Comparison of repulsive interatomic potentials calculated with an all-electron DFT approach with experimental data

The interatomic potential determines the nuclear stopping power in materials. Most ion irradiation simulation models are based on the universal-Ziegler-Biersack-Littmark (ZBL) potential (Ziegler et a1.,1983), which, however, is an average and hence may not describe the stopping of all ion-material combinations well. Here we consider pair-specific interatomic potentials determined experimentally and by density functional theory simulations with DMol approach (DMol software, 1997) to choose basic wave functions. The interatomic potentials calculated using the DMol approach demonstrate an unexpectedly good agreement with experimental data. Differences are mainly observed for heavy atom systems, which suggests they can be improved by extending a basis set and more accurately considering the relativistic effects. Experimental data prove that the approach of determining interatomic potentials from quasielastic scattering can be successfully used for modeling collision cascades in ion-solids collisions. The data obtained clearly indicate that the use of any universal potential is limited to internuclear distances R <7 a(f) (a(f) is the Firsov length). (C) 2017 Published by Elsevier B.V.Peer reviewe

Solar Oscillations and Convection: II. Excitation of Radial Oscillations

Solar p-mode oscillations are excited by the work of stochastic, non-adiabatic, pressure fluctuations on the compressive modes. We evaluate the expression for the radial mode excitation rate derived by Nordlund and Stein (Paper I) using numerical simulations of near surface solar convection. We first apply this expression to the three radial modes of the simulation and obtain good agreement between the predicted excitation rate and the actual mode damping rates as determined from their energies and the widths of their resolved spectral profiles. We then apply this expression for the mode excitation rate to the solar modes and obtain excellent agreement with the low l damping rates determined from GOLF data. Excitation occurs close to the surface, mainly in the intergranular lanes and near the boundaries of granules (where turbulence and radiative cooling are large). The non-adiabatic pressure fluctuations near the surface are produced by small instantaneous local imbalances between the divergence of the radiative and convective fluxes near the solar surface. Below the surface, the non-adiabatic pressure fluctuations are produced primarily by turbulent pressure fluctuations (Reynolds stresses). The frequency dependence of the mode excitation is due to effects of the mode structure and the pressure fluctuation spectrum. Excitation is small at low frequencies due to mode properties -- the mode compression decreases and the mode mass increases at low frequency. Excitation is small at high frequencies due to the pressure fluctuation spectrum -- pressure fluctuations become small at high frequencies because they are due to convection which is a long time scale phenomena compared to the dominant p-mode periods.Comment: Accepted for publication in ApJ (scheduled for Dec 10, 2000 issue). 17 pages, 27 figures, some with reduced resolution -- high resolution versions available at http://www.astro.ku.dk/~aake/astro-ph/0008048

3D Radiative Hydrodynamics for Disk Stability Simulations: A Proposed Testing Standard and New Results

Recent three-dimensional radiative hydrodynamics simulations of protoplanetary disks report disparate disk behaviors, and these differences involve the importance of convection to disk cooling, the dependence of disk cooling on metallicity, and the stability of disks against fragmentation and clump formation. To guarantee trustworthy results, a radiative physics algorithm must demonstrate the capability to handle both the high and low optical depth regimes. We develop a test suite that can be used to demonstrate an algorithm's ability to relax to known analytic flux and temperature distributions, to follow a contracting slab, and to inhibit or permit convection appropriately. We then show that the radiative algorithm employed by Meji\'a (2004) and Boley et al. (2006) and the algorithm employed by Cai et al. (2006) and Cai et al. (2007, in prep.) pass these tests with reasonable accuracy. In addition, we discuss a new algorithm that couples flux-limited diffusion with vertical rays, we apply the test suite, and we discuss the results of evolving the Boley et al. (2006) disk with this new routine. Although the outcome is significantly different in detail with the new algorithm, we obtain the same qualitative answers. Our disk does not cool fast due to convection, and it is stable to fragmentation. We find an effective $\alpha\approx 10^{-2}$. In addition, transport is dominated by low-order modes.Comment: Submitted to Ap

Convective intensification of magnetic fields in the quiet Sun

Kilogauss-strength magnetic fields are often observed in intergranular lanes at the photosphere in the quiet Sun. Such fields are stronger than the equipartition field B_e, corresponding to a magnetic energy density that matches the kinetic energy density of photospheric convection, and comparable with the field B_p that exerts a magnetic pressure equal to the ambient gas pressure. We present an idealised numerical model of three-dimensional compressible magnetoconvection at the photosphere, for a range of values of the magnetic Reynolds number. In the absence of a magnetic field, the convection is highly supercritical and is characterised by a pattern of vigorous, time-dependent, “granular” motions. When a weak magnetic field is imposed upon the convection, magnetic flux is swept into the convective downflows where it forms localised concentrations. Unless this process is significantly inhibited by magnetic diffusion, the resulting fields are often much greater than B_e, and the high magnetic pressure in these flux elements leads to their being partially evacuated. Some of these flux elements contain ultra-intense magnetic fields that are significantly greater than B_p. Such fields are contained by a combination of the thermal pressure of the gas and the dynamic pressure of the convective motion, and they are constantly evolving. These ultra-intense fields develop owing to nonlinear interactions between magnetic fields and convection; they cannot be explained in terms of “convective collapse” within a thin flux tube that remains in overall pressure equilibrium with its surroundings

Ambipolar Drift Heating in Turbulent Molecular Clouds

Although thermal pressure is unimportant dynamically in most molecular gas, the temperature is an important diagnostic of dynamical processes and physical conditions. This is the first of two papers on thermal equilibrium in molecular clouds. We present calculations of frictional heating by ion-neutral (or ambipolar) drift in three-dimensional simulations of turbulent, magnetized molecular clouds. We show that ambipolar drift heating is a strong function of position in a turbulent cloud, and its average value can be significantly larger than the average cosmic ray heating rate. The volume averaged heating rate per unit volume due to ambipolar drift, H_AD ~ |JxB|^2 ~ B^4/L_B^2, is found to depend on the rms Alfvenic Mach number, M_A, and on the average field strength, as H_AD ~ M_A^2^4. This implies that the typical scale of variation of the magnetic field, L_B, is inversely proportional to M_A, which we also demonstrate.Comment: 37 pages, 9 figures include

On the Saturation of Astrophysical Dynamos: Numerical Experiments with the No-cosines flow

In the context of astrophysical dynamos we illustrate that the no-cosines flow, with zero mean helicity, can drive fast dynamo action and study the dynamo's mode of operation during both the linear and non-linear saturation regime: It turns out that in addition to a high growth rate in the linear regime, the dynamo saturates at a level significantly higher than normal turbulent dynamos, namely at exact equipartition when the magnetic Prandtl number is on the order of unity. Visualization of the magnetic and velocity fields at saturation will help us to understand some of the aspects of the non-linear dynamo problem.Comment: 8 pages, 5 figures, submitted to the proceedings of "Space Climate 1" to be peer-reviewed to Solar Physic

Expression, purification and preliminary crystal analysis of the human low Mr phosphotyrosine protein phosphatase isoform 1

AbstractThe genes of the human low Mr phosphotyrosine protein phosphatase (PTPase) isoforms 1 (IF1) and 2 (IF2) were isolated by screening a human placenta cDNA library, cloned in pGEX and expressed in E. coli as fusion proteins with glutathione S-transferase. The recombinant proteins were purified by a rapid one-step procedure allowing each enzyme to purify with high final yield and specific activity. This result is important for IF1, whose purification from natural sources is difficult, due to precipitation propensity, thus hindering structural studies. The enzymes obtained showed kinetic parameters very similar to those previously determined for the enzymes purified by classical procedures from both human erythrocytes and rat liver. These recombinant enzymes can therefore be used in place of those purified from natural sources for every purpose. IF1 and IF2 crystals were also grown. IF1 crystals were X-ray-grade, diffracted to better than 2.4 Å and were suitable for high resolution X-ray structure determination

Impact of granulation effects on the use of Balmer lines as temperature indicators

Balmer lines serve as important indicators of stellar effective temperatures in late-type stellar spectra. One of their modelling uncertainties is the influence of convective flows on their shape. We aim to characterize the influence of convection on the wings of Balmer lines. We perform a differential comparison of synthetic Balmer line profiles obtained from 3D hydrodynamical model atmospheres and 1D hydrostatic standard ones. The model parameters are appropriate for F,G,K dwarf and subgiant stars of metallicity ranging from solar to 1/1000 solar. The shape of the Balmer lines predicted by 3D models can never be exactly reproduced by a 1D model, irrespective of its effective temperature. We introduce the concept of a 3D temperature correction, as the effective temperature difference between a 3D model and a 1D model which provides the closest match to the 3D profile. The temperature correction is different for the different members of the Balmer series and depends on the adopted mixing-length parameter in the 1D model. Among the investigated models, the 3D correction ranges from -300K to +300K. Horizontal temperature fluctuations tend to reduce the 3D correction. Accurate effective temperatures cannot be derived from the wings of Balmer lines, unless the effects of convection are properly accounted for. The 3D models offer a physically well justified way of doing so. The use of 1D models treating convection with the mixing-length theory do not appear to be suitable for this purpose. In particular, there are indications that it is not possible to determine a single value of the mixing-length parameter which will optimally reproduce the Balmer lines for any choice of atmospheric parameters.Comment: 6 pages, 3 figures, accepted for publication in A&

Reflection of hydrogen and deuterium atoms from the beryllium, carbon, tungsten surfaces

Particle reflection coefficients for scattering of hydrogen and deuterium atoms from amorphous beryllium, carbon and tungsten were obtained, which are of interest for thermonuclear reactor physics. For the case of deuterium scattering from tungsten the data were also calculated for polycrystalline and crystalline target. The calculations were carried out by two methods: by modeling the trajectories of the incident particles and by using the binary collision approximation. Interaction potentials between hydrogen and helium atoms and the selected materials were calculated in the scope of the density function theory using program DMol for choosing wave functions. The dependence of the reflection coefficient RN on the potential well depth was found. The results demonstrate a good agreement with the available experimental values.Peer reviewe

Intramolecular vibronic dynamics in molecular solids: C60

Vibronic coupling in solid C60 has been investigated with a combination of resonant photoemission spectroscopy (RPES) and resonant inelastic x-ray scattering (RIXS). Excitation as a function of energy within the lowest unoccupied molecular orbital resonance yielded strong oscillations in intensity and dispersion in RPES, and a strong inelastic component in RIXS. Reconciling these two observations establishes that vibronic coupling in this core hole excitation leads to predominantly inelastic scattering and localization of the excited vibrations on the molecule on a femtosecond time scale. The coupling extends throughout the widths of the frontier valence bands.