Generalized Density-Functional Tight-Binding Repulsive Potentials from Unsupervised Machine Learning

We combine the approximate density-functional tight-binding (DFTB) method with unsupervised machine learning. This allows us to improve transferability and accuracy, make use of large quantum chemical data sets for the parametrization, and efficiently automatize the parametrization process of DFTB. For this purpose, generalized pair-potentials are introduced, where the chemical environment is included during the learning process, leading to more specific effective two-body potentials. We train on energies and forces of equilibrium and nonequilibrium structures of 2100 molecules, and test on ∼130 000 organic molecules containing O, N, C, H, and F atoms. Atomization energies of the reference method can be reproduced within an error of ∼2.6 kcal/mol, indicating drastic improvement over standard DFTB

Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes

The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree–Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna–Matthews–Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future

Correction: Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes

Correction for ‘Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes’ by Beatrix M. Bold et al., Phys. Chem. Chem. Phys., 2020, 22, 10500–10518, https://doi.org/10.1039/C9CP05753F. The authors have recognised two errors in the data for the published version of this article. The first one concerns the reported QM/MM calculations on the Fenna–Matthews–Olson (FMO) complex, and the second error affects all Coulomb couplings presented. In brief, the most important changes are: (i) the ZINDO site energies for the individual pigments are closer to each other and the ZINDO site energy fluctuations are smaller; (ii) the couplings are smaller and now in better agreement with reference data; and (iii) as a consequence, the exciton splitting is decreased. These errors do not change the conclusions of the study but only lead to small corrections of the reported results, as detailed below

Effects of crystallographic anisotropy on fracture development and acoustic emission in quartz

Transgranular microcracking is fundamental for the initiation and propagation of all fractures in rocks. The geometry of these microcracks is primarily controlled by the interaction of the imposed stress field with the mineral elastic properties. However, the effects of anisotropic elastic properties of minerals on brittle fracture are not well understood. This study examines the effects of elastic anisotropy of quartz on the geometry of brittle fracture and related acoustic emissions (AE) developed during indentation experiments on single crystals at ambient pressure and temperature. A Hertzian cone crack developed during blunt indentation of a single crystal of flawless Brazilian quartz parallel to the c axis shows geometric deviation away from predictions based on the isotropic case, consistent with trigonal symmetry. The visible cone crack penetration depth varies from 3 to 5 mm and apical angle from 53 to 40. Electron backscatter diffraction (EBSD) mapping of the crack tip shows that fracturing initiates along a ~40 μm wide process zone, comprising damage along overlapping en echelon high-index crystallographic planes, shown by discrete bands of reduced electron backscatter pattern (EBSP) quality (band contrast).Coalescence of these surfaces results in a stepped fracture morphology. Monitoring of AE during indentation reveals that the elastic anisotropy of quartz has a significant effect on AE location and focal mechanisms. Ninety-four AE events were recorded during indentation and show an increasing frequency with increasing load. They correspond to the development of subsidiary concentric cracks peripheral to the main cone crack. The strong and complex anisotropy in seismic velocity (~28% Vp, ~43% Vs with trigonal symmetry) resulted in inaccurate and high uncertainty in AE locations using Geiger location routine with an isotropic velocity model. This problem was overcome by using a relative (master event) location algorithm that only requires a priori knowledge of the velocity structure within the source volume. The AE location results correlate reasonably well to the extent of the observed cone crack. Decomposition of AE source mechanisms of the Geiger relocated events shows dominantly end-member behavior between tensile and compressive vector dipole events, with some double-couple-dominated events and no purely tensile or compressive events. The same events located by the master event algorithm yield greater percentage of vector dipole components and no double-couple events, indicating that AE source mechanism solutions can depend on AE location accuracy, and therefore, relocation routine that is utilized. Calculations show that the crystallographic anisotropy of quartz causes apparent deviation of the moment tensors away from double-couple and pure tensile/compressive sources consistent with the observations. Preliminary modeling of calcite anisotropy shows a response distinct from quartz, indicating that the effects of anisotropy on interpreting AE are complex and require detailed further study

Dynamics of Disks and Warps

This chapter reviews theoretical work on the stellar dynamics of galaxy disks. All the known collective global instabilities are identified, and their mechanisms described in terms of local wave mechanics. A detailed discussion of warps and other bending waves is also given. The structure of bars in galaxies, and their effect on galaxy evolution, is now reasonably well understood, but there is still no convincing explanation for their origin and frequency. Spiral patterns have long presented a special challenge, and ideas and recent developments are reviewed. Other topics include scattering of disk stars and the survival of thin disks.Comment: Chapter accepted to appear in Planets, Stars and Stellar Systems, vol 5, ed G. Gilmore. 32 pages, 17 figures. Includes minor corrections made in proofs. Uses emulateapj.st

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Background Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors. Results Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged. Conclusions Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.Peer reviewe

An identification of the Baum-Connes and Davis-Lück assembly maps

The Baum–Connes conjecture predicts that a certain assembly map is an isomorphism. We identify the homotopy theoretical construction of the assembly map by Davis and L¨uck [8] with the category theoretical construction by Meyer and Nest [22]. This extends the result of Hambleton and Pedersen [12] to arbitrary coefficients. Our approach uses abstract properties rather than explicit constructions and is formally similar to Meyer’s and Nest’s identification of their assembly map with the original construction of the assembly map by Baum, Connes and Higson [2]