Steady state particle distribution of a dilute sedimenting suspension

Sedimentation of a non-Brownian suspension of hard particles is studied. It is shown that in the low concentration limit a two-particle distribution function ensuring finite particle correlation length can be found and explicitly calculated. The sedimentation coefficient is computed. Results are compared with experiment.Comment: 4 pages, 2 figure

Vibrational corrections to transition properties

The vibrational contributions to second-order transition properties are considered in the framework of the Born—Oppenheimer approximation. It is shown that the usual formula for vibrational second-order transition matrix elements is incomplete and needs to be supplemented by a term of purely vibrational origin. This pure vibrational contribution is calculated for vibrational transition polarizabilities in LiH and BeF and found to be quite significant. Its inclusion in theoretically calculated data for the Raman intensities appears to be necessary

Potential energy surface of the 2A' Li2+Li doublet ground state

The lowest doublet electronic state for the lithium trimer (2A') is calculated for use in three-body scattering calculations using the valence electron FCI method with atomic cores represented using an effective core potential. It is shown that an accurate description of core-valence correlation is necessary for accurate calculations of molecular bond lengths, frequencies and dissociation energies. Interpolation between 2A' ab initio surface data points in a sparse grid is done using the global interpolant moving least squares method with a smooth radial data cutoff function included in the fitting weights and bivariate polynomials as a basis set. The Jahn-Teller splitting of the 2E' surface into the 2A1 and 2B2 states is investigated using a combination of both CASSCF and FCI levels of theory. Additionally, preliminary calculations of the 2A'' surface are also presented using second order spin restricted open-shell Moller-Plesset perturbation theory.Comment: 7 pages, 5 figure

Importance of electron correlation effects and basis set superposition error in calculations of interaction energies and interaction-induced electric properties in hydrogen-bonded complexes: a model study

A detailed study of the interaction energies and interaction-induced electric dipole properties in model linear hydrogen cyanide complexes (HCN) m (m = 2–4) is carried out within the finite field HF SCF, MP2, CCSD and CCSD(T) approximations using the recently developed LPol-n (n = ds, fs, dl, fl) basis sets. The importance of high-order correlation effects and the basis set superposition error is evaluated. To correct for the latter is crucial for obtaining accurate interaction energy values, but the error can safely be neglected in the estimation of induced electric properties when the LPol-n (n = ds, fs, dl, fl) basis sets are used. Correlation effects are important in the evaluation of both the interaction energies and the induced electric properties of the systemsThis work was supported by the Spanish Ministerio de Ciencia e Innovación (CTQ2008-01861/BQU project), the Xunta de Galicia and FEDER (Axuda para Consolidación e Estructuración de Unidades de Investigación Competitivas do Sistema Universitario de Galicia 2007/050, and 2007-2013 and INCITE09 314 252 PR projects), and by the Foundation for Polish Science within the Homing Plus programme (Homing Plus/2010-1/2), cofinanced from European Regional Development Fund within Innovative Economy Operational ProgrammeS

Derivation of the Supermolecular Interaction Energy from the Monomer Densities in the Density Functional Theory

The density functional theory (DFT) interaction energy of a dimer is rigorously derived from the monomer densities. To this end, the supermolecular energy bifunctional is formulated in terms of mutually orthogonal sets of orbitals of the constituent monomers. The orthogonality condition is preserved in the solution of the Kohn-Sham equations through the Pauli blockade method. Numerical implementation of the method provides interaction energies which agree with those obtained from standard supermolecular calculations within less than 0.1% error for three example functionals: Slater-Dirac, PBE0 and B3LYP, and for two model van der Waals dimers: Ne2 and (C2H4)2, and two model H-bond complexes: (HF)2 and (NH3)2.Comment: 6 pages, 1 figure, REVTeX

KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units

Protein kinases are important targets for treating human disorders, and they are the second most targeted families after G-protein coupled receptors. Several resources provide classification of kinases into evolutionary families (based on sequence homology); however, very few systematically classify functional families (FunFams) comprising evolutionary relatives that share similar functional properties. We have developed the FunFam-MARC (Multidomain ARchitecture-based Clustering) protocol, which uses multi-domain architectures of protein kinases and specificity-determining residues for functional family classification. FunFam-MARC predicts 2210 kinase functional families (KinFams), which have increased functional coherence, in terms of EC annotations, compared to the widely used KinBase classification. Our protocol provides a comprehensive classification for kinase sequences from >10,000 organisms. We associate human KinFams with diseases and drugs and identify 28 druggable human KinFams, i.e., enriched in clinically approved drugs. Since relatives in the same druggable KinFam tend to be structurally conserved, including the drug-binding site, these KinFams may be valuable for shortlisting therapeutic targets. Information on the human KinFams and associated 3D structures from AlphaFold2 are provided via our CATH FTP website and Zenodo. This gives the domain structure representative of each KinFam together with information on any drug compounds available. For 32% of the KinFams, we provide information on highly conserved residue sites that may be associated with specificity.Adeyelu T, Bordin N, Waman VP, Sadlej M, Sillitoe I, Moya-Garcia AA, Orengo CA. KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units. Biomolecules. 2023; 13(2):277. https://doi.org/10.3390/biom1302027

Density Functional Theory Approach to Noncovalent Interactions via Interacting Monomer Densities

A recently proposed "DFT+dispersion" treatment (Rajchel et al., Phys. Rev. Lett., 2010, 104, 163001) is described in detail and illustrated by more examples. The formalism derives the dispersion-free density functional theory (DFT) interaction energy and combines it with the dispersion energy from separate DFT calculations. It consists in the self-consistent polarization of DFT monomers restrained by the exclusion principle via the Pauli blockade technique. Within the monomers a complete exchange-correlation potential should be used, but between them only the exact exchange operates. The applications to wide range of molecular complexes from rare-gas dimers to H-bonds to pi-electron interactions show good agreement with benchmark values.Comment: 9 pages, 5 figures, 2 tables, REVTeX