Deep machine learning interatomic potential for liquid silica.

The use of machine learning to develop neural network potentials (NNP) representing the interatomic potential energy surface allows us to achieve an optimal balance between accuracy and efficiency in computer simulation of materials. A key point in developing such potentials is the preparation of a training dataset of ab initio trajectories. Here we apply a deep potential molecular dynamics (DeePMD) approach to develop NNP for silica, which is the representative glassformer widely used as a model system for simulating network-forming liquids and glasses. We show that the use of a relatively small training dataset of high-temperature ab initio configurations is enough to fabricate NNP, which describes well both structural and dynamical properties of liquid silica. In particular, we calculate the pair correlation functions, angular distribution function, velocity autocorrelation functions, vibrational density of states, and mean-square displacement and reveal a close agreement with ab initio data. We show that NNP allows us to expand significantly the time-space scales achievable in simulations and thus calculating dynamical and transport properties with more accuracy than that for ab initio methods. We find that developed NNP allows us to describe the structure of the glassy silica with satisfactory accuracy even though no low-temperature configurations were included in the training procedure. The results obtained open up prospects for simulating structural and dynamical properties of liquids and glasses via NNP.

Ab initio molecular dynamics and high-dimensional neural network potential study of VZrNbHfTa melt.

The structural and dynamics properties of melts are directly related to their solidification processes, and consequently to the properties of as-cast solid alloys. Ab initio molecular dynamics (AIMD) is a powerful tool that can study both of these factors. However, the main disadvantage of this method is its low performance which is critical for simulation of the multicomponent liquids. At the same time the atomistic simulation of multicomponent liquids has found its application for prediction of the formation of high-entropy alloys-a novel class of materials with enhanced mechanical properties. An effective method to solve the problem of AIMD low performance may be the design of pair or many-body potentials for classical molecular dynamics. One of the promising approaches is high-dimensional neural networks-the method of constructing many-body potentials for classical molecular dynamics from ab initio data. Thus, in this work, the high-dimensional neural network potential for multicomponent liquid VZrNbHfTa melt was constructed. The structure of this melt obtained by AIMD and high-dimensional neural network potential was compared by analyzing partial radial distribution functions. Dynamics of the melt obtained by both methods was also compared analyzing velocity autocorrelation functions and mean-square displacement for each type of atom in multicomponent VZrNbHfTa melt. It was shown that structure and dynamics are reproduced well by high-dimensional neural network potential (HDNNP). Some differences between HDNNP- and AIMD-obtained structure and dynamics are explained by finite-size effect and lack of statistics in AIMD simulation along with inherent errors in energy and force estimations made by high-dimensional neural network potentials. Analysis of melt structure via partial radial distribution functions and chemical short range order parameters led to the conclusion that vanadium atoms are repulsed from all the atoms of another type in liquid VZrNbHfTa system, which lowers the probability of single phase disordered solid solution formation. Diffusivity in multicomponent melt was found to decrease with increasing mass and size of an atom.

Nonstoichiometric titanium dioxide nanotubes with enhanced catalytical activity under visible light.

The catalytic activity of nanotubular titanium dioxide films formed during the oxidation of acetone to carbon dioxide under the action of visible light with a wavelength of 450 nm was found to be approximately 2 times higher compared to standard titanium dioxide (Degussa P25). The nanotubular films were grown by the anodization of titanium foil using an original technique. Diffuse reflectance spectra of the films are attributed to enhanced activity in the visible spectrum by the nonstoichiometry of titanium dioxide near the interface between the nanotubular film and the titanium foil substrate.

Correction: High-temperature X-ray diffraction and thermal expansion of nanocrystalline and coarse-crystalline acanthite α-Ag2S and argentite ß-Ag2S.

Correction for 'High-temperature X-ray diffraction and thermal expansion of nanocrystalline and coarse-crystalline acanthite α-Ag2S and argentite ß-Ag2S' by S. I. Sadovnikov et al., Phys. Chem. Chem. Phys., 2016, 18, 4617-4626.

High-temperature X-ray diffraction and thermal expansion of nanocrystalline and coarse-crystalline acanthite α-Ag2S and argentite ß-Ag2S.

An in situ study of thermal expansion of polymorphic phases of coarse-crystalline and nanocrystalline silver sulfide - monoclinic acanthite α-Ag2S and cubic argentite ß-Ag2S - has been carried out for the first time using the high-temperature X-ray diffraction method. The temperature dependencies of the unit cell parameters of acanthite and argentite in the interval of 300-623 K have been determined, and the thermal expansion coefficients of acanthite and argentite have been found. It is shown that the observed difference in the thermal expansion coefficients for nano- and coarse-crystalline acanthite is due to the small particle size of nanocrystalline silver sulfide leading to the growth of anharmonicity of atomic vibrations. It is established by differential thermal analysis that a reversible polymorphic acanthite-argentite phase transformation takes place at ∼449-450 K and the phase transformation enthalpy is equal to ∼3.7-3.9 kJ mol(-1).

An in situ high-temperature scanning electron microscopy study of acanthite-argentite phase transformation in nanocrystalline silver sulfide powder.

For the first time, the α-Ag2S (acanthite)-ß-Ag2S (argentite) phase transformation in nanocrystalline and coarse-crystalline powders of silver sulfide has been observed in situ by the scanning electron microscopy method in real-time. The argentite crystals are formed on the surface of acanthite particles as a result of electron-beam heating. According to the differential thermal analysis data, the transformation occurs at a temperature of ∼449-450 K, and the enthalpy of transformation is equal to ∼3.7-3.9 kJ mol(-1). The presence of α-Ag2S (acanthite)-ß-Ag2S (argentite) phase transformation is confirmed in situ by high-temperature X-ray diffraction data.

Nonstoichiometry of nanocrystalline monoclinic silver sulfide.

Powders of silver sulfide have been synthesized by chemical bath deposition from aqueous solutions of silver nitrate and sodium sulfide in the presence of sodium citrate or EDTA-H2Na2. Colloid solutions have been prepared by a chemical condensation method from the same aqueous solutions. Synthesized silver sulfide nanopowders have a monoclinic (space group P21/c) acanthite-type structure but the occupancy of the metal sublattice sites by Ag atoms is smaller than 1. Unlike coarse-crystalline silver sulfide Ag2S, silver sulfide nanopowders with particles sizes of less than ∼50 nm are nonstoichiometric, contain vacant sites in the metal sublattice and have a composition of ∼Ag1.93S.

Quasielastic neutron scattering study of hydrogen motion in NbC(0.71)H(0.28).

In order to study the mechanism and parameters of H jump motion in the nonstoichiometric Nb carbides, we have performed quasielastic neutron scattering (QENS) measurements for NbC(0.71)H(0.28) over the temperature range 11- 475 K. Our results indicate that about 30% of H atoms in this system participate in a fast diffusive motion. The temperature dependence of the corresponding H jump rate in the range 298-475 K follows the Arrhenius law with an activation energy of 328 ± 9 meV. The Q dependence of the QENS data suggests that the observed jump motion corresponds to long-range diffusion of H atoms along chains of the off-centre sites in carbon vacancies.

Identification of lattice vacancies on the two sublattices of SiC.

The identification of atomic defects in solids is of pivotal interest for understanding atomistic processes and solid state properties. Here we report on the exemplary identification of vacancies on each of the two sublattices of SiC by making use of (i) electron irradiation, (ii) measurements of the positron lifetimes, (iii) coincident Doppler broadening studies of the positron-electron annihilation radiation, and (iv) a comparison of the experimental data with theoretical studies. After 0.3 MeV electron irradiation, carbon vacancies V(C) are identified, where, after 0.5 MeV electron irradiation, predomi-nantly silicon vacancies V(Si) are observed. After 2.5 MeV irradiation, divacancies V(Si)-V(Si) are detected. The present results are expected to be of general importance for reliable identification of defects and atomic processes in complex solids.

Glucose catabolism in cancer cells: identification and characterization of a marked activation response of the type II hexokinase gene to hypoxic conditions.

One of the most common signatures of highly malignant tumors is their capacity to metabolize more glucose to lactic acid than their tissues of origin. Hepatomas exhibiting this phenotype are dependent on the high expression of type II hexokinase, which supplies such tumors with abundant amounts of glucose 6-phosphate, a significant carbon and energy source especially under hypoxic conditions. Here we report that the distal region of the hepatoma type II hexokinase promoter displays consensus motifs for hypoxia-inducible factor (HIF-1) that overlap E-box sequences known to be related in other gene promoters to glucose response. Moreover, we show that subjecting transfected hepatoma cells to hypoxic conditions activates the type II hexokinase promoter almost 3-fold, a value that approaches 7-fold in the presence of glucose. Consistent with these findings is the induction under hypoxic conditions of the HIF-1 protein. Reporter gene analyses with a series of nested deletion mutants of the hepatoma type II hexokinase promoter show that a significant fraction of the total activation observed under hypoxic conditions localizes to the distal region where the overlapping HIF-1/E-box sequences are located. Finally, DNase I footprint analysis with a segment of the promoter containing these elements reveals the binding of several nuclear proteins. In summary, these novel studies identify and characterize a marked glucose-modulated activation response of the type II hexokinase gene to hypoxic conditions within highly glycolytic hepatoma cells, a property that may help assure that such cells exhibit a growth and survival advantage over their parental cells of origin.

Interfacial premelting and the thermomolecular force: thermodynamic buoyancy.

The presence of a substrate can alter the equilibrium state of another material near their common boundary. Examples include wetting and interfacial premelting. In the latter case, temperature gradients induce spatial variations in the thickness of the premelted film that reflect changes in the strength of the repulsion between the substrate and the solid. We show that the net thermomolecular force on a macroscopic substrate is equivalent to a thermodynamic buoyancy force-proportional to the mass of solid that can occupy the volume enclosed by the substrate and the temperature gradient.

Possible displacement of the climate signal in ancient ice by premelting and anomalous diffusion.

The best high-resolution records of climate over the past few hundred millennia are derived from ice cores retrieved from Greenland and Antarctica. The interpretation of these records relies on the assumption that the trace constituents used as proxies for past climate have undergone only modest post-depositional migration. Many of the constituents are soluble impurities found principally in unfrozen liquid that separates the grain boundaries in ice sheets. This phase behaviour, termed premelting, is characteristic of polycrystalline material. Here we show that premelting influences compositional diffusion in a manner that causes the advection of impurity anomalies towards warmer regions while maintaining their spatial integrity. Notwithstanding chemical reactions that might fix certain species against this prevailing transport, we find that-under conditions that resemble those encountered in the Eemian interglacial ice of central Greenland (from about 125,000 to 115,000 years ago)-impurity fluctuations may be separated from ice of the same age by as much as 50 cm. This distance is comparable to the ice thickness of the contested sudden cooling events in Eemian ice from the GRIP core.

FHL2, a novel tissue-specific coactivator of the androgen receptor.

The control of target gene expression by nuclear receptors requires the recruitment of multiple cofactors. However, the exact mechanisms by which nuclear receptor-cofactor interactions result in tissue-specific gene regulation are unclear. Here we characterize a novel tissue-specific coactivator for the androgen receptor (AR), which is identical to a previously reported protein FHL2/DRAL with unknown function. In the adult, FHL2 is expressed in the myocardium of the heart and in the epithelial cells of the prostate, where it colocalizes with the AR in the nucleus. FHL2 contains a strong, autonomous transactivation function and binds specifically to the AR in vitro and in vivo. In an agonist- and AF-2-dependent manner FHL2 selectively increases the transcriptional activity of the AR, but not that of any other nuclear receptor. In addition, the transcription of the prostate-specific AR target gene probasin is coactivated by FHL2. Taken together, our data demonstrate that FHL2 is the first LIM-only coactivator of the AR with a unique tissue-specific expression pattern.

Aberrant glycolytic metabolism of cancer cells: a remarkable coordination of genetic, transcriptional, post-translational, and mutational events that lead to a critical role for type II hexokinase.

For more than two-thirds of this century we have known that one of the most common and profound phenotypes of cancer cells is their propensity to utilize and catabolize glucose at high rates. This common biochemical signature of many cancers, particularly those that are poorly differentiated and proliferate rapidly, has remained until recently a "metabolic enigma." However, with many advances in the biological sciences having been applied to this problem, cancer cells have begun to reveal their molecular strategies in maintaining an aberrant metabolic behavior. Specifically, studies performed over the past two decades in our laboratory demonstrate that hexokinase, particularly the Type II isoform, plays a critical role in initiating and maintaining the high glucose catabolic rates of rapidly growing tumors. This enzyme converts the incoming glucose to glucose-6-phosphate, the initial phosphorylated intermediate of the glycolytic pathway and an important precursor of many cellular "building blocks." At the genetic level the tumor cell adapts metabolically by first increasing the gene copy number of Type II hexokinase. The enzyme's gene promoter, in turn, shows a wide promiscuity toward the signal transduction cascades active within tumor cells. It is activated by glucose, insulin, low oxygen "hypoxic" conditions, and phorbol esters, all of which enhance the rate of transcription. Also, the tumor cell uses the tumor suppressor p53, which is usually modified by mutations to debilitate cell cycle controls, to further activate hexokinase gene transcription. This results in both enhanced levels of the enzyme, which binds to mitochondrial porins thus gaining preferential access to mitochondrially generated ATP, and in a decreased susceptibility to product inhibition and proteolytic degradation. Significantly, these multiple strategies all work together to enable tumor cells to develop a metabolic strategy compatible with rapid proliferation and prolonged survival.

Glucose catabolism in cancer cells: amplification of the gene encoding type II hexokinase.

Hexokinase type II is highly overexpressed in many cancer cells, where it plays a pivotal role in the high glycolytic phenotype. Here we demonstrate by Southern blot analysis and fluorescence in situ hybridization (FISH) that in the rapidly growing rat AS-30D hepatoma cell line, enhanced hexokinase activity is associated with at least a 5-fold amplification of the type II gene relative to normal hepatocytes. This amplification is located chromosomally, extends to the whole gene, and most likely occurs at the site of the resident gene. No rearrangement of the gene could be detected. Therefore, overexpression of hexokinase type II in AS-30D hepatoma cells may be based, at least in part, on a stable gene amplification. This is the first report describing the amplification of a hexokinase gene in a tumor cell line expressing the high glycolytic phenotype.

Glucose catabolism in cancer cells: regulation of the Type II hexokinase promoter by glucose and cyclic AMP.

The increased glucose consumption of many tumor cells depends to a large extent on the overexpression of hexokinase Type II. In a previous study we isolated and sequenced the hepatoma Type II hexokinase promoter and showed that it is activated by glucose in the highly glycolytic AS-30D hepatoma cell line under study, but not activated in control hepatocytes [Mathupala, S.P., Rempel, A. and Pedersen, P.L. (1995) J. Biol. Chem. 270, 16918-16925]. Here we report that the promoter of the hexokinase Type II gene is maximally activated by glucose at concentrations above 5 mM. Moreover, the data strongly suggest that glucose can act alone without requirement for metabolism. Also, glucose-mediated promoter activation is markedly potentiated by cAMP. This response may serve as a strategy for cancer cells to maintain the hexokinase transcription rate high to ensure an efficient glucose utilization even under conditions where carbohydrates are limiting.

Glucose catabolism in cancer cells. Isolation, sequence, and activity of the promoter for type II hexokinase.

One of the most characteristic phenotypes of rapidly growing cancer cells is their propensity to catabolize glucose at high rates. Type II hexokinase, which is expressed at high levels in such cells and bound to the outer mitochondrial membrane, has been implicated as a major player in this aberrant metabolism. Here we report the isolation and sequence of a 4.3-kilobase pair proximal promoter region of the Type II hexokinase gene from a rapidly growing, highly glycolytic hepatoma cell line (AS-30D). Analysis of the sequence enabled the identification of putative promoter elements, including a TATA box, a CAAT element, several Sp-1 sites, and response elements for glucose, insulin, cAMP, Ap-1, and a number of other factors. Transfection experiments with AS-30D cells showed that promoter activity was enhanced 3.4-, 3.3-, 2.4-, 2.1-, and 1.3-fold, respectively, by glucose, phorbol 12-myristate 13-acetate (a phorbol ester), insulin, cAMP, and glucagon. In transfected hepatocytes, these same agents produced little or no effect. The results emphasize normal versus tumor cell differences in the regulation of Type II hexokinase and indicate that transcription of the Type II tumor gene may occur independent of metabolic state, thus, providing the cancer cell with a selective advantage over its cell of origin.

Elevated content of p53 protein in the absence of p53 gene mutations as a possible prognostic marker for human renal cell tumors.

p53 tumour suppressor gene expression was estimated immunohistochemically using DO-1 monoclonal antibody (recognising both wild-type and mutant p53 in 88 human renal tumours. Single strand conformation polymorphism (SSCP) analysis of possible mutations within exons 4-8 of the p53 gene was performed in 29 of the tumours (mostly immunostaining-positive cases). Obviously elevated p53 content was detected with DO-1 antibody in chromophobic cell carcinomas and most clear/chromophilic cell tumours (in chromophilic cell populations). In contrast, clear cell carcinomas demonstrated either complete absence of p53 expression or the presence of single immunopositive nuclei. Oncocytomas were completely negative. Additional immunostaining of the positive samples with mutant p53-specific Pab240 monoclonal antibody failed to detect immunopositive material. No p53 mutation was found in any of the samples analysed by SSCP. Our results suggest that the elevated p53 content in human renal cell carcinomas does not result from gene mutation and the p53 gene alterations are probably not an important mechanism in the development of human renal cell carcinomas. Accumulation of the wild-type p53 protein may be a useful prognostic marker indicating neoplastic progression malignancy.

Differences in expression and intracellular distribution of hexokinase isoenzymes in rat liver cells of different transformation stages.

The activity, intracellular distribution and mRNA expression of hexokinase isoenzymes were studied in normal rat liver, and in epithelial liver cells at different stages of neoplastic transformation, including non-tumorigenic and tumorigenic cell lines. In contrast to liver, all transformed cells exhibited only hexokinase I and II, which both showed significantly increased activity, hexokinase II being the more abundant form. In parallel, the mRNA expression of the two isoenzymes was elevated, indicating transcriptional control of gene expression. Hexokinase I and II were found in the cytosol and bound to mitochondrial membranes; the percentage of membrane-bound enzyme activity increased with the grade of transformation from 32% of total activity in normal liver up to 69% in dedifferentiated tumor cells. The ratio of hexokinase I/II was higher in the membrane fraction than in the cytosol. In all tissues studied hexokinase II could be resolved in two subtypes IIa and IIb by hydrophobic interaction chromatography. The relative proportion of cytosolic IIa and IIb varied significantly between normal liver (1:1) and transformed cells, and among cells of different transformation stages (4:1 to 1:10). IIa demonstrated the main activity in the more differentiated, IIb in the less differentiated cell lines. IIa-activity showed a good correlation with the intracellular glucose 6-phosphate concentration of the cells. The data indicate that neoplastic cell transformation is accompanied by progressive alterations in the proportion and subcellular distribution of hexokinase isoenzymes I and II.