Understanding and reducing errors in density functional calculations

We decompose the energy error of any variational DFT calculation into a contribution due to the approximate functional and that due to the approximate density. Typically, the functional error dominates, but in many interesting situations, the density-driven error dominates. Examples range from calculations of electron affinities to preferred geometries of ions and radicals in solution. In these abnormal cases, the DFT error can be greatly reduced by using a more accurate density. A small orbital gap often indicates a substantial density-driven error

Avoiding Unbound Anions in Density Functional Calculations

Converged approximate density functional calculations usually do not bind anions, due to large self-interaction error. But Hartree-Fock calculations have no such prob- lem, producing negative HOMO energies. A recently proposed scheme for calculating DFT energies on HF densities is shown to work very well for molecules, better than the common practice of restricting the basis set, except for cases like CN, where the HF density is too inaccurate due to spin contamination

Can Sodium Abundances of A-Type Stars Be Reliably Determined from Na I 5890/5896 Lines?

An extensive non-LTE abundance analysis based on Na I 5890/5896 doublet lines was carried out for a large unbiased sample of ~120 A-type main-sequence stars (including 23 Hyades stars) covering a wide v_e sin i range of ~10--300 km/s, with an aim to examine whether the Na abundances in such A dwarfs can be reliably established from these strong Na I D lines. The resulting abundances ([Na/H]_{58}), which were obtained by applying the T_eff-dependent microturbulent velocities of \xi ~2--4 km/s with a peak at T_eff ~ 8000 K (typical for A stars), turned out generally negative with a large diversity (from ~-1 to ~0), while showing a sign of v_e sin i-dependence (decreasing toward higher rotation). However, the reality of this apparently subsolar trend is very questionable, since these [Na/H]_{58} are systematically lower by ~0.3--0.6 dex than more reliable [Na/H]_{61} (derived from weak Na I 6154/6161 lines for sharp-line stars). Considering the large \xi-sensitivity of the abundances derived from these saturated Na I D lines, we regard that [Na/H]_{58} must have been erroneously underestimated, suspecting that the conventional \xi values are improperly too large at least for such strong high-forming Na I 5890/5896 lines, presumably due to the depth-dependence of \xi decreasing with height. The nature of atmospheric turbulent velocity field in mid-to-late A stars would have to be more investigated before we can determine reliable sodium abundances from these strong resonance D lines.Comment: 14 pages, 8 figures, accepted for publication in Publ. Astron. Soc. Japan, Vol. 61, No. 5 (2009

Multi-Cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space

Cells interacting through an extracellular matrix (ECM) exhibit emergent behaviors resulting from collective intercellular interaction. In wound healing and tissue development, characteristic compaction of ECM gel is induced by multiple cells that generate tensions in the ECM fibers and coordinate their actions with other cells. Computational prediction of collective cell-ECM interaction based on first principles is highly complex especially as the number of cells increase. Here, we introduce a computationally-efficient method for predicting nonlinear behaviors of multiple cells interacting mechanically through a 3-D ECM fiber network. The key enabling technique is superposition of single cell computational models to predict multicellular behaviors. While cell-ECM interactions are highly nonlinear, they can be linearized accurately with a unique method, termed Dual-Faceted Linearization. This method recasts the original nonlinear dynamics in an augmented space where the system behaves more linearly. The independent state variables are augmented by combining auxiliary variables that inform nonlinear elements involved in the system. This computational method involves a) expressing the original nonlinear state equations with two sets of linear dynamic equations b) reducing the order of the augmented linear system via principal component analysis and c) superposing individual single cell-ECM dynamics to predict collective behaviors of multiple cells. The method is computationally efficient compared to original nonlinear dynamic simulation and accurate compared to traditional Taylor expansion linearization. Furthermore, we reproduce reported experimental results of multi-cell induced ECM compaction

Validation Test of Geant4 Simulation of Electron Backscattering

Backscattering is a sensitive probe of the accuracy of electron scattering algorithms implemented in Monte Carlo codes. The capability of the Geant4 toolkit to describe realistically the fraction of electrons backscattered from a target volume is extensively and quantitatively evaluated in comparison with experimental data retrieved from the literature. The validation test covers the energy range between approximately 100 eV and 20 MeV, and concerns a wide set of target elements. Multiple and single electron scattering models implemented in Geant4, as well as preassembled selections of physics models distributed within Geant4, are analyzed with statistical methods. The evaluations concern Geant4 versions from 9.1 to 10.1. Significant evolutions are observed over the range of Geant4 versions, not always in the direction of better compatibility with experiment. Goodness-of-fit tests complemented by categorical analysis tests identify a configuration based on Geant4 Urban multiple scattering model in Geant4 version 9.1 and a configuration based on single Coulomb scattering in Geant4 10.0 as the physics options best reproducing experimental data above a few tens of keV. At lower energies only single scattering demonstrates some capability to reproduce data down to a few keV. Recommended preassembled physics configurations appear incapable of describing electron backscattering compatible with experiment. With the support of statistical methods, a correlation is established between the validation of Geant4-based simulation of backscattering and of energy deposition

Investigation of Geant4 Simulation of Electron Backscattering

A test of Geant4 simulation of electron backscattering recently published in this journal prompted further investigation into the causes of the observed behaviour. An interplay between features of geometry and physics algorithms implemented in Geant4 is found to significantly affect the accuracy of backscattering simulation in some physics configurations