present ELH in the context of high-order finite-differencing methods and of the equations of general-relativistic hydrodynamics. We study the performance of ELH in a series of classical astrophysical tests in general relativity involving isolated, rotating and nonrotating neutron stars, and including a case of gravitational collapse to black hole. We present a detailed comparison of ELH with the fifth-order monotonicity preserving method MP5 (Suresh and Huynh in J. Comput. Phys. 136(1):83-99, 1997, doi:10.1006/jcph.1997.5745), one of the most common high-order schemes currently employed in numerical-relativity simulations. We find that ELH achieves comparable and, in many of the cases studied here, better accuracy than more traditional methods at a fraction of the computational cost (up to ∼50% speedup). Given its accuracy and its simplicity of implementation, ELH is a promising framework for the development of new special- and general-relativistic hydrodynamics codes well adapted for massively parallel supercomputers.