Design of thin-film materials and explanation of their properties by atomic-level simulations

Disertační práce se zabývá teoretickým popisem pevných látek pomocí teorie funkcionálu hustoty. Studuje a rozvíjí vybrané prvky metodiky a předpovídá struktury a vlastnosti vybraných materiálů, převážně těch, jež jsou na katedře připravovány jako tenké vrstvy. Teoretické výsledky jsou proto často uváděny do souvislosti s experimentálními. Jednou ze skupin studovaných materiálů jsou kubické a hexagonální nitridy přechodových kovů včetně svých tuhých roztoků, ternárních nitridů (Hf,M)N (M = Y, Ho, Ta, Mo). Je zkoumána jejich stabilita a mechanické vlastnosti. Formovací energie roztoků závisí kromě krystalické struktury také na rozložení atomů Hf a M a pro některá složení a rozložení též na případném provedení geometrické optimalizace pozic atomů. Vypočítané vlastnosti krystalických MN and (Hf,M)N jsou dále vztaženy k vlastnostem amorfních Hf-M-Si-B-C-N, modelovaných pomocí ab initio molekulární dynamiky. Formovací energie MN je užitečnou měrou hybné síly k tvorbě vazeb M-N v Hf-M-Si-B-C-N. Její postupný nárůst s růstem číslem sloupce prvku M v periodické tabulce koreluje s poklesem podílu vazeb M-N na všech vazbách atomů M v Hf-M-Si-B-C-N či s delokalizací elektronových stavů a zúžením zakázaného pásu. Trend růstu kovovosti potvrzují i experimentální výsledky jako růst elektrické vodivosti a extinkčního koeficientu. Korelaci lze nalézt i mezi mechanickými vlastnostmi pro tenkovrstvé Hf-M-Si-B-C-N a modelované MN, a snadné výpočty vlastností MN tak jsou užitečnou metodu předpovědi trendů vlastností Hf-M-Si-B-C-N. Pro případ Hf-Y-Si-B-C-N je korelace modelu s experimentem prokázána také při rostoucím obsahu dusíku: vypočítaný pokles zastoupení vazeb neobsahujících N a vzdálení elektronových stavů od Fermiho meze vysvětlují pokles experimentálního extinkčního koeficientu a odpovídající rozšíření zakázaného pásu. Zvláštní pozornost je věnována magnetickému nitridu HoN. Výpočty ab initio týkající se elektronových struktur a souvisejících vlastností takového materiálu by měly správně reprodukovat jeho magnetický moment. Nejprve je určen počet neobsazených elektronových stavů, který zaručuje, že zjištěné energetické minimum je globální. Dále je vyvinuta metoda, která umožňuje, aby experimentální hodnota magnetizace tvořila energetické minimum, a je kladen důraz na příznivé rozložení spinů ve velké simulační buňce. Je prozkoumána závislost vybraných charakteristik HoN na velikosti buňky a magnetizaci. Tyto výsledky poskytují teoretický vhled do spinové struktury nitridů kovů vzácných zemin a umožňují použít správnou metodiku podobných výpočtů vlastností silně korelovaných materiálů. Pro bixbyitové Ta2N3 a Ta2N2O jsou vypočítány hustoty elektronových stavů, které jsou v případě Ta2N2O užity k vysvětlení jeho experimentálních vlastností, zejména existence jednoho optického a dvou elektrických zakázaných pásů. Je zkoumán také diborid (Ti,Zr,Hf,Ta)B2, zejména vliv poruch (jednak vakancí, a jednak atomů C, poruch relevantních pro četné experimenty) na charakteristiky materiálu. Jsou prozkoumány různé druhy, koncentrace i rozložení poruch a jsou rozpoznána uspořádání vedoucí na nejnižší formovací energie. Náhrada atomů B atomy C je méně výhodná než tvorba bórových vakancí. Vakance dále upřednostňují shlukování do rozsáhlejší plošné oblasti bez atomů, a minimalizují tak počet přerušených vazeb B-B, zatímco uhlíkové substituce na bórových pozicích shlukování neupřednostňují a mají sklon minimalizovat počet vazeb C-C. S koncentrací vakancí zároveň roste objem na atom. Tyto výsledky jsou využity k vysvětlení experimentálních jevů, jako je uvolnění kompresního pnutí při žíhání diboridů. Je kvantifikován také vliv vakancí na mechanické a elektronické vlastnosti.ObhájenoThe Ph.D. thesis deals with a theoretical description of the solid state by density-functional theory. It studies and develops selected components of the methodology and predicts the structures and properties of selected materials, predominantly those prepared as thin films at the department. Thus, the theoretical results are often associated to experimental ones. One class of the studied materials consists of cubic and hexagonal transition-metal nitrides, including their solid solutions, ternary nitrides (Hf,M)N (M = Y, Ho, Ta, Mo). We study their stability and mechanical properties. The solution formation energy depends not only on the crystal structure but also on the distribution of Hf and M atoms and, for some cases, on the decision to perform structural relaxation. The calculated properties of crystalline MN and (Hf,M)N are then associated with the properties of amorphous Hf-M-Si-B-C-N, modelled by ab initio molecular dynamics. Formation energy of MN is a useful measure of the driving force towards M-N bond formation in Hf-M-Si-B-C-N. Its increase with the M periodic-table group number correlates with the decrease in the ratio of the number of M-N bonds to the total number of M bonds in Hf-M-Si-B-C-N as well as with the delocalisation of electronic states and narrowing of the band gap. The growing trend in the metallicity is confirmed also by experimental results such as the growth of electrical conductivity and extinction coefficient. In addition, correlation is found between mechanical properties of thin-film Hf-M-Si-B-C-N and modelled MN, so the easy calculations of MN properties are a useful method for the prediction of the trends in the Hf-M-Si-B-C-N properties. For the case of Hf-Y-Si-B-C-N, the correlation of the model and experiment is proven also at growing nitrogen content: the calculated decrease in the number of N-less bonds and the retreat of the electronic states from the Fermi level explain the decrease of the experimental extinction coefficient and the corresponding band-gap broadening. Attention is paid to the magnetic nitride HoN. Ab initio calculations of electronic structures and related properties should correctly reproduce its magnetic moment. First, the number of unoccupied electronic states is identified which guarantees that the energy minimum identified is the global one. A method is then developed which allows the experimental magnetisation to constitute an energy minimum, emphasising the favourable spin distribution in a large simulation cell. The dependence of selected HoN characteristics on cell size and magnetisation is examined. These findings provide a theoretical insight into the spin structure of rare-earth metal nitrides and allow one to use the correct methodology of similar calculations of properties of strongly correlated materials. For bixbyite Ta2N3 and Ta2N2O, densities of electronic states are calculated and in the case of Ta2N2O used to explain experimental properties like the existence of one optical and two electrical band gaps. The diboride (Ti,Zr,Hf,Ta)B2 is studied, too, mainly the effect of defects (either vacancies or C atoms, both relevant for numerous experiments) on material characteristics. Different types, concentrations and distributions of defects are investigated, and the configurations leading to the lowest formation energies are identified. The replacement of B by C is more unfavourable than the formation of B vacancies. Furthermore, vacancies prefer to coalesce into a larger planar void, minimising the number of broken B-B bonds, while C substitutions at B sites do not prefer coalescence and minimise the number of C-C bonds. In parallel, the volume per atom increases with the vacancy concentration. These results are used to explain experimental phenomena such as the stress release during annealing. In addition, the effect of vacancies on mechanical and electronic properties is quantified

Tracking by 3D Model Estimation of Unknown Objects in Videos

Most model-free visual object tracking methods formulate the tracking task as object location estimation given by a 2D segmentation or a bounding box in each video frame. We argue that this representation is limited and instead propose to guide and improve 2D tracking with an explicit object representation, namely the textured 3D shape and 6DoF pose in each video frame. Our representation tackles a complex long-term dense correspondence problem between all 3D points on the object for all video frames, including frames where some points are invisible. To achieve that, the estimation is driven by re-rendering the input video frames as well as possible through differentiable rendering, which has not been used for tracking before. The proposed optimization minimizes a novel loss function to estimate the best 3D shape, texture, and 6DoF pose. We improve the state-of-the-art in 2D segmentation tracking on three different datasets with mostly rigid objects

Vacancies and substitutional defects in multicomponent diboride Ti0.25Zr0.25Hf0.25Ta0.25B2

SVK1-2022-01

Preconception counseling, fertility, and pregnancy complications after abdominal organ transplantation: a survey and cohort study of 532 recipients

Background Pregnancy after solid organ transplant is a significant priority for transplant recipients but how patients report being counseled is unknown. Methods We performed a single‐center retrospective cohort study and telephone survey of female patients ages 18–49 at the time of kidney, pancreas, or liver transplant from 2000 to 2012 (n = 532). Data on pregnancy counseling, fertility, and maternal, fetal‐ and transplant‐specific outcomes were collected. Multivariate Cox models assessed the impact of pregnancy on graft‐specific outcomes. Results The survey response rate was 29% (n = 152). One‐third (n = 51) of women were actively counseled against pregnancy by one or more providers. A total of 17 pregnancies occurred among nine patients (5.9%), with 47% live births, 47% early embryonic demises, 5.9% stillbirths. Of live births, 50% were premature. Gestational complications, including diabetes, hypertension, and preeclampsia were present in 88% of mothers. Pregnancy after transplant was associated with higher rates of acute rejection than nulliparous transplant recipients (33% vs. 5.6%, p = 0.07) but did not significantly affect graft survival ( HR  = 1.00, 95% CI 0.99–1.01), after stratifying by organ and adjusting for clinical factors. Conclusion This study suggests that transplant patients are being counseled against pregnancy despite acceptable risks of complications and no specific effects on long‐term graft function.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108677/1/ctr12393.pd

Tectonic evolution of Variscan Iberia: Gondwana–Laurussia

An integrated interpretation of the late Paleozoic structural and geochronological record of the Iberian Massif is presented and discussed under the perspective of a Gondwana-Laurussia collision giving way to the Variscan orogen. Compressional and extensional structures developed during the building of the Variscan orogenic crust of Iberia are linked together into major tectonic events operating at lithosphere scale. A review of the tectonometamorphic and magmatic evolution of the IberianMassif reveals backs and forths in the overall conver- gence between Gondwana and Laurussia during theamalgamation of Pangea in late Paleozoic times. Stages dom- inated by lithosphere compression are characterized by subduction, both oceanic and continental, development of magmatic arcs, (over- and under-) thrusting of continental lithosphere, and folding. Variscan convergence re- sulted in the eventual transference of a large allochthonous set of peri-Gondwanan terranes, the Iberian Allochthon, onto the Gondwana mainland. The Iberian Allochthon bears the imprint of previous interaction be- tween Gondwana and Laurussia, including their juxtaposition after the closure of the Rheic Ocean in Lower De- vonian times. Stages governed by lithosphere extension are featured by the opening of two short-lived oceanic basins that dissected previous Variscan orogenic crust, first in the Lower-Middle Devonian, following the closure of the Rheic Ocean, and then in the early Carboniferous, following the emplacement of the peri-Gondwanan allochthon. An additional, major intra-orogenic extensional event in the early-middle Carboniferous dismem- bered the Iberian Allochthon into individual thrust stacks separated by extensional faults and domes. Lateral tec- tonics played an important role through the Variscan orogenesis, especially during the creation of new tectonic blocks separated by intracontinental strike-slip shear zones in the late stages of continental convergence

Use of human splenocytes in an innovative humanised mouse model for prediction of immunotherapy-induced cytokine release syndrome.

OBJECTIVES: Humanised mice have emerged as valuable models for pre-clinical testing of the safety and efficacy of immunotherapies. Given the variety of models available, selection of the most appropriate humanised mouse model is critical in study design. Here, we aimed to develop a model for predicting cytokine release syndrome (CRS) while minimising graft-versus-host disease (GvHD). METHODS: To overcome donor-induced variation, we directly compared the in vitro and in vivo immune phenotype of immunodeficient NSG mice reconstituted with human bone marrow (BM) CD34+ haematopoietic stem cells (HSCs), peripheral blood mononuclear cells (PBMCs) or spleen mononuclear cells (SPMCs) from the same human donors. SPMC engraftment in NSG-dKO mice, which lack MHC class I and II, was also evaluated as a strategy to limit GvHD. Another group of mice was engrafted with umbilical cord blood (UCB) CD34+ HSCs. Induction of CRS in vivo was investigated upon administration of the anti-CD3 monoclonal antibody OKT3. RESULTS: PBMC- and SPMC-reconstituted NSG mice showed short-term survival, with engrafted human T cells exhibiting mostly an effector memory phenotype. Survival in SPMC-reconstituted NSG-dKO mice was significantly longer. Conversely, both BM and UCB-HSC models showed longer survival, without demonstrable GvHD and a more naïve T-cell phenotype. PBMC- and SPMC-reconstituted mice, but not BM-HSC or UCB-HSC mice, experienced severe clinical signs of CRS upon administration of OKT3. CONCLUSION: PBMC- and SPMC-reconstituted NSG mice better predict OKT3-mediated CRS. The SPMC model allows generation of large experimental groups, and the use of NSG-dKO mice mitigates the limitation of early GvHD

Biaxial tensile tests identify epidermis and hypodermis as the main structural elements of sweet cherry skin

The skin of developing soft and fleshy fruit is subjected to considerable growth stress, and failure of the skin is associated with impaired barrier properties in water transport and pathogen defence. The objectives were to establish a standardized, biaxial tensile test of the skin of soft and fleshy fruit and to use it to characterize and quantify mechanical properties of the sweet cherry (Prunus avium) fruit skin as a model. A segment of the exocarp (ES) comprising cuticle, epidermis, hypodermis and adhering flesh was mounted in the elastometer such that the in vivo strain was maintained. The ES was pressurized from the inner surface and the pressure and extent of associated bulging were recorded. Pressure: strain responses were almost linear up to the point of fracture, indicating that the modulus of elasticity was nearly constant. Abrading the cuticle decreased the fracture strain but had no effect on the fracture pressure. When pressure was held constant, bulging of the ES continued to increase. Strain relaxation upon releasing the pressure was complete and depended on time. Strains in longitudinal and latitudinal directions on the bulging ES did not differ significantly. Exocarp segments that released their in vivo strain before the test had higher fracture strains and lower moduli of elasticity. The results demonstrate that the cherry skin is isotropic in the tangential plane and exhibits elastic and viscoelastic behaviour. The epidermis and hypodermis, but not the cuticle, represent the structural 'backbone' in a cherry skin. This test is useful in quantifying the mechanical properties of soft and fleshy fruit of a range of species under standardized conditions.DFG/KN402/8-