Ligandbook — an online repository for small and drug-like molecule force field parameters

International audienceLigandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Availability and Implementation: Ligandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit

Fano-type interference in quantum dots coupled between metallic and superconducting leads

We analyze the quantum interference effects appearing in the charge current through the double quantum dots coupled in T-shape configuration to an isotropic superconductor and metallic lead. Owing to proximity effect the quantum dots inherit a pairing which has the profound influence on nonequilibrium charge transport, especially in the subgap regime |eV| < Delta. We discuss under what conditions the Fano-type lineshapes might appear in such Andreev conductance and consider a possible interplay with the strong correlation effects.Comment: 7 pages, 7 figure

Ag(II) as spin super-polarizer in metal fluoride clusters

Using quantum mechanical calculations, we examine magnetic (super)exchange interactions in prototypal molecular fluoride clusters containing late transition metals or selected lanthanides, as well as Ag(II). By referencing to analogous species comprising closed shell Cd(II) we provide evidence that the presence of Ag(II) may modify the magnetic properties of such systems (including metal metal superexchange) to an unprecedented degree, specifically both coupling sign and strength may markedly change. Remarkably, this happens in spite of the fact that the fluoride ligand is the least susceptible to spin polarization among all monoatomic ligands known in chemistry. Ag(II), with one hole in its d shell, stands as spin superpolarizer, and this feature could be exploited in spintronics and diverse molecular devices.Comment: 6 pages, 3 figures, 2 tables, and 19 pages of supplementary informatio

Atomistic mechanism of transmembrane helix association

Transmembrane helix association is a fundamental step in the folding of helical membrane proteins. The prototypical example of this association is formation of the glycophorin dimer. While its structure and stability have been well-characterized experimentally, the detailed assembly mechanism is harder to obtain. Here, we use all-atom simulations within phospholipid membrane to study glycophorin association. We find that initial association results in the formation of a non-native intermediate, separated by a significant free energy barrier from the dimer with a native binding interface. We have used transition-path sampling to determine the association mechanism. We find that the mechanism of the initial bimolecular association to form the intermediate state can be mediated by many possible contacts, but seems to be particularly favoured by formation of non-native contacts between the C-termini of the two helices. On the other hand, the contacts which are key to determining progression from the intermediate to the native state are those which define the native binding interface, reminiscent of the role played by native contacts in determining folding of globular proteins. As a check on the simulations, we have computed association and dissociation rates from the transition-path sampling. We obtain results in reasonable accord with available experimental data, after correcting for differences in native state stability. Our results yield an atomistic description of the mechanism for a simple prototype of helical membrane protein folding

TEORIA WZMOCNIENIA JEDNOFOLIOWEGO DETEKTORA Z GAZOWYM POWIELANIEM ELEKTRONÓW

Gain prediction theory of single foil Gas Electron Multiplier detector was developed. Gas electron multiplier (GEM) detector with single foil was developed. Soft X-ray spectra with an energy of 5.9 keV emitted by the isotope Fe-55 were measured. On this basis, the dependence of gain and energy resolution from the detector voltage was determined. The simple theory of gain dependence on various detector parameters was developed. Preliminary results of the study confirmed the potential usefulness of the GEM detector as a substitute for the multiwire proportional chamber.Opracowano teorię wzmocnienia jednofoliowego detektora z gazowym powielaniem elektronów. Opracowano detektor z gazowym powielaniem elektronów z pojedynczą folią. Zmierzono widmo miękkiego promieniowania X, o energii 5,9 keV, emitowanego przez izotop Fe-55. Na tej podstawie wyznaczono zależność wzmocnienia i energetycznej zdolności rozdzielczej od napięcia zasilającego detektor. Opracowano prosta teorią zależności wzmocnienia od różnych parametrów detektora. Wstępne rezultaty badań potwierdzają potencjalną przydatność detektora GEM jako substytutu wielodrutowej komory proporcjonalnej

Expression of KIM-1, VEGF and bFGF in the transplanted kidney as predictive factors of kidney allograft function

Introduction: Transplantation is now a common treatment for kidney failure. However, it is associated with numerous complications, among which is rejection. Currently, factors that can predict the function of the transplanted kidney are being sought. This study aimed to investigate whether the expression of KIM-1 (kidney injury molecule-1), VEGF (vascular endothelial growth factor) and bFGF (basic fibroblast growth factor) assessed in the transplanted kidney before transplantation can be a predictive marker of the later function of the transplanted kidney and the occurrence of complications such as delayed graft function (DGF) and acute rejection (AR). Material and methods: The study group included 44 kidney allograft recipients who underwent kidney transplantation. Results: There were no statistically significant correlations between KIM-1, VEGF and bFGF gene expression in transplanted kidney biopsies and the occurrence of DGF and AR. The expression of the bFGF gene correlated significantly with the creatinine levels before and on the first day after transplantation. There were no statistically significant correlations between creatinine levels and expression of the KIM-1 and VEGF genes. There was also no statistically significant correlation between bFGF, KIM-1 and VEGF gene expression in the transplanted kidney and later eGFR and diuresis values. A statistically significant negative correlation was found between bFGF and serum potassium levels before transplantation and up to one month after transplantation. KIM-1 expression correlated significantly negatively with pre-transplant serum potassium levels. VEGF expression correlated significantly negatively with potassium levels 2 and 24 months after transplantation. Conclusions: The present results suggest that the expression of KIM-1, VEGF and bFGF assessed in the transplanted kidney before transplantation is not a significant predictor of the later function of the transplanted kidney. The expression of the bFGF gene correlates with the creatinine levels before and on the first day after transplantation. The expression of KIM-1, VEGF and bFGF may correlate with potassium serum levels

REFLECT – Research flight of EURADOS and CRREAT: Intercomparison of various radiation dosimeters onboard aircraft

Aircraft crew are one of the groups of radiation workers which receive the highest annual exposure to ionizing radiation. Validation of computer codes used routinely for calculation of the exposure due to cosmic radiation and the observation of nonpredictable changes in the level of the exposure due to solar energetic particles, requires continuous measurements onboard aircraft. Appropriate calibration of suitable instruments is crucial, however, for the very complex atmospheric radiation field there is no single reference field covering all particles and energies involved. Further intercomparisons of measurements of different instruments under real flight conditions are therefore indispensable. In November 2017, the REFLECT (REsearch FLight of EURADOS and CRREAT) was carried out. With a payload comprising more than 20 different instruments, REFLECT represents the largest campaign of this type ever performed. The instruments flown included those already proven for routine dosimetry onboard aircraft such as the Liulin Si-diode spectrometer and tissue equivalent proportional counters, as well as newly developed detectors and instruments with the potential to be used for onboard aircraft measurements in the future. This flight enabled acquisition of dosimetric data under well-defined conditions onboard aircraft and comparison of new instruments with those routinely used. As expected, dosimeters routinely used for onboard aircraft dosimetry and for verification of calculated doses such as a tissue equivalent proportional counter or a silicon detector device like Liulin agreed reasonable with each other as well as with model calculations. Conventional neutron rem counters underestimated neutron ambient dose equivalent, while extended-range neutron rem counters provided results comparable to routinely used instruments. Although the responses of some instruments, not primarily intended for the use in a very complex mixed radiation field such as onboard aircraft, were as somehow expected to be different, the verification of their suitability was one of the objectives of the REFLECT. This campaign comprised a single short flight. For further testing of instruments, additional flights as well as comparison at appropriate reference fields are envisaged. The REFLECT provided valuable experience and feedback for validation of calculated aviation doses

Numerical simulations of generation of high-energy ion beams driven by a petawatt femtosecond laser

This contribution presents results of a Particle-in-Cell simulation of ion beam acceleration via the interaction of a petawatt 25 fs laser pulse of high intensity (up to ~1021 W/cm2) with thin hydrocarbon (CH) and erbium hydride (ErH3) targets of equal areal mass density (of 0.6 g/m2). A special attention is paid to the effect that the laser pulse polarization and the material composition of the target have on the maximum ion energies and the number of high energy (>10 MeV) protons. It is shown that both the mean and the maximum ion energies are higher for the linear polarization than for the circular one. A comparison of the maximum proton energies and the total number of protons generated from the CH and ErH3 targets using a linearly polarized beam is presented. For the ErH3 targets the maximum proton energies are higher and they reach 50 MeV for the laser pulse intensity of 1021 W/cm2. The number of protons with energies higher than 10 MeV is an order of magnitude higher for the ErH3 targets than that for the CH targets