Computational study of dynamic motions and possibility of crossing between surfaces in 3-hydroxy-5-(1H-pyrrol-2-yl)-2H-pyrrol-2-one

Potential energy surfaces (PESs) for tautomerism and two dynamic motions of 3-hydroxy-5-(1H-pyrrol-2-yl)-2H-pyrrol-2-one and its tautomer were calculated using density functional theory. Calculated energies confirm that T1 is 10.95 kJ mol^? 1 more stable than T2. Dynamic study of possible motions shows the high energy-level transition state at D8 = 90° for ring rotation and at D15 = 80° and 90° for rotation of OH bond, respectively, in T1 and T2. In addition, calculated rate constant for conversion of T1 to T2 (tautomerism) is 116 M^? 1 s^? 1, for relative rotations of rings in T1 and T2 are, respectively, 5.62 × 10^? 2 and 1.53 M^? 1 s^? 1 and for rotations of OH bond in T1 and T2 are, respectively, 3.56 × 10⁵ and 6.15 × 10⁴ M^? 1 s^? 1. In the next part of the study, orbital occupancies, natural bond orbitals (NBO) charges and hybridisation in relative rotation of rings and internal reaction coordinate (IRC) steps have been extracted to study the possibility of level crossing. These data show that PESs for IRC and ring rotation have different symmetries. So that these two potential curves cannot have effective non-adiabatic level crossing. However, the levels are weakly avoided or the possibility of level crossing is higher than related system because the energy difference between their barrier energies is not very high.     

Reaction Kinetics of the Invertase from Yeast (S. Cerevisiae)

Invertase converts sucrose to glucose and fructose. The reaction mechanism for the formation of glucose and fructose was studied by stopped flow spectrophotometer and circular dichroism. The reaction mechanism follows biphasic mode with rate constants of k₁0.0053 s^?1?±?0.001 s^?1 and k₂ 0.030 s^?1?±?0.01 s^?1 for 25 mM concentration of sucrose. Far UV circular dichroic spectrum of invertase in presence of sucrose shows 18 % increase in β conformation as a function of time. Taken together, the invertase hydrolysis follows biphasic mode where it undergoes conformational changes followed by hydrolysis of the sucrose.     

Influence of flow rate variation on the development of Escherichia coli biofilms

This work investigates the effect of flow rate variation on mass transfer and on the development of Escherichia coli biofilms on a flow cell reactor under turbulent flow conditions. Computational fluid dynamics (CFD) was used to assess the applicability of this reactor for the simulation of industrial and biomedical biofilms and the numerical results were validated by streak photography. Two flow rates of 374 and 242 L h^?1 (corresponding to Reynolds numbers of 6,720 and 4,350) were tested and wall shear stresses between 0.183 and 0.511 Pa were predicted in the flow cell reactor. External mass transfer coefficients of 1.38 × 10^?5 and 9.64 × 10^?6 m s^?1 were obtained for the higher and lower flow rates, respectively. Biofilm formation was favored at the lowest flow rate because shear stress effects were more important than mass transfer limitations. This flow cell reactor generates wall shear stresses that are similar to those found in some industrial and biomedical settings, thus it is likely that the results obtained on this work can be used in the development of biofilm control strategies in both scenarios.     

Investigation of human platelet adhesion under low shear conditions in a rotational flow chamber

Even though blood pumps have come into clinical usage, thrombo-embolic complications still pose a major problem, and they have not yet been clarified and quantified. However, it is known that the basis of thrombus formation is platelet adhesion, which is thought to be closely associated with the shear rate. Therefore, our current interest focuses on the effect of shear conditions on platelet adhesion. We have designed and carried out an experimental setup allowing fluorescent microscopy of whole blood within a rotational viscometer under controllable shear conditions. A small area of the bottom plate was coated with type I collagen, which provided a model of the injured vessel as a target for platelet adhesion. Using this setup, the time course of platelet adhesion under several different shear rates, ranging from 127 to 723 s^?1, was studied. Platelet adhesion increased along with shear rates up to 283 s^?1, followed by a gradual decrease when the shear rate exceeded 346 s^?1. The adhesion amounts were statistically significant between 283 and 173 s^?1 (p = 0.02), 173 and 127 s^?1 (p = 0.035), and 283 and 503 s^?1 (p = 0.03), respectively. This result suggests that there is an optimal shear condition around 300 s^?1 for platelet adhesion to type I collagen.     

Determining possible thrombus sites in an extracorporeal device,using computational fluid dynamics-derived relative residence time

The prediction of conditions that may result in thrombus formation is a useful application of computational fluid dynamics. A number of techniques exist, based on the consideration of wall shear stress and regions of low blood flow; however, no clear guideline exists for the best practice of their use. In this paper, the sensitivity of each parameter and the specific mechanical forces are explained, before the optimal indicator of thrombosis risk is outlined. An extracorporeal access device cavity provides a suitable geometry to test the methodology. The recommended method for thrombus prediction considers areas with a calculated residence time (RT) and shear strain rate (SSR) thresholds, here set to RT>1 and SSR < 10 s^? 1. Evidence of thrombosis was found for physiological waveforms with an absence of reverse flow, which is expected to ‘wash out’ the cavity. The predicted thrombosis sites compare well with evidence collected from explanted devices.     

Mechanism for the depolymerization of cellulose under alkaline conditions

The mechanism for the hydroxyl-radical-induced depolymerization of cellulose under alkaline conditions in air was investigated using density functional theory at the B3LYP/6-31+G(d,p) level as well as electron transfer theory. The pathway for the depolymerization of cellulose was obtained theoretically and H abstraction from the C(3) atom of the pyran ring during the cleavage of the glucosidic bond was found to be the rate-limiting step due to its high energy barrier (16.81 kcal/mol) and low reaction rate constant (4.623?×?10⁴ mol L^?1 s^?1). Calculations of the electron transfer between O₂ and the saccharide radical performed with the HARLEM software package revealed that following the H abstraction, the oxygen molecule approaches C(2) on the saccharide radical and obtains an electron from the radical, even though no bond forms between the oxygen molecule and the radical. The rate constant for electron transfer could be as high as 1.572?×?10¹¹ s^?1. Furthermore, an enol intermediate is obtained during the final stage of the depolymerization.     

Engineered bone culture in a perfusion bioreactor: a 2D computational study of stationary mass and momentum transport

Successful bone cell culture in large implants still is a challenge to biologists and requires a strict control of the physicochemical and mechanical environments. This study analyses from the transport phenomena viewpoint the limiting factors of a perfusion bioreactor for bone cell culture within fibrous and porous large implants (2.5 cm in length, a few cubic centimetres in volume, 250 μm in fibre diameter with approximately 60% porosity).

A two-dimensional mathematical model, based upon stationary mass and momentum transport in these implants is proposed and numerically solved. Cell oxygen consumption, in accordance theoretically with the Michaelis–Menten law, generates non linearity in the boundary conditions of the convection diffusion equation. Numerical solutions are obtained with a commercial code (Femlab® 3.1; Comsol AB, Stockholm, Sweden). Moreover, based on the simplification of transport equations, a simple formula is given for estimating the length of the oxygen penetration within the implant.

Results show that within a few hours of culture process and for a perfusion velocity of the order of 10^? 4 m s^? 1, the local oxygen concentration is everywhere sufficiently high to ensure a suitable cell metabolism. But shear stresses induced by the fluid flow with such a perfusion velocity are found to be locally too large (higher than 10^? 3 Pa). Suitable shear stresses are obtained by decreasing the velocity at the inlet to around 2 × 10^? 5 m s^? 1. But consequently hypoxic regions (low oxygen concentrations) appear at the downstream part of the implant.

Thus, it is suggested here that in the determination of the perfusion flow rate within a large implant, a compromise between oxygen supply and shear stress effects must be found in order to obtain a successful cell culture.     

Influence of mixing and shear stress on Chlorella vulgaris, Scenedesmus obliquus, and Chlamydomonas reinhardtii

Photosynthetic activity (PA) and growth of different microalgae species (Chlorella vulgaris, Scenedesmus obliquus, and Chlamydomonas reinhardtii) depends in addition to other factors on mixing (tip speed) and shear stress (friction velocity) and was studied in a stirring tank (microcosm). In order to detect cause–effect relationships for an increase in photosynthetic activity, experiments were conducted under different pH values (6.0–8.5) and CO₂ concentrations (0.038 and 4 % (v/v)). The PA was determined as the effective quantum yield by pulse amplitude modulation during a stepwise increase of the tip speed from 0 to 589 cm s^?1 (friction velocity: 0–6.05 cm s^?1) in short-term experiments. The increase caused a distinctive pattern of PA of each species. Compared to 0 cm s^?1, C. vulgaris and S. obliquus showed a 4.0 and 4.8 % higher PA at the optimum tip speed of 126 cm s^?1 (friction velocity of 2.09 cm s^?1) and a 48 and 71 % higher growth, respectively. At 203 cm s^?1, the PA dropped to the value of the unstirred control, while at 589 cm s^?1, the PA decreased of up to 7 and 8 %. In contrast, C. reinhardtii showed 7 % stronger growth at 126 cm s^?1, while the PA decreased about 15 % at an increase of tip speed to 589 cm s^?1. For all investigated microalgae, the pattern of PA and higher growth was not only explained by the main contributing factors like light supply, nutrient supply, and overcoming diffusion gradients. The results indicate that hydrodynamic forces have a stimulating effect on the physiological processes within the cells.     

Sequence-dependent nucleotide dynamics revealed by intercalated ring rotation in DNA-bisnaphthalimide complexes

Bisnaphthalimide intercalators are anti-tumour agents composed of two planar rings linked by a flexible diazanonylene chain. The intercalated rings of three bisnaphthalimide analogues complexed to DNA are found here to undergo 180° rotating motions that do not affect the diazanonylene linker atoms bound to the major groove. These ring rotations are detected by NMR spectroscopy in a broad range of sequence contexts and duplex lengths. A comparative analysis of the frequency and activation energies of such excited states in different complexes and conditions indicates that these motions (i) are unrelated to drug dissociation; (ii) are a consequence of concerted, sequence-dependent nucleotide movements taking place on the millisecond time scale; and (iii) may occur inside the DNA duplexes. The rotation frequencies range from 2 to 25 s⁻¹ at 25°C, depending on DNA composition and the size of the rotating rings. The detected nucleotide dynamics are likely to play an important role in the binding kinetics of the numerous proteins and drugs that require base unstacking when interacting with DNA.     

Kinetics of the stacking of ethidium bromide by the raman laser temperature-jump method

Raman laser temperature-jump measurements have been made on concentrated solutions of ethidium bromide. Two relaxations were observed. The faster has a lifetime of less than 30 ns and is attributed to rotation of the phenyl ring. The slower relaxation is concentration dependent and is due to the parallel stacking of two dye molecules. The forward and reverse rates for this process are (4.6 ± 1.4) × 10⁸ M^?1s^?1 and (6.7 ± 1.4)× 10⁶ s^?1, respectively, at 25°C. 0.25 M ionic strength, and pH 6.9. This reverse rate and those of three similar reactions are found to fit a linear free energy plot. The implications of these results for studies of nucleic acid base stacking are discussed.     

Kinetics and mathematical modeling of infrared thin-layer drying of garlic slices

Drying of garlic slices in thin-layer have been studied with Infrared (IR) at 0.075, 0.15, 0.225 and 0.3 W cm^?2 radiation intensity and 0.75 and 1.25 m s^?1 air flow velocity. The results showed increasing in drying rate and decreasing at the time of drying with decreasing air flow velocity and increasing IR radiation intensity. The effective moisture diffusivity (D_eff) was obtained using Fick’s diffusion equation and its mean values ranged between 5.83×10^?11 and 7.66×10^?10 m² s^?1 for all investigated conditions. In addition, a third-order polynomial equation linking the effective moisture diffusivity and moisture content was found. Average activation energy increased with the decrease of IR radiation and increase of air flow velocity. Thirteen different mathematical models were verified with non-linear regression analysis for describing the garlic drying process. Modified Henderson and Pabis model presented the best prediction of the drying of garlic slices.     

Alpine dwarf shrubs show high proportions of nonfunctional xylem: Visualization and quantification of species-specific patterns

Xylem conductive capacity is a key determinant of plant hydraulic function and intimately linked to photosynthesis and productivity, but can be impeded by temporary or permanent conduit dysfunctions. Here we show that persistent xylem dysfunctions in unstressed plants are frequent in Alpine dwarf shrubs and occur in various but species-specific cross-sectional patterns. Combined synchrotron micro-computed tomography (micro-CT) imaging, xylem staining, and flow measurements in saturated samples of six widespread Ericaceae species evidence a high proportion (19%–50%) of hydraulically nonfunctional xylem areas in the absence of drought stress, with regular distribution of dysfunctions between or within growth rings. Dysfunctions were only partly reversible and reduced the specific hydraulic conductivity to 1.38 to 3.57 ×10^?4 m² s^?1 MPa^?1. Decommission of inner growth rings was clearly related to stem age and a higher vulnerability to cavitation of older rings, while the high proportion of nonfunctional conduits in each annual ring needs further investigations. The lower the xylem fraction contributing to the transport function, the higher was the hydraulic efficiency of conducting xylem areas. Improved understanding of the functional lifespan of xylem elements and the prevalence and nature of dysfunctions is critical to correctly assess structure-function relationships and whole-plant hydraulic strategies.     

Synthesis,DNA and protein interactions and human topoisomerase inhibition of novel Spiroacridine derivatives

Nine new spiroacridine derivatives were synthetized by introducing cyano-N-acylhydrazone group between the acridine and phenyl-substituted rings followed by spontaneous cyclization. The new compounds were assayed for their DNA binding properties, human topoisomerase IIα inhibition and bovine serum albumin (BSA) interaction. Besides, docking analysis were performed in order to better understanding the biomolecule-compounds interactions. All compounds interacted with BSA which was demonstrated by the fluorescence suppression constant of 10⁴?M^?1. Compounds with chloro and NO₂ substituents at that para-position on phenyl ring demonstrated the best results for BSA interaction. DNA binding constant determined by UV–vis data demonstrated high values for AMTAC-11 and AMTAC-14, 1.1?×?10⁸?M^?1 and 4.8?×?10⁶?M^?1, respectively, and all others presented constant values of 10⁵?M^?1. AMTAC-06 with chloro at para-position on phenyl ring presented a topoisomerase II inhibition of 84.34% in comparison to the positive controls used. Docking studies indicated that AMTAC-06 is able to intercalate the DNA base pairs at topoisomerase IIα active site, preventing DNA connection after break, in a process known as poisoning. Topoisomerase enzyme inhibition result was correlated to BSA interaction profile, since AMTAC-06 showed the best results in both analysis. The findings obtained here proved that methoxy or chloro substitution on phenyl ring at para-position is fundamental for in vitro activity of new spiroacridine derivatives, and indicates that AMTAC-06 is a promising entity and should serve as a lead compound in the development of new DNA and protein binders, as well as human topoisomerase II inhibitors.     

2-Methylisoborneol production characteristics of <Emphasis Type="Italic">Pseudanabaena</Emphasis> sp. FACHB 1277 isolated from Xionghe Reservoir,China

The cyanobacterium Pseudanabaena sp. FACHB 1277, a 2-methylisoborneol (2-MIB) producer isolated from Xionghe Reservoir, was identified by molecular biological methods based on the 16S rDNA sequence. Pseudanabaena sp. FACHB 1277 is a planktonic freshwater species with relatively high 2-MIB per cell density value (7.76?×?10^?6 ng cell^?1) and specific growth rate (0.25?±?0.01 d^?1). The effects of temperature and light intensity on 2-MIB production of Pseudanabaena sp. FACHB 1277 were investigated. Of the six temperatures tested, 10, 15, 20, 25, 30, and 35 °C, the maximum total 2-MIB per cell density and minimum cell density were observed at 10 °C, while the total 2-MIB and dissolved 2-MIB (including extracellular and dissolved intracellular 2-MIB) increased with increasing temperature. Among the six tested light intensities (10, 25, 40, 55, 70, and 85 μmol photons m^?2 s^?1), the minimum total 2-MIB per cell density and maximum cell density were observed at 25 μmol photons m^?2 s^?1. The total 2-MIB and extracellular 2-MIB increased with light intensity increasing from 10 to 40 μmol photons m^?2 s^?1, while no significant increase was observed when the light intensity was higher than 40 μmol photons m^?2 s^?1. The maximum intracellular 2-MIB (including dissolved and bound) occurred at 25 μmol photons m^?2 s^?1. The present study indicates that increasing temperature could favor the conversion of bound intracellular to dissolved 2-MIB, while increasing light intensity stimulates the release of dissolved intracellular 2-MIB into the environment.     

Impact of flow velocity on the dynamic behaviour of biofilm bacteria

Abstract

The impact of flow velocity (FV) on the growth dynamics of biofilms and bulk water heterotrophic plate count (HPC) bacteria in drinking water distribution systems was quantified and modeled by combining a logistic growth model with mass balance equations. The dynamic variations in the specific growth and release rates of biofilm bacteria were also quantified. The experimental results showed that the maximum biofilm biomass did not change when flow velocity was increased from 20 to 40 cm s^?1, but was significantly affected when flow velocity was further increased to 60 cm s^?1. Although the concentration of biofilm bacteria was substantially reduced by the higher shear stress, the concentration of bacteria in the bulk fluid was slightly increased. From this it is estimated that the specific growth rate and specific release rate of biofilm bacteria had doubled. The specific release (detachment) rate was dependent on the specific growth rate of the biofilm bacteria.     

Mathematical modeling and analysis of the flocculation process in chambers in series

In this study, the flocculation process in continuous systems with chambers in series was analyzed using the classical kinetic model of aggregation and break-up proposed by Argaman and Kaufman, which incorporates two main parameters: K _a and K _b. Typical values for these parameters were used, i. e., K _a = 3.68 × 10^?5–1.83 × 10^?4 and K _b = 1.83 × 10^?7–2.30 × 10^?7 s^?1. The analysis consisted of performing simulations of system behavior under different operating conditions, including variations in the number of chambers used and the utilization of fixed or scaled velocity gradients in the units. The response variable analyzed in all simulations was the total retention time necessary to achieve a given flocculation efficiency, which was determined by means of conventional solution methods of nonlinear algebraic equations, corresponding to the material balances on the system. Values for the number of chambers ranging from 1 to 5, velocity gradients of 20–60 s^?1 and flocculation efficiencies of 50–90 % were adopted.     

Adhesion study of silicone coatings: the interaction of thickness,modulus and shear rate on adhesion force

Abstract

Interactions between coating thickness, modulus and shear rate on pseudobarnacle adhesion to a platinum-cured silicone coating were studied using a statistical experimental design. A combined design method was used for two mixture components and two process variables. The two mixture components, vinyl end-terminated polydimethylsiloxanes (V21: MW = 6 kg mole^?1 and V35: MW = 4 9.5 kg mole^?1, Gelest Inc.) were mixed at five different levels to vary the modulus. The dry coating thickness was varied from 160 – 740 μm and shear tests were performed at four different shear rates (2, 7, 12, and 22 μm s^?1). The results of the statistical analysis showed that the mixture components were significant factors on shear stress, showing an interaction with the process variable. For the soft silicone coating based on the high molecular weight polydimethylsiloxane (E = 0.08 MPa), shear stress significantly increased as coating thickness decreased, while shear rate slightly impacted shear force especially at 160 μm coating thickness. As the modulus was increased (E = 1.3 MPa), more force was required to detach the pseudobarnacle from the coatings, but thickness and rate dependence on shear stress became less important.     

Feeding efficiency of Chaoborus flavicans (Insecta, Diptera) under turbulent conditions

Turbulence can affect predator–prey interactions. The effect of turbulence on the feeding efficiency of an ambush predator was tested with laboratory experiments. The experiments were conducted in 100-L aquaria in which ten individuals of fourth instar Chaoborus flavicans larvae were placed as predators. Two prey densities (3 and 10 ind. of Daphnia pulex L^?1) and two durations (30 and 120 min) were tested in a nonturbulent treatment and five different turbulence levels [average root-mean-square (RMS) velocities ranging from 0 to 7.3 cm s^?1, corresponding dissipation rates from 7.2 × 10^?7 to 1.3 × 10^?3 m² s^?3]. We hypothesized that the feeding rate of C. flavicans would be enhanced by turbulence due to increasing encounter rates up to a turbulence level above which a disturbance in post-encounter processes would lead to reduced feeding efficiency. However, the results showed no significant increase in the feeding rate of C. flavicans at intermediate turbulence. At high turbulence we found the expected significant negative response in the feeding rate of Chaoborus larvae. The feeding rate declined below the rates at nonturbulent and intermediate turbulence conditions as the average RMS velocity exceeded 3.1 cm s^?1 (dissipation rate 9.9 × 10^?5 m² s^?3, respectively).     

Hypolimnetic turbulence generation associated with superposition of large-scale internal waves in a strongly stratified lake: Lake Biwa, Japan

A 48-h microstructure experiment captured the variation of turbulence in Lake Biwa, Japan, during a strong stratification period, 1 week after a typhoon event. A free-fall microstructure profiler (TurboMAP) and a fine-scale profiler (F-probe) were deployed. An array of five ADCPs positioned close to the experiment site provided current measurements associated with the internal-wave field for a period of one week. Strong winds related to the passage of a typhoon close to the lake generated two low-frequency internal waves: a Kelvin wave and an inertial wave. Both waves were in the first baroclinic mode. This study pictures the superposition of two large-scale internal waves and a stronger current resulting from the two waves being in phase. The synchronization of the waves provoked enhanced shear in the hypolimnion, more than 10 m above the bottom, as well as high dissipation (10^?7 W kg^?1) and vertical diffusivity reaching 10^?4 m² s^?1. The enhanced shear event seems to be related to the current amplitude since it occurred when the current amplitude was increased by the diel wind. Assuming the same turbulence intensity for the enhanced hypolimnetic shear events, this superposition may affect nutrient transfer in the hypolimnion. Also, we witnessed sediment resuspension, consisting of high turbidity and high fluorescence intensity, likely due to a combination of bottom stress and enhanced turbulence.