Exploring the Implementation of GaAsBi Alloys as Strain-Reducing Layers in InAs/GaAs Quantum Dots.

This paper investigates the effect of GaAsBi strain reduction layers (SRLs) on InAs QDs with different Bi fluxes to achieve nanostructures with improved temperature stability. The SRLs are grown at a lower temperature (370 °C) than the usual capping temperature for InAs QDs (510 °C). The study finds that GaAs capping at low temperatures reduces QD decomposition and leads to larger pyramidal dots but also increases the threading dislocation (TD) density. When adding Bi to the capping layer, a significant reduction in TD density is observed, but unexpected structural changes also occur. Increasing the Bi flux does not increase the Bi content but rather the layer thickness. The maximum Bi content for all layers is 2.4%. A higher Bi flux causes earlier Bi incorporation, along with the formation of an additional InGaAs layer above the GaAsBi layer due to In segregation from QD erosion. Additionally, the implementation of GaAsBi SRLs results in smaller dots due to enhanced QD decomposition, which is contrary to the expected function of an SRL. No droplets were detected on the surface of any sample, but we did observe regions of horizontal nanowires within the epilayers for the Bi-rich samples, indicating nanoparticle formation.

Invariant dynamics in a united-atom model of an ionic liquid.

We study a united-atom model of the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethyl)sulfonylamide to determine to what extent there exist curves in the phase diagram along which the microscopic dynamics are invariant when expressed in dimensionless, or reduced, form. The initial identification of these curves, termed isodynes, is made by noting that contours of reduced shear viscosity and reduced self-diffusion coefficient coincide to a good approximation. Choosing specifically the contours of reduced viscosity as nominal isodynes, further simulations were carried out for state points on these, and other aspects of dynamics were investigated to study their degree of invariance. These include the mean-squared displacement, shear-stress autocorrelation function, and various rotational correlation functions. These were invariant to a good approximation, with the main exception being rotations of the anion about its long axis. The dynamical features that are invariant have in common that they are aspects that would be relevant for a coarse-grained description of the system; specifically, removing the most microscopic degrees of freedom in principle leads to a simplification of the potential energy landscape, which allows for the existence of isodynes.

Evolutionary conservation of Trichomonas-mycoplasma symbiosis across the host species barrier.

Introduction: The protozoan parasite Trichomonas vaginalis is the most common cellular sexually transmitted disease in humans, and the closely related species Trichomonas gallinae is an avian parasite of ecological and economic importance. Phylogenetic evidence suggests T. vaginalis arose during bird to human transmission of a T. gallinae-like ancestor. Trichomonas vaginalis shares a strong clinical association with the independent sexually transmitted pathogen Metamycoplasma (formerly Mycoplasma) hominis, and the uncultured bacterium "Candidatus Malacoplasma (formerly Mycoplasma) girerdii," with the latter association being an order of magnitude stronger. Both bacterial species have been shown to profoundly influence T. vaginalis growth, energy production and virulence-associated mechanisms. Methods: Evidence for a novel Malacoplasma sp. was discovered by in vivo Illumina metatranscriptomics sequencing of the T. gallinae-infected pigeon mouth. We leveraged published 16S rDNA profiling data from digestive tract of 12 healthy and 24 T. gallinae-infected pigeons to investigate association between the novel Malacoplasma sp. and T. gallinae. We utilised Illumina metagenomics sequencing targeted to pigeon oral and crop samples infected with the novel Malacoplasma sp. to generate its full-length genome sequence. Sequence similarity network analysis was used to compare annotated proteins from the novel Malacoplasma sp. with a range of other related species. Results: Here we present evidence for a novel Malacoplasma species, related to "Ca. M. girerdii," that is strongly associated with T. gallinae in the upper digestive tract of domestic pigeons. Analysis of the genome sequence revealed gene features apparently specific to a Trichomonas-symbiotic Malacoplasma lineage. Discussion: These data support a model of long-term association between Trichomonas and Malacoplasma spp. that has been conserved across diversification of the Trichomonas lineage and the host species barrier from birds to human.

Identification of D-arabinan-degrading enzymes in mycobacteria.

Bacterial cell growth and division require the coordinated action of enzymes that synthesize and degrade cell wall polymers. Here, we identify enzymes that cleave the D-arabinan core of arabinogalactan, an unusual component of the cell wall of Mycobacterium tuberculosis and other mycobacteria. We screened 14 human gut-derived Bacteroidetes for arabinogalactan-degrading activities and identified four families of glycoside hydrolases with activity against the D-arabinan or D-galactan components of arabinogalactan. Using one of these isolates with exo-D-galactofuranosidase activity, we generated enriched D-arabinan and used it to identify a strain of Dysgonomonas gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan, including members of the DUF2961 family (GH172) and a family of glycoside hydrolases (DUF4185/GH183) that display endo-D-arabinofuranase activity and are conserved in mycobacteria and other microbes. Mycobacterial genomes encode two conserved endo-D-arabinanases with different preferences for the D-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.

Isomorphs in sheared binary Lennard-Jones glass: Transient response.

We have studied shear deformation of binary Lennard-Jones glasses to investigate the extent to which the transient part of the stress strain curves is invariant when the thermodynamic state point is varied along an isomorph. Shear deformations were carried out on glass samples of varying stability, determined by cooling rate, and at varying strain rates, at state points deep in the glass. Density changes up to and exceeding a factor of two were made. We investigated several different methods for generating isomorphs but none of the previously developed methods could generate sufficiently precise isomorphs given the large density changes and nonequilibrium situation. Instead, the temperatures for these higher densities were chosen to give state points isomorphic to the starting state point by requiring the steady-state flow stress for isomorphic state points to be invariant in reduced units. In contrast to the steady-state flow stress, we find that the peak stress on the stress strain curve is not invariant. The peak stress decreases by a few percent for each ten percent increase in density, although the differences decrease with increasing density. Analysis of strain profiles and nonaffine motion during the transient phase suggests that the root of the changes in peak stress is a varying tendency to form shear bands, with the largest tendency occurring at the lowest densities. We suggest that this reflects the effective steepness of the potential; a higher effective steepness gives a greater tendency to form shear bands.

Revisiting fecal metatranscriptomics analyses of macaques with idiopathic chronic diarrhoea with a focus on trichomonad parasites.

Trichomonads, anaerobic microbial eukaryotes members of the phylum Parabasalia, are common obligate extracellular symbionts that can lead to pathological or asymptomatic colonization of various mucosal surfaces in a wide range of animal hosts. Results from previous in vitro studies have suggested a number of intriguing mucosal colonization strategies by Trichomonads, notably highlighting the importance of interactions with bacteria. However, in vivo validation is currently lacking. A previous metatranscriptomics study into the cause of idiopathic chronic diarrhoea in macaques reported the presence of an unidentified protozoan parasite related to Trichomonas vaginalis. In this work, we performed a reanalysis of the published data in order to identify the parasite species present in the macaque gut. We also leveraged the information-rich metatranscriptomics data to investigate the parasite behaviour in vivo. Our results indicated the presence of at least 3 genera of Trichomonad parasite; Tetratrichomonas, Pentatrichomonas and Trichomitus, 2 of which had not been previously reported in the macaque gut. In addition, we identified common in vivo expression profiles shared amongst the Trichomonads. In agreement with previous findings for other Trichomonads, our results highlighted a relationship between Trichomonads and mucosal bacterial diversity which could be influential in health and disease.

Effect of the Symbiosis with Mycoplasma hominis and Candidatus Mycoplasma Girerdii on Trichomonas vaginalis Metronidazole Susceptibility.

Trichomoniasis, the most common non-viral sexually transmitted infection worldwide, is caused by the protozoon Trichomonas vaginalis. The 5- nitroimidazole drugs, of which metronidazole is the most prescribed, are the only effective drugs to treat trichomoniasis. Resistance against metronidazole is increasingly reported among T. vaginalis isolates. T. vaginalis can establish an endosymbiosis with two Mycoplasma species, Mycoplasma hominis and Candidatus Mycoplasma girerdii, whose presence has been demonstrated to influence several aspects of the protozoan pathobiology. The role of M. hominis in T. vaginalis resistance to metronidazole is controversial, while the influence of Ca. M. girerdii has never been investigated. In this work, we investigate the possible correlation between the presence of Ca. M. girerdii and/or M. hominis and the in vitro drug susceptibility in a large group of T. vaginalis isolated in Italy and in Vietnam. We also evaluated, via RNA-seq analysis, the expression of protozoan genes involved in metronidazole resistance in a set of syngenic T. vaginalis strains, differing only for the presence/absence of the two Mycoplasmas. Our results show that the presence of M. hominis significantly increases the sensitivity to metronidazole in T. vaginalis and affects gene expression. On the contrary, the symbiosis with Candidatus Mycoplasma girerdii seems to have no effect on metronidazole resistance in T. vaginalis.

Two Different Species of Mycoplasma Endosymbionts Can Influence Trichomonas vaginalis Pathophysiology.

Trichomonas vaginalis can host the endosymbiont Mycoplasma hominis, an opportunistic pathogenic bacterium capable of modulating T. vaginalis pathobiology. Recently, a new noncultivable mycoplasma, "Candidatus Mycoplasma girerdii," has been shown to be closely associated with women affected by trichomoniasis, suggesting a biological association. Although several features of "Ca. M. girerdii" have been investigated through genomic analysis, the nature of the potential T. vaginalis-"Ca. M. girerdii" consortium and its impact on the biology and pathogenesis of both microorganisms have not yet been explored. Here, we investigate the association between "Ca. M. girerdii" and T. vaginalis isolated from patients affected by trichomoniasis, demonstrating their intracellular localization. By using an in vitro model system based on single- and double-Mycoplasma infection of Mycoplasma-free isogenic T. vaginalis, we investigated the ability of the protist to establish a relationship with the bacteria and impact T. vaginalis growth. Our data indicate likely competition between M. hominis and "Ca. M. girerdii" while infecting trichomonad cells. Comparative dual-transcriptomics data showed major shifts in parasite gene expression in response to the presence of Mycoplasma, including genes associated with energy metabolism and pathogenesis. Consistent with the transcriptomics data, both parasite-mediated hemolysis and binding to host epithelial cells were significantly upregulated in the presence of either Mycoplasma species. Taken together, these results support a model in which this microbial association could modulate the virulence of T. vaginalis. IMPORTANCE T. vaginalis and M. hominis form a unique case of endosymbiosis that modulates the parasite's pathobiology. Recently, a new nonculturable mycoplasma species ("Candidatus Mycoplasma girerdii") has been described as closely associated with the protozoon. Here, we report the characterization of this endosymbiotic relationship. Clinical isolates of the parasite demonstrate that mycoplasmas are common among trichomoniasis patients. The relationships are studied by devising an in vitro system of single and/or double infections in isogenic protozoan recipients. Comparative growth experiments and transcriptomics data demonstrate that the composition of different microbial consortia influences the growth of the parasite and significantly modulates its transcriptomic profile, including metabolic enzymes and virulence genes such as adhesins and pore-forming proteins. The data on modulation from RNA sequencing (RNA-Seq) correlated closely with those of the cytopathic effect and adhesion to human target cells. We propose the hypothesis that the presence and the quantitative ratios of endosymbionts may contribute to modulating protozoan virulence. Our data highlight the importance of considering pathogenic entities as microbial ecosystems, reinforcing the importance of the development of integrated diagnostic and therapeutic strategies.

Valence band engineering of GaAsBi for low noise avalanche photodiodes.

Avalanche Photodiodes (APDs) are key semiconductor components that amplify weak optical signals via the impact ionization process, but this process' stochastic nature introduces 'excess' noise, limiting the useful signal to noise ratio (or sensitivity) that is practically achievable. The APD material's electron and hole ionization coefficients (α and ß respectively) are critical parameters in this regard, with very disparate values of α and ß necessary to minimize this excess noise. Here, the analysis of thirteen complementary p-i-n/n-i-p diodes shows that alloying GaAs with ≤ 5.1 % Bi dramatically reduces ß while leaving α virtually unchanged-enabling a 2 to 100-fold enhancement of the GaAs α/ß ratio while extending the wavelength beyond 1.1 µm. Such a dramatic change in only ß is unseen in any other dilute alloy and is attributed to the Bi-induced increase of the spin-orbit splitting energy (∆so). Valence band engineering in this way offers an attractive route to enable low noise semiconductor APDs to be developed.

Quantifying dynamical and structural invariance in a simple molten salt model.

Recent experimental results for the structure in the ionic liquid PYR14 +TFSI- have shown invariance in the main structure factor peak along curves of equal electrical conductivity [Hansen et al., Phys. Chem. Chem. Phys. 22, 14169 (2020)]. The charge peak decreases slightly with increasing temperature at fixed conductivity, however. For simple liquids, curves with invariant dynamics and structure, known as isomorphs, can be identified as configurational adiabats. While liquids with strong-Coulomb interactions do not have good isomorphs, ionic liquids could be an intermediate case with approximate isomorphs along which some aspects of structure and dynamics are invariant. We study a simple molten salt model using molecular dynamics simulations to test this hypothesis. Simple measures of structure and dynamics are investigated along with one transport property, the shear viscosity. We find that there is a substantial degree of invariance of the self-intermediate scattering function, the mean square displacement, and the viscosity along configurational adiabats over a wide range of densities for the three adiabats simulated. The density range studied is more than a factor of two and extends from the strong-Coulomb regime at low densities to the weak-Coulomb regime at high densities. The structure is not invariant over the full range of density, but in the weak-Coulomb regime, we see behavior similar to that seen experimentally over density changes of order 15%. In view of the limited structural invariance but substantial dynamical invariance, we designate the configurational adiabats as isodynes.

Sporadic isolation of Tetratrichomonas species from the cattle urogenital tract.

Tritrichomonas foetus is a venereal trichomonad parasite which causes reproductive issues in cattle. No other trichomonads are known to be urogenital pathogens in cattle, but there are several reports of Tetratrichomonas and Pentatrichomonas isolates of unclear origin from the cattle urogenital tract (UGT) in the Americas. This study reports the first case of a non-T. foetus cattle urogenital trichomonad isolate in Europe. Molecular analysis of the internal transcribed spacer (ITS) 1-5.8S ribosomal RNA-ITS 2 and 18S ribosomal RNA loci suggest that the isolate is a Tetratrichomonas species from a lineage containing other previously described bull preputial isolates. We identified close sequence similarity between published urogenital and gastrointestinal Tetratrichomonas spp., and this is reviewed alongside further evidence regarding the gastrointestinal origin of non-T. foetus isolates. Routine screening for T. foetus is based on culture and identification by microscopy, and so considering other trichomonad parasites of the bovine UGT is important to avoid misdiagnosis.

Slow lactate gluconate exchange in calcium complexes during precipitation from supersaturated aqueous solutions.

Saturated solutions of calcium l-lactate in water or in deuterium oxide continuously dissolve calcium l-lactate by addition of solid sodium d-gluconate and become strongly supersaturated in calcium d-gluconate due to no or slow precipitation. The quantification of total dissolved calcium allied with the calcium complexes equilibrium constants allowed an ion speciation, which shows an initial non-thermal and spontaneous supersaturation of more than a factor of 50 at 25 °C only slowly decreasing after initiation of precipitation of calcium d-gluconate after a lag phase of several hours. A mathematical model is proposed, based on numerical solution of coupled differential equations of dynamics of l-lactate and d-gluconate exchange during the lag phase for precipitation and during precipitation. A slow exchange of l-lactate coordinated to calcium with d-gluconate is indicated with a time constant of 0.20 h-1 in water and of 0.15 h-1 in deuterium oxide and a kinetic deuterium/hydrogen isotope effect of 1.25. Such spontaneous non-thermal supersaturation and slow ligand exchange with a pseudo first order equilibration process with a half-life of 3.5 h in water for calcium hydroxycarboxylates can help to understand the higher calcium bioavailability from calcium hydroxycarboxylates compared to simple salts.

Isomorph invariance of dynamics of sheared glassy systems.

We study hidden scale invariance in the glassy phase of the Kob-Andersen binary Lennard-Jones system. After cooling below the glass transition, we generate a so-called isomorph from the fluctuations of potential energy and virial in the NVT ensemble: a set of density, temperature pairs for which structure and dynamics are identical when expressed in appropriate reduced units. To access dynamical features, we shear the system using the SLLOD algorithm coupled with Lees-Edwards boundary conditions and study the statistics of stress fluctuations and the particle displacements transverse to the shearing direction. We find good collapse of the statistical data, showing that isomorph theory works well in this regime. The analysis of stress fluctuations, in particular the distribution of stress changes over a given strain interval, allows us to identify a clear signature of avalanche behavior in the form of an exponential tail on the negative side. This feature is also isomorph invariant. The implications of isomorphs for theories of plasticity are discussed briefly.

Hidden scale invariance at high pressures in gold and five other face-centered-cubic metal crystals.

Recent density functional theory simulations showed that metals have a hitherto overlooked symmetry termed "hidden scale invariance" [Hummel et al., Phys. Rev. B 92, 174116 (2015)PRBMDO1098-012110.1103/PhysRevB.92.174116]. This scaling property implies the existence of lines in the thermodynamic phase diagram, so-called isomorphs, along which structure and dynamics are invariant to a good approximation when given in properly reduced units. This means that the phase diagram becomes effectively one-dimensional with regard to several physical properties. This paper investigates consequences and implications of the isomorph theory in six metallic crystals: Au, Ni, Cu, Pd, Ag, and Pt. The data are obtained from molecular dynamics simulations employing many-body effective medium theory (EMT) to model the atomic interactions realistically. We test the predictions from isomorph theory for structure and dynamics by means of the radial distribution and the velocity autocorrelation functions, as well as the prediction of instantaneous equilibration after a jump between two isomorphic state points. Many properties of crystals tend to be dominated by defects, and many of the properties associated with these defects are expected to be isomorph invariant as well. This is investigated in this paper for the case of vacancy diffusion. In regard to the perfect crystal properties, we find the predicted invariance of structure and also, though less perfectly, of dynamics. We show results on the variation of the density-scaling exponent γ, which can be related to the Grüneisen parameter, for all six metals. We consider large density changes up to a factor of two, corresponding to very high pressures. Unlike systems modeled using the Lennard-Jones potential where the density-scaling exponent γ is almost constant, this quantity varies substantially when using the EMT potential and is also strongly material dependent.

Thermodynamics of freezing and melting.

Although the freezing of liquids and melting of crystals are fundamental for many areas of the sciences, even simple properties like the temperature-pressure relation along the melting line cannot be predicted today. Here we present a theory in which properties of the coexisting crystal and liquid phases at a single thermodynamic state point provide the basis for calculating the pressure, density and entropy of fusion as functions of temperature along the melting line, as well as the variation along this line of the reduced crystalline vibrational mean-square displacement (the Lindemann ratio), and the liquid's diffusion constant and viscosity. The framework developed, which applies for the sizable class of systems characterized by hidden scale invariance, is validated by computer simulations of the standard 12-6 Lennard-Jones system.

Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study.

The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

Density scaling and quasiuniversality of flow-event statistics for athermal plastic flows.

Athermal steady-state plastic flows were simulated for the Kob-Andersen binary Lennard-Jones system and its repulsive version in which the sign of the attractive terms is changed to a plus. Properties evaluated include the distributions of energy drops, stress drops, and strain intervals between the flow events. We show that simulations at a single density in conjunction with an equilibrium-liquid simulation at the same density allow one to predict the plastic flow-event statistics at other densities. This is done by applying the recently established "hidden scale invariance" of simple liquids to the glass phase. The resulting scaling of flow-event properties reveals quasiuniversality, i.e., that the probability distributions of energy drops, stress drops, and strain intervals in properly reduced units are virtually independent of the microscopic pair potentials.

Variation of the dynamic susceptibility along an isochrone.

Koperwas et al. showed in a recent paper [Phys. Rev. Lett. 111, 125701 (2013)] that the dynamic susceptibility χ4 as estimated by dielectric measurements for certain glass-forming liquids decreases substantially with increasing pressure along a curve of constant relaxation time. This observation is at odds with other measures of dynamics being invariant and seems to pose a problem for theories of glass formation. We show that this variation is in fact consistent with predictions for liquids with hidden scale invariance: Measures of dynamics at constant volume are invariant along isochrones, called isomorphs in such liquids, but contributions to fluctuations from long-wavelength fluctuations can vary. This is related to the known noninvariance of the isothermal bulk modulus. Considering the version of χ4 defined for the NVT ensemble, data from simulations of a binary Lennard-Jones liquid show in fact a slight increase with increasing density. This is a true departure from the formal invariance expected for this quantity.

Estimating the density-scaling exponent of a monatomic liquid from its pair potential.

This paper investigates two conjectures for calculating the density dependence of the density-scaling exponent γ of a single-component, pair-potential liquid with strong virial potential-energy correlations. The first conjecture gives an analytical expression for γ directly in terms of the pair potential. The second conjecture is a refined version of this involving the most likely nearest-neighbor distance determined from the pair-correlation function. The conjectures are tested by simulations of three systems, one of which is the standard Lennard-Jones liquid. While both expressions give qualitatively correct results, the second is more accurate.

Statistical mechanics of Roskilde liquids: configurational adiabats, specific heat contours, and density dependence of the scaling exponent.

We derive exact results for the rate of change of thermodynamic quantities, in particular, the configurational specific heat at constant volume, CV, along configurational adiabats (curves of constant excess entropy Sex). Such curves are designated isomorphs for so-called Roskilde liquids, in view of the invariance of various structural and dynamical quantities along them. The slope of the isomorphs in a double logarithmic representation of the density-temperature phase diagram, γ, can be interpreted as one third of an effective inverse power-law potential exponent. We show that in liquids where γ increases (decreases) with density, the contours of CV have smaller (larger) slope than configurational adiabats. We clarify also the connection between γ and the pair potential. A fluctuation formula for the slope of the CV-contours is derived. The theoretical results are supported with data from computer simulations of two systems, the Lennard-Jones fluid, and the Girifalco fluid. The sign of dγ∕dρ is thus a third key parameter in characterizing Roskilde liquids, after γ and the virial-potential energy correlation coefficient R. To go beyond isomorph theory we compare invariance of a dynamical quantity, the self-diffusion coefficient, along adiabats and CV-contours, finding it more invariant along adiabats.