Density-functional approaches to noncovalent interactions: a comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmark-quality evaluations of binding strength compiled for molecular complexes of diverse size and nature. In particular, the efficacy of functionals deliberately crafted to encompass long-range forces, a posteriori DFT+dispersion corrections (DFT-D2 and DFT-D3), and exchange-hole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 [revised in J. Chem. Phys. 132, 144104 (2010)] and JSCH test sets of minimum-energy structures, as well as collections of dispersion-bound (NBC10) and hydrogen-bonded (HBC6) dissociation curves and a pairwise decomposition of a protein-ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBE-D, BP86-D, B97-D, PBE0-D, B3LYP-D, B970-D, M05-2X, M06-2X, ωB97X-D, B2PLYP-D, XYG3, and B3LYP-XDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible double-ζ or robust triple-ζ basis set regimes and among hydrogen-bonded or dispersion-dominated complexes. For overall results, M05-2X, B97-D3, and B970-D2 yield superior values in conjunction with aug-cc-pVDZ, for a mean absolute deviation of 0.41 - 0.49 kcal/mol, and B3LYP-D3, B97-D3, ωB97X-D, and B2PLYP-D3 dominate with aug-cc-pVTZ, affording, together with XYG3/6-311+G(3df,2p), a mean absolute deviation of 0.33 - 0.38 kcal/mol.     

Evidence for the central origin of lexical tone normalization (L)

Huang and Holt [(2009). J. Acoust. Soc. Am. 125, 3983-3994] suggest that listeners may dynamically tune lexical tone perception via general auditory sensitivity to the mean f0 of the preceding context, effectively normalizing pitch differences across talkers. The present experiments further examine the effect using the missing-f0 phenomenon as a means of determining the level of auditory processing at which lexical tone normalization occurs. Speech contexts filtered to remove or mask low-frequency f0 energy elicited contrastive context effects. Central, rather than peripheral, auditory processes may be responsible for the context-dependence that has been considered to be lexical tone normalization.     

Search for a dark matter annihilation signal from the galactic center halo with H.E.S.S

A search for a very-high-energy (VHE; ≥100 GeV) γ-ray signal from self-annihilating particle dark matter (DM) is performed towards a region of projected distance r～45-150 pc from the Galactic center. The background-subtracted γ-ray spectrum measured with the High Energy Stereoscopic System (H.E.S.S.) γ-ray instrument in the energy range between 300 GeV and 30 TeV shows no hint of a residual γ-ray flux. Assuming conventional Navarro-Frenk-White and Einasto density profiles, limits are derived on the velocity-weighted annihilation cross section (σv) as a function of the DM particle mass. These are among the best reported so far for this energy range and in particular differ only little between the chosen density profile parametrizations. In particular, for the DM particle mass of ～1 TeV, values for (σv) above 3×10(-25) cm(3)?s(-1) are excluded for the Einasto density profile.     

Alterations in diffusion properties of white matter in Williams syndrome

Diffusion tensor imaging (DTI) was used to investigate the involvement of brain white matter in Williams syndrome (WS), a genetic neurodevelopmental disorder. Whole-brain DTIs were obtained from 16 young adults with WS and 16 normal controls. A voxel-based analysis was performed to compare fractional anisotropy (FA) values between the two groups. A tract-based analysis was also performed to compare FA values between the two groups along two major white matter tracts that pass through the external capsule: the uncinate and inferior fronto-occipital fasciculi. Several regions of both increased and decreased FA were found within major white matter tracts that connect functional regions that have previously been implicated in the cognitive and neurological symptoms of the syndrome. The tract-based analysis provided additional insight into the involvement of specific white matter tracts implicated in the voxel-based analysis within the external capsule. The results from this study support previously reported changes in white matter diffusion properties in WS and demonstrate the potential usefulness for tract-based analysis in future studies of the disorder.     

Data Formats for Elementary Gas‐Phase Kinetics: Part 2. Unique Representations of Reactions

A method of extending the IUPAC International Chemical Identifier (InChI) to describe and identify elementary reactions in a standard computer‐readable notation is developed. Denoted InChI‐ER, the method is based on the existing InChI formalism, with certain refinements for the better identification of molecular entities as proposed in Part 1 published previously in this journal. Using this base notation, an identifier for elementary reactions on a molecular level is created by adding additional layers in a conceptually similar and extensible manner. Two of the layers describe the atoms involved in the transition state and the connectivity changes that occur during the reaction. Additional layers classify the reactions on the basis of the connectivity changes, providing chemical information useful in organizing and searching kinetic data sets found in databases or used in detailed kinetic modeling. Important aspects of the method are that the proposed layers are optional, that they do not interfere with existing InChI specifications, and that they retain extensibility should further refinements be desired in the future.     

Needle and seed segmentation in intra-operative 3D ultrasound-guided prostate brachytherapy

In order to guide the needle to the correct location in 3D US-guided brachytherapy, the needle is continuously tracked as it is being inserted. A pre-scan before the needle insertion and a post-scan after the needle insertion are subtracted to obtain a difference image containing the needle. The image is projected along two orthogonal directions approximately perpendicular to the needle, and the 3D needle is reconstructed from the segmented needles in the two projected images. The seeds implanted with the needle are located in the cropped volume along the needle. Thus, the seeds are segmented using a tri-bar model and 3D line segment patterns. Finally, the positions of the seeds are determined using a peak detection technique. Experiments with agar and turkey/chicken phantoms as well as patient data demonstrated that our needle segmentation technique could segment the needle in near real-time with an accuracy of 0.6 mm in position and 1.0 degrees in orientation. The true-positive rate for seed segmentation is 100% for the agar phantom and 93% for the chicken phantom. The average distance to manual seed segmentation was 1.0mm for the agar phantom and 1.7 mm for the chicken phantom.     

Schwarz method for earthquake source dynamics

Dynamic faulting under slip-dependent friction in a linear elastic domain (in-plane and 3D configurations) is considered. The use of an implicit time-stepping scheme (Newmark method) allows much larger values of the time step than the critical CFL time step, and higher accuracy to handle the non-smoothness of the interface constitutive law (slip weakening friction).The finite element form of the quasi-variational inequality is solved by a Schwarz domain decomposition method, by separating the inner nodes of the domain from the nodes on the fault. In this way, the quasi-variational inequality splits into two subproblems. The first one is a large linear system of equations, and its unknowns are related to the mesh nodes of the first subdomain (i.e. lying inside the domain). The unknowns of the second subproblem are the degrees of freedom of the mesh nodes of the second subdomain (i.e. lying on the domain boundary where the conditions of contact and friction are imposed). This nonlinear subproblem is solved by the same Schwarz algorithm, leading to some local nonlinear subproblems of a very small size.Numerical experiments are performed to illustrate convergence in time and space, instability capturing, energy dissipation and the influence of normal stress variations. We have used the proposed numerical method to compute source dynamics phenomena on complex and realistic 2D fault models (branched fault systems).     

Group contribution method for the estimation of contact angle trends on modified polymer surfaces

Group contribution methods can be used as an aid in evaluating contact angle data on modified polymer surfaces. Good correlation was seen between experimental contact angle titration data on a hydrolyzed polyimide surface and equations involving water-octanol partition coefficients using parameters derived from group contribution methods. The methods used captured features of the experimental contact angle titration data observed during ionization of surface functional groups.