196 research outputs found
Correlated ab-initio calculations for ground-state properties of II-VI semiconductors
Correlated ab-initio ground-state calculations, using relativistic
energy-consistent pseudopotentials, are performed for six II-VI semiconductors.
Valence () correlations are evaluated using the coupled cluster approach
with single and double excitations. An incremental scheme is applied based on
correlation contributions of localized bond orbitals and of pairs and triples
of such bonds. In view of the high polarity of the bonds in II-VI compounds, we
examine both, ionic and covalent embedding schemes for the calculation of
individual bond increments. Also, a partitioning of the correlation energy
according to local ionic increments is tested. Core-valence ()
correlation effects are taken into account via a core-polarization potential.
Combining the results at the correlated level with corresponding Hartree-Fock
data we recover about 94% of the experimental cohesive energies; lattice
constants are accurate to \sim 1%; bulk moduli are on average 10% too large
compared with experiment.Comment: 10 pages, twocolumn, RevTex, 3 figures, accepted Phys. Rev.
AXL and CAV-1 play a role for MTH1 inhibitor TH1579 sensitivity in cutaneous malignant melanoma
Cutaneous malignant melanoma (CMM) is the deadliest form of skin cancer and clinically challenging due to its propensity to develop therapy resistance. Reactive oxygen species (ROS) can induce DNA damage and play a significant role in CMM. MTH1 protein protects from ROS damage and is often overexpressed in different cancer types including CMM. Herein, we report that MTH1 inhibitor TH1579 induced ROS levels, increased DNA damage responses, caused mitotic arrest and suppressed CMM proliferation leading to cell death both in vitro and in an in vivo xenograft CMM zebrafish disease model. TH1579 was more potent in abrogating cell proliferation and inducing cell death in a heterogeneous co-culture setting when compared with CMM standard treatments, vemurafenib or trametinib, showing its broad anticancer activity. Silencing MTH1 alone exhibited similar cytotoxic effects with concomitant induction of mitotic arrest and ROS induction culminating in cell death in most CMM cell lines tested, further emphasizing the importance of MTH1 in CMM cells. Furthermore, overexpression of receptor tyrosine kinase AXL, previously demonstrated to contribute to BRAF inhibitor resistance, sensitized BRAF mutant and BRAF/NRAS wildtype CMM cells to TH1579. AXL overexpression culminated in increased ROS levels in CMM cells. Moreover, silencing of a protein that has shown opposing effects on cell proliferation, CAV-1, decreased sensitivity to TH1579 in a BRAF inhibitor resistant cell line. AXL-MTH1 and CAV-1-MTH1 mRNA expressions were correlated as seen in CMM clinical samples. Finally, TH1579 in combination with BRAF inhibitor exhibited a more potent cell killing effect in BRAF mutant cells both in vitro and in vivo. In summary, we show that TH1579-mediated efficacy is independent of BRAF/NRAS mutational status but dependent on the expression of AXL and CAV-1
Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces
Allosteric Modulators of Steroid Hormone Receptors : Structural Dynamics and Gene Regulation
Peer reviewedPublisher PD
Resonant inelastic soft-x-ray scattering spectra at the N1s and C1s edges of poly(pyridine-2,5-diyl)
Resonant inelastic scattering measurements of poly(pyridine-2,5-diyl) have
been performed at the N1s and C1s edges using synchrotron radiation. For
comparison, molecular orbital calculations of the spectra have been carried out
with the repeat unit as a model molecule of the polymer chain. The resonant
emission spectra show depletion of the p electron bands which is consistent
with symmetry selection and momentum conservation rules. The depletion is most
obvious in the resonant inelastic scattering spectra of carbon while the
nitrogen spectra are dominated by lone pair n orbital emission of s symmetry
and are less excitation energy dependent. By comparing the measurements to
calculations an isomeric dependence of the resonant spectra is found giving
preference to two of the four possible isomers in the polymer.Comment: 6 pages, 3 figures,
http://www.sciencedirect.com/science/article/pii/S036820489800354
The electronic structure of poly(pyridine-2,5-diyl) investigated by soft x-ray absorption and emission spectroscopies
The electronic structure of the poly-pyridine conjugated polymer has been
investigated by resonant and nonresonant inelastic X-ray scattering and X-ray
absorption spectroscopies using synchrotron radiation. The measurements were
made for both the carbon and nitrogen contents of the polymer. The analysis of
the spectra has been carried out in comparison with molecular orbital
calculations taking the repeat-unit cell as a model molecule of the polymer
chain. The simulations indicate no significant differences in the absorption
and in the non-resonant X-ray scattering spectra for the different isomeric
geometries, while some isomeric dependence of the resonant spectra is
predicted. The resonant emission spectra show depletion of the {\pi} electron
bands in line with symmetry selection and momentum conservation rules. The
effect is most vizual for the carbon spectra; the nitrogen spectra are
dominated by lone pair n orbital emission of {\sigma} symmetry and are less
frequency dependent.Comment: 11 pages, 7 figures, 1 table,
http://www.sciencedirect.com/science/article/pii/S030101049800262
A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry
We present here a review of the fundamental topics of Hartree-Fock theory in
Quantum Chemistry. From the molecular Hamiltonian, using and discussing the
Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock
equations for the electronic problem. Special emphasis is placed in the most
relevant mathematical aspects of the theoretical derivation of the final
equations, as well as in the results regarding the existence and uniqueness of
their solutions. All Hartree-Fock versions with different spin restrictions are
systematically extracted from the general case, thus providing a unifying
framework. Then, the discretization of the one-electron orbitals space is
reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition
of the basic underlying concepts related to the construction and selection of
Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we
close the review with a section in which the most relevant modern developments
(specially those related to the design of linear-scaling methods) are commented
and linked to the issues discussed. The whole work is intentionally
introductory and rather self-contained, so that it may be useful for non
experts that aim to use quantum chemical methods in interdisciplinary
applications. Moreover, much material that is found scattered in the literature
has been put together here to facilitate comprehension and to serve as a handy
reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and
subeqn package
Identification of hot-spot residues in protein-protein interactions by computational docking
<p>Abstract</p> <p>Background</p> <p>The study of protein-protein interactions is becoming increasingly important for biotechnological and therapeutic reasons. We can define two major areas therein: the structural prediction of protein-protein binding mode, and the identification of the relevant residues for the interaction (so called 'hot-spots'). These hot-spot residues have high interest since they are considered one of the possible ways of disrupting a protein-protein interaction. Unfortunately, large-scale experimental measurement of residue contribution to the binding energy, based on alanine-scanning experiments, is costly and thus data is fairly limited. Recent computational approaches for hot-spot prediction have been reported, but they usually require the structure of the complex.</p> <p>Results</p> <p>We have applied here normalized interface propensity (<it>NIP</it>) values derived from rigid-body docking with electrostatics and desolvation scoring for the prediction of interaction hot-spots. This parameter identifies hot-spot residues on interacting proteins with predictive rates that are comparable to other existing methods (up to 80% positive predictive value), and the advantage of not requiring any prior structural knowledge of the complex.</p> <p>Conclusion</p> <p>The <it>NIP </it>values derived from rigid-body docking can reliably identify a number of hot-spot residues whose contribution to the interaction arises from electrostatics and desolvation effects. Our method can propose residues to guide experiments in complexes of biological or therapeutic interest, even in cases with no available 3D structure of the complex.</p
Transancestral mapping and genetic load in systemic lupus erythematosus
Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (∼50% of these regions have multiple independent associations); these include 24 novel SLE regions (P<5 × 10-8), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.info:eu-repo/semantics/publishedVersio
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