132 research outputs found
Molar crown and root size relationship in anthropoid primates: 14th International Symposium on Dental Morphology, Greifswald
No full textAbstract not availableJ.A. Kieser, T. Tkatchenko, M.C. Dean, M.E.H. Jones, W. Duncan, N.J. Nelso
Overexpression of Hoxc13 in differentiating keratinocytes results in downregulation of a novel hair keratin gene cluster and alopecia
No full textStudying the roles of Hox genes in normal and pathological development of skin and hair requires identification of downstream target genes in genetically defined animal models. We show that transgenic mice overexpressing Hoxc13 in differentiating keratinocytes of hair follicles develop alopecia, accompanied by a progressive pathological skin condition that resembles ichthyosis. Large-scale analysis of differential gene expression in postnatal skin of these mice identified 16 previously unknown and 13 known genes as presumptive Hoxc13 targets, The majority of these targets are downregulated and belong to a subgroup of genes that encode hair-specific keratin-associated proteins (KAPs). Genomic mapping using a mouse hamster radiation hybrid panel showed these genes to reside in a novel KAP gene cluster on mouse chromosome 16 in a region of conserved linkage with human chromosome 21q22.11, Furthermore, data obtained by Hoxc13/lacZ reporter gene analysis in mice that overexpress Hoxc13 suggest negative autoregulatory feedback control of Hoxc13 expression levels, thus providing an entry point for elucidating currently unknown mechanisms that are required for regulating quantitative levels of Hox gene expression, Combined, these results provide a framework for understanding molecular mechanisms of Hoxc13 function in hair growth and development
Etude des reactions d'oligomerisation, isomerisation et polymerisation de substrats insatures catalysees par des complexes allyle cationiques du nickel
No full textResumo não disponíve
Noncovalent Interactions of DNA Bases with Naphthalene and Graphene
No full textpeer reviewedThe complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base naphthalene complexes are scrutinized at high levels of ab initio theory including coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. The stacked configurations are the most stable, where the CCSD(T)/CBS binding energies of guanine, adenine, thymine, and cytosine are 9.31 8.48, 8.53, 7.30 kcal/mol, respectively. The energy components are investigated using symmetry-adapted perturbation theory based on density functional theory including the dispersion energy. We compared the CCSD(T)/CBS results with several density functional methods applicable to periodic systems. Considering accuracy and availability, the optB86b nonlocal functional and the Tkatchenko-Scheffler functional are used to study the binding energies of nucleobases on graphene. The predicted values are 18-24 kcal/mol, though many-body effects on screening and energy need to be further considered
The three-center two-positron bond
No full textComputational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic stability of a system containing two positrons and three hydride anions, namely 2e(+)[H(3)(3−)]. To this aim, we performed a preliminary scan of the potential energy surface of the system with both electrons and positrons in a spin singlet state, with a multi-component MP2 method, that was further refined with variational and diffusion Monte Carlo calculations, and confirmed an equilibrium geometry with D(3h) symmetry. The local stability of 2e(+)[H(3)(3−)] is demonstrated by analyzing the vertical detachment and adiabatic energy dissociation channels. Bonding properties of the positronic compound, such as the equilibrium interatomic distances, force constants, dissociation energies, and bonding densities are compared with those of the purely electronic H(3)(+) and Li(3)(+) systems. Through this analysis, we find compelling similarities between the 2e(+)[H(3)(3−)] compound and the trilithium cation. Our results strongly point out the formation of a non-electronic three-center two-positron bond, analogous to the well-known three-center two-electron counterparts, which is fundamentally distinct from the two-center two-positron bond [D. Bressanini, J. Chem. Phys., 2021, 155, 054306], thus extending the concept of positron bonded molecules
Extending the applicability of the Tkatchenko-Scheffler dispersion correction via iterative Hirshfeld partitioning
No full textInternational audienceRecently we have demonstrated that the applicability of the Tkatchenko-Scheffler (TS) method for calculating dispersion corrections to density-functional theory can be extended to ionic systems if the Hirshfeld method for estimating effective volumes and charges of atoms in molecules or solids (AIM's) is replaced by its iterative variant [T. Bucko, S. Lebegue, J. Hafner, and J. Angyan, J. Chem. Theory Comput. 9, 4293 (2013)]. The standard Hirshfeld method uses neutral atoms as a reference, whereas in the iterative Hirshfeld (HI) scheme the fractionally charged atomic reference states are determined self-consistently. We show that the HI method predicts more realistic AIM charges and that the TS/HI approach leads to polarizabilities and C-6 dispersion coefficients in ionic or partially ionic systems which are, as expected, larger for anions than for cations (in contrast to the conventional TS method). For crystalline materials, the new algorithm predicts polarizabilities per unit cell in better agreement with the values derived from the Clausius-Mosotti equation. The applicability of the TS/HI method has been tested for a wide variety of molecular and solid-state systems. It is demonstrated that for systems dominated by covalent interactions and/or dispersion forces the TS/HI method leads to the same results as the conventional TS approach. The difference between the TS/HI and TS approaches increases with increasing ionicity. A detailed comparison is presented for isoelectronic series of octet compounds, layered crystals, complex intermetallic compounds, and hydrides, and for crystals built of molecules or containing molecular anions. It is demonstrated that only the TS/HI method leads to accurate results for systems where both electrostatic and dispersion interactions are important, as illustrated for Li-intercalated graphite and for molecular adsorption on the surfaces in ionic solids and in the cavities of zeolites
Δ-Machine Learning to Elevate DFT-Based Potentials and a Force Field to the CCSD(T) Level Illustrated for Ethanol
No full textProgress in machine learning has facilitated the development of potentials that offer both the accuracy of first-principles techniques and vast increases in the speed of evaluation. Recently, Delta-machine learning has been used to elevate the quality of a potential energy surface (PES) based on low-level, e.g., density functional theory (DFT) energies and gradients to close to the gold-standard coupled cluster level of accuracy. We have demonstrated the success of this approach for molecules, ranging in size from H3O+ to 15-atom acetyl-acetone and tropolone. These were all done using the B3LYP functional. Here, we investigate the generality of this approach for the PBE, M06, M06-2X, and PBE0 + MBD functionals, using ethanol as the example molecule. Linear regression with permutationally invariant polynomials is used to fit both low-level and correction PESs. These PESs are employed for standard RMSE analysis for training and test data sets, and then general fidelity tests such as energetics of stationary points, normal-mode frequencies, and torsional potentials are examined. We achieve similar improvements in all cases. Interestingly, we obtained significant improvement over DFT gradients where coupled cluster gradients were not used to correct the low-level PES. Finally, we present some results for correcting a recent molecular mechanics force field for ethanol and comment on the possible generality of this approach
Quantum Machine Learning Corrects Classical Force Fields: Stretching DNA Base Pairs in Explicit Solvent
No full textIn order to improve the accuracy of molecular dynamics simulations, classical
force fields are supplemented with a kernel-based machine learning method
trained on quantum-mechanical fragment energies. As an example application, a
potential-energy surface is generalised for a small DNA duplex, taking into
account explicit solvation and long-range electron exchange--correlation
effects. Study of the corrected potential energy versus extension shows that
leading classical DNA models have excessive stiffness with respect to
stretching. This discrepancy is found to be common across multiple forcefields.
The quantum correction is in qualitative agreement to the experimental
thermodynamics for larger DNA double helices, providing a candidate explanation
for the general and long-standing discrepancy between single molecule
stretching experiments and classical calculations of DNA stretching. The new
dataset of quantum calculations and the associated Kernel Modified Molecular
Dynamics (KMMD) method should be of general utility in biomolecular
simulations. KMMD is made available as part of the AMBER22 simulation software.Comment: Publisher postprint (with minor corrections) is open access at J Chem
Phys https://doi.org/10.1063/5.009472
Interactions between large molecules pose a puzzle for reference quantum mechanical methods
No full textQuantum-mechanical methods of benchmark quality are widely used for describing molecular interactions. The present work shows that interaction energies by CCSD(T) and DMC are not in consistent agreement for a set of polarizable supramolecules calling for cooperative efforts solving this conundrum
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