Geometric effects in the infinite-layer nickelates

Geometric effects in the infinite-layer nickelates $R$NiO$_2$ associated with the relative size of the $R$-site atom are investigated via first-principles calculations. We consider, in particular, the prospective YNiO$_2$ material to illustrate the impact of these effects. Compared to LaNiO$_2$, we find that the La $\to$ Y substitution is equivalent to a pressure of 19 GPa and that the presence of topotactic hydrogen can be precluded. However, the electronic structure of YNiO$_2$ departs from the cuprate-like picture due to an increase in both self-doping effect and $e_g$ hybridization. Furthermore, we find that geometric effects introduce a quantum critical point in the $R$NiO$_2$ series. This implies a $P4/mmm \leftrightarrow I4/mcm$ structural transformation associated to a $A_3^+$ normal mode, according to which the oxygen squares undergo an in-plane rotation around Ni that alternates along $c$. We find that such a $A_3^+$-mode instability has a generic character in the infinite-layer nickelates and can be tuned via either the effective $R$-site atom size or epitaxial strain.Comment: 6 pages, 4 figures, 4 table

Time-Dependent Density Functional Theory Investigation on the Electronic and Optical Properties of Poly-C,Si,Ge-acenes

We report a comparative computational investigation on the first six members of linear poly-C,Si,Ge-acenes (X4n+2H2n+4, X = C,Si,Ge; n = 1, 2, 3, 4, 5, 6). We performed density functional theory (DFT) and time-dependent DFT calculations to compare morphological, electronic, and optical properties. While C-acenes are planar, Si-and Ge-acenes assume a buckled configuration. Electronic properties show similar trends as a function of size for all families. In particular, differently from C-based compounds, in the case of both Si-and Ge-acenes, the excitation energies of the strongest low-lying electronic transition (β peaks) span the visible region of the spectrum, demonstrating their size tunability. For all families, we assessed the plasmonic character of this transition and found a linear relationship for the wavelength-dependence of the β peaks as a function of the number of rings. A similar slope of about 56 nm is observed for Si-and Ge-acenes, although the peak positions of the former are located at lower wavelengths. Outcomes of this study are compared with existing theoretical results for 2D lattices and nanoribbons, and experiments where available

Molecular interactions of carbapenem antibiotics with the multidrug efflux transporter acrb of escherichia coli

The drug/proton antiporter AcrB, engine of the major efflux pump AcrAB(Z)-TolC of Escherichia coli and other bacteria, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multi-drug resistance (MDR) phenotype. Although hundreds of small molecules are known to be AcrB substrates, only a few co-crystal structures are available to date. Computational methods have been therefore intensively employed to provide structural and dynamical fingerprints related to transport and inhibition of AcrB. In this work, we performed a systematic computational investigation to study the interaction between representative carbapenem antibiotics and AcrB. We focused on the interaction of carbapenems with the so-called distal pocket, a region known for its importance in binding inhibitors and substrates of AcrB. Our findings reveal how the different physico-chemical nature of these antibiotics is reflected on their binding preference for AcrB. The molecular-level information provided here could help design new antibiotics less susceptible to the efflux mechanism

Fundamentals of tin iodide perovskites:A promising route to highly efficient, lead-free solar cells

Hybrid tin-iodide perovskites are investigated as potential lead-free replacement of the lead-iodide perovskites; however, the intrinsic operational limit of these systems has not been described in detail, so far. In this work we combine advanced ab initio calculations with XRD and absorption measurements to lay out the fundamentals of formamidinium (FASnI3) and methylammonium (MASnI3) tin iodide perovskites, in comparison with the lead-halide MAPbI3 prototype. Our theoretical analysis reveals that the tin-based materials display an intrinsic photoconversion efficiency on a par with the lead perovskites, and even superior in the thick-layer limit, where the theoretical PCE reaches 30.5% for lead-halides, and 32.3% for tin-halides under AM1.5G illumination; this is the result of two competing factors: a smaller absorption cross section at the onset for stannates, and their smaller band gap of 1.36 eV, thus very close to the ideal Shockley-Queisser limit. We found the rate of photoluminescence emission extremely sensitive to the absorption spectral weight at the band extrema, resulting in B-factor as different as 7.6 × 10-9 s-1 cm3 for MASnI3 and 0.4 × 10-10 s-1 cm3 for FASnI3. The additional impact of Urbach energy and hole doping, giving rise to large Burstein-Moss effect, is described in detail. This journal i

Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria

Modern medicine relies upon antibiotics, but we have arrived to the point where our inability to come up with new effective molecules against resistant pathogens, together with the declining private investment, is resulting in the number of untreatable infections increasing worldwide at worrying pace. Among other pathogens, widely recognized institutions have indicated Gram-negative bacteria as particularly challenging, due to the presence of the outer membrane. The very first step in the action of every antibiotic or adjuvant is the permeation through this membrane, with small hydrophilic drugs usually crossing through protein channels. Thus, a detailed understanding of their properties at a molecular level is crucial. By making use of Molecular Dynamics simulations, we compared the two main porins of four members of the Enterobacteriaceae family, and, in this paper, we show their shared geometrical and electrostatic characteristics. Then, we used metadynamics simulations to reconstruct the free energy for permeation of selected diazobicyclooctans through OmpF. We demonstrate how porins features are coupled to those of the translocating species, modulating their passive permeation. In particular, we show that the minimal projection area of a molecule is a better descriptor than its molecular mass or the volume. Together with the magnitude and orientation of the electric dipole moment, these are the crucial parameters to gain an efficient compensation between the entropic and enthalpic contributions to the free energy barrier required for permeation. Our results confirm the possibility to predict the permeability of molecules through porins by using a few molecular parameters and bolster the general model according to which the free energy increase is mostly due to the decrease of conformational entropy, and this can be compensated by a favorable alignment of the electric dipole with respect to the channel intrinsic electric field

Anomalous relaxations and chemical trends at III-V nitride non-polar surfaces

Relaxations at nonpolar surfaces of III-V compounds result from a competition between dehybridization and charge transfer. First principles calculations for the (110) and (10$\bar{1}$0) faces of zincblende and wurtzite AlN, GaN and InN reveal an anomalous behavior as compared with ordinary III-V semiconductors. Additional calculations for GaAs and ZnO suggest close analogies with the latter. We interpret our results in terms of the larger ionicity (charge asymmetry) and bonding strength (cohesive energy) in the nitrides with respect to other III-V compounds, both essentially due to the strong valence potential and absence of $p$ core states in the lighter anion. The same interpretation applies to Zn II-VI compounds.Comment: RevTeX 7 pages, 8 figures included; also available at http://kalix.dsf.unica.it/preprints/; improved after revie

Volumetry versus linear diameter lung nodule measurement: an ultra-low-dose computed tomography lung cancer screening study

BACKGROUND: The DutchBelgian Randomized Lung Cancer Screening Trial (NELSON) used a volume-based protocol and significantly reduced the prevalence of false-positive results (2.1%). AIM: To compare the performance of manual linear diameter and semi-automated volumetric nodule measurement in the pilot project Moscow Lung Cancer Screening ultra-low-dose computed tomography pilot study. MATERIALS AND METHODS: The study included individuals with a lung nodule of at least 4 mm on baseline-computed tomography of the Moscow lung cancer screening between February 2017 and February 2018, without verified lung cancer diagnosis until 2020. The radiation dose was selected individually and did not exceed 1 mSv. All scans were assessed by three blinded readers to measure the maximum and minimum transversal nodule diameter and extrapolated volume. As a reference value of size and volume, the average value from the results of expert measurements was obtained. A false-positive nodule was defined as a nodule 6 mm/100 mm3 and a false-negative nodule as a nodule 6 mm/100 mm3. RESULTS: Overall, 293 patients were included (166 men; mean age, 64.6 5.3years); 199 lung nodules were 6 mm/100 mm3 and 94 were 6 mm/100 mm3. Regarding volumetric measurements, 32 [10.9%; 4 false-positive, 28 false-negative], 29 [9.9%; 17 false-positive, 12 false-negative], and 30 [10.2%; 6 false-positive, 24 false-negative] nodule discrepancies were reported by readers 1, 2, and 3 respectively. For linear diameter measurement, 92 [65.5%; 107 false-positive, 85 false-negative], 146 [49.8%; 58 false-positive, 88 false-negative], and 102 [34.8%; 23 false-positive, 79 false-negative] nodule discrepancies were reported by readers 1, 2, and 3 respectively. CONCLUSIONS: The use of lung nodule volumetry strongly reduces the number of false-positive and false-negative nodules compared with nodule diameter measurements, in an ultra-low-dose computed tomography lung cancer screening program

Сравнительный анализ плотности печени по данным КТ и низкодозной КТ органов грудной клетки

The introduction of LDCT-based screening programs into clinical practice allows an additional assessment of the liver. It is known that medium-to-severe steatosis can be detected using LDCT. However, taking into account the increased image noise level and the fact that the liver is always only partly in the scan area, the question arises as to how accurately the liver density can be determined in LDCT relative to routine CT.Purpose. Thus, the following objectives of this study have been established:• To identify the differences between the mean density of the liver as measured by a CT and an LNDT.• To compare the mean density between CT and LDCT in different patient subgroups depending on the mean liver density (<40 HU, 40–50 HU, 50–60 HU, and >60 HU).• To determine the effect of image noise level on the mean liver density values on LDCT compared to CT.Materials and methods. We analyzed 30000 patient records from 2017 to 2019.Inclusion criteria: We included patients with both thoracic non-contrast CT and an LDCT and the time interval between the studies of less than 27 days.Exclusion criteria: The absence of CT-LDCT pair, presence of focal liver lesions, known liver diseases, operated liver, anemia with blood density decrease below 40 HU, hands along the body instead of overhead.Study protocol: LDCT was performed at 135 kV. The routine CT was at 120 kV. Scan length: from lung apex to pleural sinuses. The average radiation dose with LDCT was 0.6–0.8 mSv, and 2.8–4.6 mSv with routine CT. All scans were performed on two 64-detector units from the same manufacturer.We measured liver density with the CTLiverExam software algorithm for automatic liver densitometry.The statistical processing was done using the Stata14 program.Results. We used data from 61 patients for statistical analysis. The average age was 53 years. The ratio of men to women was 23:38.We did not observe statistically significant differences between CT and LDCT. With a breakdown by the initial liver density level, it turned out that in the subgroup 40-50 HU, the differences were statistically significant. No correlation between liver density and standard deviation for CT was revealed (p = 0.338). There was a mild anticorrelation for LDCT with a coefficient of -0.686 (p < 0.0001).Conclusion. Our study shows that liver density measurement in thoracic LDCT is valid. In the context of lung cancer screening programs. An analysis of the image noise/liver density ratio on the LDCT shows an inversely proportional relationship: the higher the noise level, the more significant a “decrease” in liver density. This factor must be taken into account when interpreting the results CT and LDCT.Жировой гепатоз – распространенный вид патологии, своевременное выявление которой позволяет избежать прогрессирования заболевания и развития необратимых изменений. Известно, что по данным стандартной компьютерной томографии (КТ) и низкодозной КТ (НДКТ) можно достоверно выявлять стеатоз средней и тяжелой степеней, в том числе при исследовании органов грудной клетки (ОГК). Таким образом внедрение в клиническую практику скрининговых программ с помощью НДКТ позволяет проводить дополнительную оценку состояния печени.Цель исследования: оценка возможностей корректного определения средней плотности печени при НДКТ ОГК для выявления признаков жирового гепатоза при проведении скрининговых исследований.Материал и методы. Проанализированы результаты КТ и НДКТ ОГК 30 000 пациентов, выполненных за период 2017–2019 гг. Критериями включения в разработку являлось наличие у пациента данных КТ и НДКТ в промежутке менее 27 дней между исследованиями. Исследования, при которых в печени выявлены образования, пациенты после операций на печени, с анемией, при снижении плотности крови менее 40 HU, с опущенными вдоль туловища руками во время исследования и при некорректной сегментации печени при обработке изображений не включались в анализ.Исследования НДКТ и КТ были выполнены на 64-срезовых томографах. Протяженность сканирования: от верхушки легких до плевральных синусов. Напряжение при низкодозном протоколе было равно 135 кВ, при стандартном – 120 кВ. Средняя лучевая нагрузка при НДКТ составила 0,6–0,8 мЗв, при стандартной КТ – 2,8–4,6 мЗв.Автоматический анализ изображений проводился с помощью разработанного ПО для автоматического измерения плотности печени, статистический анализ – с помощью программы Stata14 (StataCorp LLC, College Station, Texas, США).Результаты. Отобраны результаты исследований 61 пациента, которые соответствовали заданным критериям. Соотношение мужчин к женщинам составило 23:38, средний возраст – 53 года.При сравнительной оценке рентгенологической плотности печени при КТ и НДКТ на всей выборке  статистически значимых отличий не выявлено (p < 0,480), при этом отмечалось незначительное повышение средних значений плотности при использовании низкодозных протоколов сканирования: 52,81 HU при НДКТ и 51,88 HU при КТ.Оценка исследований, разбитых на подгруппы в зависимости от плотности печени, показала, что в подгруппе  40–50 HU полученные данные отличаются статистической значимостью (p < 0,0003), тогда как в остальных группах подобная взаимосвязь не выявлена (p < 0,753, p < 0,269, p < 0,077). При НДКТ отмечена средняя антикорреляция между плотностью и среднеквадратическим отклонением с коэффициентом -0,686 (p < 0,0001).Обсуждение. Результат статистического анализа показал, что данные плотности печени при НДКТ сопоставимы с КТ. Это позволяет выявлять пациентов с жировым гепатозом средней и тяжелой степеней,не повышая дозу лучевой нагрузки.Анализ влияния шумовых помех на плотность печени при НДКТ показал, что чем выше уровень шума, тем интенсивнее снижаются данные плотности печени, что необходимо учитывать при трактовке результатов. Отсутствие единых значений плотности печени, различающих ее нормальные значения от сниженных, затрудняет интерпретацию данных, находящихся в диапазоне 40–50 HU, что требует проведения дальнейших исследований