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.     

Precipitation of sparingly soluble salts in packed sandbeds in the presence of miscible and immiscible organic substances

Sparingly soluble salts precipitation, e.g. calcium carbonate or calcium sulfate, results in pore clogging in rock formations and in the concomitant reduction of the local permeability of oil wells during the oil extraction processes. On the other hand, in situ controlled salt precipitation is desirable in various applications e.g. waterproofing of concrete constructions suffering from leakages, etc. In the present study, calcium carbonate (CaCO₃) precipitation in sandbeds was investigated, in the presence of organic solvents simulating the conditions prevalent in oil‐well zones. CaCO₃ precipitation was investigated from supersaturated solutions prepared by in‐situ mixing of NaHCO₃ and CaCl₂.2H₂O solutions before the inlet of sandbeds. The solution resulting from the mixing of the two solutions was supersaturated with respect to all calcium carbonate polymorphs. Three types of experiments were performed depending on the supersaturated solutions: a) aqueous solutions b) aqueous supersaturated solutions in contact with sandbeds pre‐saturated with n‐dodecane c) aqueous solutions containing monoethylene glycol (MEG). Results showed that oil–water interfaces enhanced the heterogeneity of the supersaturated solutions and accelerated crystal growth of calcium carbonate at the inlet of the sandbed, resulting in early pore clogging and limitation of local permeability. Maximum sandbed consolidation was obtained with the solutions containing MEG.     

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).     

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...     

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.     

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.     

Democracy in action: Quantization, saturation, and compressive sensing

Recent theoretical developments in the area of compressive sensing (CS) have the potential to significantly extend the capabilities of digital data acquisition systems such as analog-to-digital converters and digital imagers in certain applications. To date, most of the CS literature has been devoted to studying the recovery of sparse signals from a small number of linear measurements. In this paper, we study more practical CS systems where the measurements are quantized to a finite number of bits; in such systems some of the measurements typically saturate, causing significant nonlinearity and potentially unbounded errors. We develop two general approaches to sparse signal recovery in the face of saturation error. The first approach merely rejects saturated measurements; the second approach factors them into a conventional CS recovery algorithm via convex consistency constraints. To prove that both approaches are capable of stable signal recovery, we exploit the heretofore relatively unexplored property that many CS measurement systems are democratic, in that each measurement carries roughly the same amount of information about the signal being acquired. A series of computational experiments indicate that the signal acquisition error is minimized when a significant fraction of the CS measurements is allowed to saturate (10–30% in our experiments). This challenges the conventional wisdom of both conventional sampling and CS.     

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.     

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.