Local perturbations of periodic systems. Chemisorption and point defects by GoGreenGo.

We present a software package GoGreenGo-an overlay aimed to model local perturbations of periodic systems due to either chemisorption or point defects. The electronic structure of an ideal crystal is obtained by worldwide-distributed standard quantum physics/chemistry codes, and then processed by various tools performing projection to atomic orbital basis sets. Starting from this, the perturbation is addressed by GoGreenGo with use of the Green's functions formalism, which allows evaluating its effect on the electronic structure, density matrix, and energy of the system. In the present contribution, the main accent is made on processes of chemical nature, such as chemisorption or doping. We address a general theory and its computational implementation supported by a series of test calculations of the electronic structure perturbations for benchmark model solids: simple, face-centered, and body-centered cubium systems. In addition, more realistic problems of local perturbations in graphene lattice, such as lattice substitution, vacancy, and "on-top" chemisorption, are considered.

Relative stability of diamond and graphite as seen through bonds and hybridizations.

The relative stability of the two most important forms of elemental carbon, diamond and graphite, is readdressed from a newly developed perspective as derived from historically well-known roots. Unlike other theoretical studies mostly relying on numerical methods, we consider an analytical model to gain fundamental insight into the reasons for the quasi-degeneracy of diamond and graphite despite their extremely different covalent bonding patterns. We derive the allotropes' relative energies and provide a qualitative picture predicting a quasi-degenerate electronic ground state for graphite (graphene) and diamond at zero temperature. Our approach also gives numerical estimates of the energy difference and interatomic separations in good agreement with experimental data and recent results of hybrid DFT modeling, although obtained with a much smaller numerical but highly transparent effort. An attempt to extend this treatment to the lowest energy allotropes of silicon proves to be successful as well.

Deductive molecular mechanics of four-coordinated carbon allotropes.

Deductive molecular mechanics is applied to study the relative stability and mechanical properties of carbon allotropes containing isolated σ-bonds. Our approach demonstrates numerical accuracy comparable to that of density-functional theory, but achieved with dramatically lower computational costs. We also show how the relative stability of carbon allotropes may be explained from a chemical perspective using the concept of strain of bonds (or rings) in close analogy to theoretical organic chemistry. Besides that, the role of nonbonding electrostatic interactions as the key factor causing the differences in mechanical properties (in particular, hardness) of the allotropes is emphasized and discussed. The ADAMAS program developed on the basis of this study fairly reproduces spatial and electronic structure as well as mechanical properties of carbon allotropes.

Detection of coronaviruses in insectivorous bats of Fore-Caucasus, 2021.

Coronaviruses (CoVs) pose a huge threat to public health as emerging viruses. Bat-borne CoVs are especially unpredictable in their evolution due to some unique features of bat physiology boosting the rate of mutations in CoVs, which is already high by itself compared to other viruses. Among bats, a meta-analysis of overall CoVs epizootiology identified a nucleic acid observed prevalence of 9.8% (95% CI 8.7-10.9%). The main objectives of our study were to conduct a qPCR screening of CoVs' prevalence in the insectivorous bat population of Fore-Caucasus and perform their characterization based on the metagenomic NGS of samples with detected CoV RNA. According to the qPCR screening, CoV RNA was detected in 5 samples, resulting in a 3.33% (95% CI 1.1-7.6%) prevalence of CoVs in bats from these studied locations. BetaCoVs reads were identified in raw metagenomic NGS data, however, detailed characterization was not possible due to relatively low RNA concentration in samples. Our results correspond to other studies, although a lower prevalence in qPCR studies was observed compared to other regions and countries. Further studies should require deeper metagenomic NGS investigation, as a supplementary method, which will allow detailed CoV characterization.

X-ray micro-computed tomography in the assessment of penile cavernous fibrosis in a rabbit castration model.

BACKGROUND: Current assessment methods of penile cavernous fibrosis in animal models have limitations due to the inability to provide complex and volume analysis of fibrotic alterations. OBJECTIVE: The aim was to evaluate micro-computed tomography for assessment of cavernous fibrosis and compare it with histological, histochemical, immunohistochemical, and RT-PCR analysis. MATERIALS AND METHODS: A controlled trial was performed involving 25 New Zealand male rabbits with induced testosterone deficiency by orchidectomy. Penile samples were obtained before and after 7, 14, 21, and 84 days from orchidectomy. We consistently performed (a) gray value analysis of corpora cavernosa 3D models reconstructed after micro-computed tomography, (b) morphometry of smooth muscles/connective tissue ratio, collagen type I/III ratio, and area of TGF-beta-1 expression in corpora cavernosa, and (c) RT-PCR of TGF-beta-1 expression. RESULTS: Micro-computed tomography allowed visualization of penile structures at a resolution comparable to light microscopy. Gray values of corpora cavernosa decreased from 1673 (1512-1773) on the initial day to 1184 (1089-1232) on the 21st day (p < 0.005). However, on the 84th day, it increased to 1610 (1551-1768). On 21st and 84th days, there was observed a significant decrease in smooth muscle/connective tissue ratio and a significant increase in collagen type I/III ratio (p < 0.05). TGF-beta1 expression increased on the 84th day according to immunohistochemistry (p < 0.005). RT-PCR was impossible to conduct due to the absence of RNA in obtained samples after micro-CT. DISCUSSION AND CONCLUSIONS: Micro-computed tomography provided 3D visualization of entire corpora cavernosa and assessment of radiodensity alterations by gray value analysis in fibrosis progression. We speculate that gray value changes at early and late fibrosis stages could be related to tissue reorganization. RT-PCR is impossible to conduct on tissue samples studied by micro-CT due to RNA destruction. We also suggest that micro-computed tomography could negatively affect the immunohistochemical outcome, as a significant increase of TGF-beta-1 expression occurs later than histological fibrotic signs.