Numerical fluorescence correlation spectroscopy for the analysis of molecular dynamics under nonstandard conditions

The suitability of mathematical models used to extract kinetic information from correlated data constitutes a significant issue in fluorescence correlation spectroscopy (FCS). Standard FCS equations are derived from a simple Gaussian approximation of the optical detection volume, but some investigations have suggested this traditional practice can lead to inaccurate and misleading conclusions under many experimental circumstances, particularly those encountered in one-photon confocal measurements. Furthermore, analytical models cannot be derived for all measurement scenarios. We describe a novel numerical approach to FCS that circumvents conventional analytical models, enabling meaningful analyses even under extraordinarily unusual measurement conditions. Numerical fluorescence correlation spectroscopy (NFCS) involves quantitatively matching experimental correlation curves with synthetic curves generated via diffusion simulation or direct calculation based on an experimentally determined 3D map of the detection volume. Model parameters are adjusted iteratively to minimize the residual differences between synthetic and experimental correlation curves. In order to reduce analysis time, we distribute calculations across a network of processors. As an example of this new approach, we demonstrate that synthetic autocorrelation curves correspond well with experimental data and that NFCS diffusion measurements of Rhodamine B remain constant, regardless of the distortion present in a confocal detection volume.     

Measurement of the overall size of an aircraft under turbulence conditions based on inverse aperture synthesis

An algorithm is proposed for processing reflected signals providing compensation of the action of the turbo-propeller effect and radial movement of an aircraft. Results are presented for a full-scale experiment confirming the possibility of adequate evaluation of the transverse size of an aircraft from the frequency range of its Doppler profile using the algorithm developed. __________ Translated from Izmeritel'naya Tekhnika, No. 8. pp. 24–28, August, 2008.     

Immunoassay for phenylurea herbicides: application of molecular modeling and quantitative structure-activity relationship analysis on an antigen-antibody interaction study

An indirect competitive enzyme-linked immunosorbent assay (icELISA) for 12 phenylurea herbicides (PUHs) was established with the half-maximum inhibition concentration (IC(50)) of 1.7-920.7 μg L(-1). A method of computer-aided molecular modeling was established in quantitative structure-activity relationship (QSAR) studies to obtain a deeper insight into the PUHs' antibody interactions on how and which molecular properties of the analytes quantitatively affect the antibody recognition. A two-dimensional (2D)-QSAR model based on the Hansch equation and a hologram QSAR (HQSAR) model were constructed, and both showed highly predictive abilities with cross-validation q(2) values of 0.820 and 0.752, respectively. It was revealed that the most important impact factor of the antibody recognition was the PUHs' hydrophobicity (log P), which provided a quadratic correlation to the antibody recognition. Hapten-carrier linking groups were less exposed to antibodies during immunization; thus, groups of the analytes in the same position were generally considered to be less contributive to antibody recognition during immunoassay. But the results of substructure-level analysis showed that these groups played an important role in the antigen-antibody interaction. In addition, the frontier-orbital energy parameter E(LUMO) was also demonstrated as a related determinant for this reaction. In short, the result demonstrated that the hydrophobicity and the lowest unoccupied molecular orbital energy (E(LUMO)) of PUH molecules were mainly responsible for antibody recognition.     

Properties of iron under Earth’s core conditions: Molecular dynamics simulation with an embedded-atom method potential

Using an earlier proposed embedded-atom method potential, we have performed molecular dynamics simulations of the thermodynamic, structural, and diffusional properties of iron under Earth’s core conditions (temperatures of up to 5000 K and densities of up to 12.5 g/cm³). The results attest to spontaneous crystallization of liquid iron at certain parameters of state. We have derived equations of state for the liquid and solid phases and have calculated their heat capacities at constant pressure and temperature, thermal expansion coefficients, isothermal and adiabatic bulk moduli, and sound velocities under various conditions. In addition, we have calculated the heat of fusion of iron and the change in its molar volume on melting. The results agree with literature data. The self-diffusion coefficient of iron decreases linearly with increasing density, vanishes at the densities corresponding to the liquid-solid phase boundary, and is a roughly linear function of temperature.     

Thermally responsive polymeric hydrogel brushes: synthesis, physical properties and use for the culture of chondrocytes

Hydrogel brushes are materials composed of a water-swollen network, which contains polymer chains that are grafted with another polymer. Using a thermally responsive polymer, poly(N-isopropyl acrylamide) (polyNIPAM), as the graft component we are able to maintain the critical solution temperature (Tcrit), independent of the overall composition of the material, at approximately 32 degrees C. The change in swelling at Tcrit is a function of the amount of polyNIPAM in the system. However, there is a much smaller change in the surface contact angles at Tcrit. PolyNIPAM-based materials have generated considerable interest, as 'smart' substrates for the culture of cells and here, we show the utility of hydrogel brushes in cell culture. Chondrocytes attached to the hydrogel brushes and yielded viable cell cultures. Moreover, the chondrocytes could be released from the hydrogel brushes without the use of proteases by reducing the temperature of the cultures to below Tcrit to induce a change in the conformation of the polyNIPAM chain at Tcrit. The importance of the crosslink hydrogel component is illustrated by significant changes in cell attachment/cell viability as the crosslink density is changed.     

Application of molecular imprinting to the development of aqueous buffer and organic solvent based radioligand binding assays for (s)-propranolol

Antibody mimics have been prepared by molecular imprinting of (S)-propranolol and applied in the development of radioligand binding assays for the imprint species. In the assays, polymer particles, radioligand, and analyte were incubated either in an organic solvent or an aqueous buffer, with similarly high sensitivity under both set of conditions. Optimization of the assay conditions led to 100-1000-fold improvements in the limit of determination and 100-1000-fold reductions of the amount of imprinted polymer used, compared with previous studies of this novel type of assay. The present assay uses only 10-50 μg of polymer, and the limit of determination is about 6 nM. The toluene-based assay showed excellent enantioselectivity, the cross-reactivity of the R enantiomer being only 1%, which is better than that demonstrated by biological antibodies. The aqueous buffer based assay showed high substrate selectivity for propranolol in the presence of structurally similar β-blockers. The different selectivity profiles obtained are due to a different balance between hydrophobic and polar interactions in toluene and water, since polar interactions, such as hydrogen bonds, are strong in apolar solvents and hydrophobic interactions are strong in water.     

Comparing ignitability for in situ burning of oil spills for an asphaltenic,a waxy and a light crude oil as a function of weathering conditions under arctic conditions

In situ burning of oil spills in the Arctic is a promising countermeasure. In spite of the research already conducted more knowledge is needed especially regarding burning of weathered oils. This paper uses a new laboratory burning cell (100 mL sample) to test three Norwegian crude oils, Grane (asphalthenic), Kobbe (light oil) and Norne (waxy), for ignitability as a function of ice conditions and weathering degree. The crude oils (9 L) were weathered in a laboratory basin (4.8 m³) under simulated arctic conditions (0, 50 and 90% ice cover). The laboratory burning tests show that the ignitability is dependent on oil composition, ice conditions and weathering degree. In open water, oil spills rapidly become “not ignitable” due to the weathering e.g. high water content and low content of residual volatile components. The slower weathering of oil spills in ice (50 and 90% ice cover) results in longer time-windows for the oil to be ignitable. The composition of the oils is important for the window of opportunity. The asphalthenic Grane crude oil had a limited time-window for in situ burning (9 h or less), while the light Kobbe crude oil and the waxy Norne crude oil had the longest time-windows for in situ burning (from 18 h to more than 72 h). Such information regarding time windows for using in situ burning is very important for both contingency planning and operational use of in situ burning.     

Dependence of the Bragg condition on an external electric field for a polymeric photorefractive material

We investigated the effect of an applied electric field on the Bragg condition of degenerate four-wave mixing a polymeric photorefractive material with a low glass-transition temperatue. For a polymeric photorefractive material the application of an external electric field is necessary for photorefractivity leads to birefringence of the material by poling of the nonlinear optical chromophore. Because the propagation vectors of the pumping and reading beams inside the material are influenced by the refractive index of the material, the Bragg condition depends on the magnitude of the external field. Using an oriented gas model and the-coupled-mode theory, we numerically analyzed the Bragg-mismatch effect that causes a reduction in diffraction efficiency as a function of an external field. We present the boundary conditions for sample thickness and grating spacing for which the Bragg-mismatch effect must be taken into account.     

Melting of Ni and Fe nanoparticles: a molecular dynamics study with application to carbon nanotube synthesis

Molecular dynamics simulations with many-body interatomic potentials are used to study melting of Ni and Fe nanoparticles with diameters that range between 2 and 12 nm. Two different embedded-atom method interatomic potentials are used for each element. The capability of each interatomic potential to model (i) size-dependent melting in nanoparticles and (ii) the bulk melting temperature of Ni or Fe is explored. In agreement with existing theory, molecular dynamics simulations show that the melting temperature of non-supported nanoparticles decreases with decreasing nanoparticle size, displaying a linear relationship with the inverse of nanoparticle diameter. However, molecular dynamics simulations using the interatomic potentials considered in this work provide a lower estimate than existing theory for the sensitivity of the melting temperature to nanoparticle size (slope of linear relationship). Molecular dynamics simulations demonstrate that melting is surface initiated and that a finite temperature range exists in which partial melting of the nanoparticle occurs. This observation is very important in the development of advanced vapor-liquid-solid models for catalyst-assisted single-walled carbon nanotube synthesis.     

Engineering method of computing the radiation flux to a permeable surface under aerodynamic heating conditions

Formulas are proposed for the computation of the radiation heat transfer at the frontal point of an axisymmetric blunt body with a carbon-based destructible coating around which a hypersonic air stream flows.Translated from Inzhenerno-Fizicheskii Zhurnal, Vol. 55, No. 5, pp. 763–767, November, 1988.     

A stochastic lifing method for materials operating under long service conditions: with application to the creep life of a commercial titanium alloy

This paper extends the theta prediction methodology so that life predictions for materials operating under long service conditions can be made that also have a degree of confidence associated with them. Ways in which this model can be applied to the fatigue as well as the creep of all materials is also discussed. For comparison purposes two failure criteria are built into the stochastic model and the determinants of failure derived. This stochastic theta model is then used to investigate the nature of the creep failure time distribution for the Ti 6.2.4.6 alloy under constant uniaxial conditions. The distributions for each _j were found to be very different—with only some of them being normally distributed. The others had very pronounced skews to both the left and right. The empirical distributions for predicted failure times were also found to have long tails reaching out to higher failure times—although the failure time distributions were more symmetric when using the Monkman—Grant failure criteria. For Titanium 6.2.4.6 operating at 773 K and 580 MPa the chances of failure before 410 hours is 1%. At 480 MPa and 773 K the chances of failure before 780 hours is 1%.     

Application of DEM to evaluate and compare process parameters for a particle failure under different loading conditions

The paper presents an application of Discrete Element Modelling (DEM) in understanding the micro-process parameters of a particle failure under different loading conditions. A composite particle has been modelled using many primary particles to represent a quasi-homogeneous particle. Some of the examples of quasi-homogeneous particles are constituents of tablets, pellets, granules and concrete. These particles can behave differently under identical loading conditions even though they consist of same primary particles and proportions. This is a typical behaviour of such particles which is governed by the imperfections present in the particles. A DEM has been used to model the composite particle consisting of bi-modal distribution (smaller particles—matrices and larger particles—aggregates) of primary particles. The particle has been loaded under single plate compression, double plate compression and normal impact on different types of target. The single plate compression and normal impact experiments have also been performed. Process parameters like, fracture pattern, particle size distribution, liberation degree and new surface generation have been evaluated and compared. The results are applicable in understanding the particle failure under different processing operations like, transportation, handling and comminution. The results are also useful in selecting the better loading method for liberating aggregates from cheaper matrices for recycling.     

Facile and selective approach towards synthesis of a series ZSM-5/ZSM-12 catalysts for methanol to hydrocarbons reactions: Applying different synthesis driving force and conditions

The use of ultrasonic waves was developed for synthesis of zeolites at shorter crystallization time with improving their desirable properties. A series of nanostructured ZSM-5/ZSM-12 composite zeolites with different Si/Al ratios and alkalinity using organic templates were prepared by hydrothermal and sonochemical synthesis methods. The physicochemical properties of synthesized nanocatalysts such as structure, morphology, textural, and acidity were characterized via XRD, FESEM, N₂ physisorption, FTIR, TPD-NH₃, TGA-DTG techniques. The results revealed that increasing the Si/Al ratio and alkalinity in the hydrothermal samples enhanced the crystallization, formation of amorphous microcrystals, and dominant phase of MFI with decreasing MTW competitive phase. Zeolites synthesized by high-temperature and short-time sonochemical method had higher crystallinity, less dominant phase of ZSM-5, smaller crystals, greater surface areas, higher concentration of Brønsted acid sites, and stronger strength of moderate/strong acid sites. The catalytic performance of the zeolites for MTH conversion was evaluated under a reaction temperature of 450 °C at different times on stream. The results showed that the sonochemical zeolite had a higher methanol conversion (100%), higher selectivity toward olefins (28% vs. 19%) with more C₃⁼/C₂⁼ ratio (0.79 vs. 0.58), and lower alkanes selectivity (66% vs. 72%) after 240 min TOS.     

An analytical method for determination of the performance of a fin assembly under dehumidifying conditions: A comparative study

The present paper establishes an analytical method for determining the performance of a fully wet fin assembly under dehumidifying conditions. A cubic relationship between the humidity ratio of the saturated air and its temperature is taken for calculating driving force for the mass transfer. With this relationship, the governing equation of a fin assembly becomes nonlinear. The Adomian decomposition method is suggested for the solution. The performance parameters, namely, surface efficiency and augmentation factor, are furnished as a function of different design variables. To establish the merit of the work, present results are compared with those values obtained from the previous model and a reasonable difference in results has been noticed. In this point, it can be highlighted that the error associated with the previous model increases with the relative humidity. Finally, the present model is equally useful to predict the performance of a wet fin assembly with the consideration of any other nonlinear effect.     

Rayleigh equation for the growth of a gas bubble under conditions of finite liquid volume

An equation is presented for the growth of a stationary spherical gas bubble in a finite spherical liquid volume, for which the familiar Rayleigh equation is the zero-order approximation. The results of computer solutions of the derived equation and the Rayleigh equation are compared.     

An analytical model of the stress-strain state of an axisymmetric elastic body under conditions of a two-dimensional temperature field

We have derived an analytical solution for the thermoelasticity problem involving the stress-strain state of an axisymmetric body subjected to the action of a two-dimensional temperature field.Translated from Inzhenerno-Fizicheskii Zhurnal, Vol. 56, No. 4, pp. 650–657, April, 1989.