A cutoff phenomenon in accelerated stochastic simulations of chemical kinetics via flow averaging (FLAVOR-SSA)

We present a simple algorithm for the simulation of stiff, discrete-space, continuous-time Markov processes. The algorithm is based on the concept of flow averaging for the integration of stiff ordinary and stochastic differential equations and ultimately leads to a straightforward variation of the the well-known stochastic simulation algorithm (SSA). The speedup that can be achieved by the present algorithm [flow averaging integrator SSA (FLAVOR-SSA)] over the classical SSA comes naturally at the expense of its accuracy. The error of the proposed method exhibits a cutoff phenomenon as a function of its speed-up, allowing for optimal tuning. Two numerical examples from chemical kinetics are provided to illustrate the efficiency of the method.     

Assessment of T1, T1ρ, and T2 values of the ulnocarpal disc in healthy subjects at 3 tesla

Objective

The purpose of this study was to implement clinically feasible imaging techniques for determination of T₁, T_1ρ, and T₂ values of the ulnocarpal disc and to assess those values in a cohort of asymptomatic subjects at 3 tesla. Resulting values were compared between different age groups, since former histological findings of the ulnocarpal disc indicated frequent early degenerative changes of this tissue starting in the third decade of life, even in asymptomatic subjects.

Materials and methods

Twenty-seven healthy subjects were included in this study. T₁ measurements were performed using 3D spoiled gradient-echo (GRE) sequence with variable flip angle. A series of T_1ρ and T₂-weighted images was acquired by a 3D GRE sequence after suitable magnetization preparation. T_1,T_1ρ, and T₂ maps of the ulnocarpal disc were calculated pixel-wise. Representative mean values from extended regions were analysed.

Results

Mean T₁ values of the ulnocarpal disc ranged from 722 ms in a 39 year-old subject to 1264 ms in a 65 year-old subject, T_1ρ ranged from 9.2 ms (26 year-old subject) to 25.9 ms (65 year-old subject). Calculated T₂ values showed a large range from 4.1 ms to 22.3 ms. T_1ρ and T₁ values tended to increase with age (p < 0.05), whereas T₂ did not.

Conclusions

MR relaxometry of the ulnocarpal disc is feasible, and T_1,T_1ρ, and T₂ values show modest variance in asymptomatic subjects. The potential of relaxation mapping to reveal relevant structural changes in patients has to be investigated in further studies.     

Phonon lifetimes from first-principles self-consistent lattice dynamics

Phonon lifetime calculations from first principles usually rely on time-consuming molecular dynamics calculations, or density functional perturbation theory where the zero-temperature crystal structure is assumed to be dynamically stable. Here is presented a new and effective method for calculating phonon lifetimes from first principles. This method is not limited to crystallographic phases stable at 0 K and provides a scheme more effective than most corresponding molecular dynamics calculations. The method is based on the recently developed self-consistent ab initio lattice dynamical method and is here tested by calculating the bcc phase phonon lifetimes of Li, Na, Ti and Zr as representative examples.     

Sand consolidation with calcium phosphate-polyelectrolyte composites

A new method for the consolidation of loose sand formations has been developed. The method involves in situ precipitation of a composite calcium phosphate-polyelectrolyte salt that binds together with loose sand grains, thus resulting to their consolidation. Three different polyelectrolytes (PE) were tested, i.e., polyacrylic acid (PAA), polyallylamine hydrochloride (PAH), and polyethylenimine (PEI). The effect of PE tested on the thermodynamics and the kinetics of precipitation of calcium phosphate salts was investigated. Three types of experiments were done. Investigation of the adsorption of PE on either hydroxyapatite (Ca(5)(PO(4))(3)OH, HAP) crystals or on sand grains. Measurement of the kinetics of heterogeneous nucleation of HAP on the solid substrates and the mechanical properties of the obtained crystals in batch experiments of low and high supersaturation solutions, respectively. Evaluation of the consolidation in sand packs in order to investigate the effectiveness of the method. The crystallization rates, R(p), on HAP crystals in the presence of the PE tested were found in the order R(p)(PAA)>R(p)(PEI)>R(p)(PAH), while nucleation and crystal growth on silicate sand took place only in the absence of adsorbed PE. PAH favored strongly the consolidation process, whereas PEI and PAA resulted in the formation of poorly consolidated grain agglomerates.     

Adsorption of CF4 on graphite preplated with a monolayer of CF3Cl

We report a study of the adsorption of CF(4) on graphite preplated with a monolayer of CF(3)Cl, using infrared reflection absorption spectroscopy combined with ellipsometry. The saturated vapor pressure of CF(3)Cl is nearly 3 orders of magnitude smaller than that of CF(4) at the same temperature, so the main control variables are the temperature and the pressure (or chemical potential) of CF(4), together with the initial coverage of CF(3)Cl. The temperature range covered is 60-105 K. We find that, if the initial monolayer of CF(3)Cl is liquid, CF(4) continuously displaces CF(3)Cl by substitution in the monolayer. If the initial monolayer of CF(3)Cl is solid, due to either lower temperature or compression, CF(4) condenses as a second layer on the top of the CF(3)Cl layer, with only slight mixing with the original layer. This behavior persists to multiple layers of CF(4).     

Emission (57Co) Mössbauer spectroscopy as a tool for probing speciation and metabolic transformations of cobalt(II) in bacterial cells

The emission (⁵⁷Co) variant of Mössbauer spectroscopy, rarely used in biology-related studies, was applied to study binding and possible transformations of ⁵⁷Co^II traces in live and dead (hydrothermally treated) cells of the rhizobacterium Azospirillum brasilense (strain Sp7) at T?=?80 K in frozen aqueous suspensions and as their dried residues. The Mössbauer parameters calculated from the spectra were compared with the similarly obtained data reported earlier for another A. brasilense strain, Sp245 (which differs from strain Sp7 by the ecological niche occupied in the rhizosphere and was found earlier to exhibit different metabolic responses under similar environmental conditions). Similarly to strain Sp245, live cells of strain Sp7, rapidly frozen 2 min and 1 h after their contact with ⁵⁷Co²⁺ (measured in frozen suspensions), showed marked differences in their Mössbauer parameters, reflecting metabolic transformations of ⁵⁷Co²⁺ occurring within an hour. However, the parameters for strains Sp7 (this work) and Sp245 (reported earlier), obtained under similar conditions, were found to significantly differ, implying dissimilarity in their metabolic response to Co²⁺. This is in line with their different metabolic responses to several heavy metals, including Co²⁺, detected earlier using Fourier transform infrared spectroscopy.     

Applications of the MFI-UF to measure and predict particulate fouling in RO systems

The MFI-UF was developed to include smaller colloidal particles not measured in the existing Silt Density Index (SDI) and MFI_0.45 fouling indices. This research investigates the application of the MFI-UF to measure and predict the particulate fouling potential of reverse osmosis (RO) feedwater and also to assess pretreatment efficiency. MFI-UF measurements were carried out at the IJssel Lake and River Rhine RO pilot plants of the influent feedwater, RO concentrate and after pretreatment processes. Pretreatment efficiency was compared based on MFI-UF, MFI_0.45, and SDI measurements. The MFI-UF of the influent feedwater was approximately 700–2400 times higher than the corresponding MFI_0.45 and SDI, due to the retention of smaller particles. A pretreatment efficiency of ≥80%, was found by the MFI-UF at both pilot plants. For the larger particles the MFI_0.45 gave a 90–100% reduction. Minimum predicted run times for a 15% flux decline from MFI-UF measurements were shorter than that observed at the IJssel Lake pilot plant. This may be explained by problems with the ultrafiltration (UF) pretreatment at the time and/or almost negligible particle deposition in the RO pilot systems. Moreover, it was shown that cake resistance increased with ionic strength in MFI-UF tap water experiments and therefore, a correction of the MFI-UF index is required for salinity effects in RO concentrate.     

Crocins from Crocus sativus L. in the Management of Hyperglycemia. In Vivo Evidence from Zebrafish

Diabetes mellitus is a disease characterized by persistent high blood glucose levels and accompanied by impaired metabolic pathways. In this study, we used zebrafish to investigate the effect of crocins isolated from Crocus sativus L., on the control of glucose levels and pancreatic β-cells. Embryos were exposed to an aqueous solution of crocins and whole embryo glucose levels were measured at 48 h post-treatment. We showed that the application of crocins reduces zebrafish embryo glucose levels and enhances insulin expression. We also examined whether crocins are implicated in the metabolic pathway of gluconeogenesis. We showed that following a single application of crocins and glucose level reduction, the expression of phosphoenolpyruvate carboxykinase 1 (pck1), a key gene involved in glucose metabolism, is increased. We propose a putative role for the crocins in glucose metabolism and insulin management.     

Dehydration of rhyolite: activation energy,water speciation and morphological investigation

Journal of Thermal Analysis and Calorimetry - Rhyolite is an extrusive, igneous rock of aluminosilicate composition that upon rapid cooling forms obsidian. Obsidian is amorphous and contains...     

Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity

This article focuses on designing mutations of the PA-IIL lectin from Pseudomonas aeruginosa that lead to change in specificity. Following the previous results revealing the importance of the amino acid triad 22–23–24 (so-called specificity-binding loop), saturation in silico mutagenesis was performed, with the intent of finding mutations that increase the lectin’s affinity and modify its specificity. For that purpose, a combination of docking, molecular dynamics and binding free energy calculation was used. The combination of methods revealed mutations that changed the performance of the wild-type lectin and its mutants to their preferred partners. The mutation at position 22 resulted in 85 % in inactivation of the binding site, and the mutation at 23 did not have strong effects thanks to the side chain being pointed away from the binding site. Molecular dynamics simulations followed by binding free energy calculation were performed on mutants with promising results from docking, and also at those where the amino acid at position 24 was replaced for bulkier or longer polar chain. The key mutants were also prepared in vitro and their binding properties determined by isothermal titration calorimetry. Combination of the used methods proved to be able to predict changes in the lectin performance and helped in explaining the data observed experimentally.