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PubMed2003

Theory of the lattice Boltzmann method: acoustic and thermal properties in two and three dimensions.

The focus of the present work is to provide an analysis for the acoustic and thermal properties of the energy-conserving lattice Boltzmann models, and a solution to the numerical defects and instability associated with these models in two and three dimensions. We discover that a spurious algebraic coupling between the shear and energy modes of the linearized evolution operator is a defect universal to the energy-conserving Boltzmann models in two and three dimensions. This spurious mode coupling is highly anisotropic and may occur at small values of wave number k along certain directions, and it is a direct consequence of the following key features of the lattice Boltzmann equation: (1) its simple spatial-temporal dynamics, (2) the linearity of the relaxation modeling for collision operator, and (3) the energy-conservation constraint. To eliminate the spurious mode coupling, we propose a hybrid thermal lattice Boltzmann equation (HTLBE) in which the mass and momentum conservation equations are solved by using the multiple-relaxation-time model due to d'Humières, whereas the diffusion-advection equation for the temperature is solved separately by using finite-difference technique (or other means). Through the Chapman-Enskog analysis we show that the hydrodynamic equations derived from the proposed HTLBE model include the equivalent effect of gamma=C(P)/C(V) in both the speed and attenuation of sound. Appropriate coupling between the energy and velocity field is introduced to attain correct acoustics in the model. The numerical stability of the HTLBE scheme is analyzed by solving the dispersion equation of the linearized collision operator. We find that the numerical stability of the lattice Boltzmann scheme improves drastically once the spurious mode coupling is removed. It is shown that the HTLBE scheme is far superior to the existing thermal LBE schemes in terms of numerical stability, flexibility, and possible generalization for complex fluids. We also present the simulation results of the convective flow in a rectangular cavity with different temperatures on two opposite vertical walls and under the influence of gravity. Our numerical results agree well with the pseudospectral result.

Journal Article↗
PubMed2004

Detection and characterization of partially unfolded oligomers of the SH3 domain of alpha-spectrin.

For the purpose of equilibrium and kinetic folding-unfolding studies, the SH3 domain of alpha-spectrin (spc-SH3) has long been considered a classic two-state folding protein. In this work we have indeed observed that the thermal unfolding curves of spc-SH3 measured at pH 3.0 by differential scanning calorimetry, circular dichroism, and NMR follow apparently the two-state model when each unfolding profile is considered individually. Nevertheless, we have found that protein concentration has a marked effect upon the thermal unfolding profiles. This effect cannot be properly explained in terms of the two-state unfolding model and can only be interpreted in terms of the accumulation of intermediate associated states in equilibrium with the monomeric native and unfolded states. By chemical cross-linking and pulsed-field gradient NMR diffusion experiments we have been able to confirm the existence of associated states formed during spc-SH3 unfolding. A three-state model, in which a dimeric intermediate state is assumed to be significantly populated, provides the simplest interpretation of the whole set of thermal unfolding data and affords a satisfactory explanation for the concentration effects observed. Whereas at low concentrations the population of the associated intermediate state is negligible and the unfolding process consequently takes place in a two-state fashion, at concentrations above approximately 0.5 mM the population of the intermediate state becomes significant at temperatures between 45 degrees C and 80 degrees C and reaches up to 50% at the largest concentration investigated. The thermodynamic properties of the intermediate state implied by this analysis fall in between those of the unfolded state and the native ones, indicating a considerably disordered conformation, which appears to be stabilized by oligomerization.

Animals↗
PubMed1999

Probing porous media with gas diffusion NMR.

We show that gas diffusion nuclear magnetic resonance (GD-NMR) provides a powerful technique for probing the structure of porous media. In random packs of glass beads, using both laser-polarized and thermally polarized xenon gas, we find that GD-NMR can accurately measure the pore space surface-area-to-volume ratio, S/V rho, and the tortuosity, alpha (the latter quantity being directly related to the system's transport properties). We also show that GD-NMR provides a good measure of the tortuosity of sandstone and complex carbonate rocks.

Calcium Carbonate↗
PubMed2004

The effect of cellular receptor diffusion on receptor-mediated viral binding using Brownian adhesive dynamics (BRAD) simulations.

Brownian adhesive dynamics (BRAD) is a new method for simulating the attachment of viruses to cell surfaces. In BRAD, the motion of the virus is subject to stochastic bond formation and breakage, and thermal motion owing to collisions from the solvent. In the model, the virus is approximated as a rigid sphere and the cell surface is approximated as a rigid plane coated with receptors. In this article, we extend BRAD to allow for the mobility of receptors in the plane of the membrane, both before and after they are ligated by viral attachment proteins. Allowing the proteins to move within the membrane produced several differences in behavior from when the receptors are immobilized. First, the mean steady-state bond number is unaffected by changes in cellular receptor density because proteins are now free to diffuse into the contact area, and the extent of binding is dictated by the availability of viral attachment proteins. Second, the time required to reach steady-state binding increases as both the cellular receptor number decreases and the receptor mobility decreases. This is because receptor diffusion is a slower process than the binding kinetics of the proteins. Decreasing the rate of protein binding was found to decrease the fraction of viruses bound to steady state, but not the extent of binding for those viruses that were bound. Increasing the binding rate increased the fraction of viruses bound, until no further viruses could bind. Alterations in receptor binding kinetics had no discernable effect on the mean steady-state bond number between virus and cell, because interactions were of sufficiently high affinity that all available receptor-viral attachment proteins were destined to bind at steady state.

Algorithms↗
PubMed1990

[Chemical and thermal compatibility of all-ceramic systems].

The chemical and thermal compatibility of the all-ceramic systems Vitadur-N, Hi-Ceram and In-Ceram as well as the combinations of Dicor with Vitadur-N, Dicor with NBK 1000 and Dicor with Vivodent, respectively, were investigated by means of electronmicroscopy and microprobe measurements at the interface of each compound, and thermomechanical analyses of the components were performed. The results show good contact at the interface of all combinations investigated. No evidence was found for diffusion at the interface except in the In-Ceram system, were a migration of K+ from Vitadur-N dentine into the glassy phase of In-Ceram occurs. The thermomechanical analyses showed a good thermal compatibility of all compounds investigated.

Biocompatible Materials↗
PubMed2006

Diffusion NMR studies on fish antifreeze proteins and synthetic analogues.

Pulsed field gradient spin echo NMR spectroscopy was used to measure diffusion coefficients of the alpha-helical type I antifreeze protein from the winter flounder, two synthetic derivatives in which the four Thr residues were replaced with Val and Ala, respectively, and the low molecular weight fraction antifreeze glycoprotein. Under the conditions studied, the natural type I antifreeze protein and low molecular weight glycoprotein gave diffusion values that were consistent with the presence of monomeric protein in solution. While significant aggregation of the Ala analogue was observed (2-10 mM), there was no evidence for aggregation in the Val analogue (1-3 mM). These results are compared with previously reported solubility and thermal hysteresis data and the implications for the design of synthetic antifreeze proteins are discussed.

Amino Acid Sequence↗
PubMed2004

Amino acid substitutions in the C-terminal AAA+ module of Hsp104 prevent substrate recognition by disrupting oligomerization and cause high temperature inactivation.

Hsp104 is an important determinant of thermotolerance in yeast and is an unusual molecular chaperone that specializes in the remodeling of aggregated proteins. The structural requirements for Hsp104-substrate interactions remain unclear. Upon mild heat shock Hsp104 formed cytosolic foci in live cells that indicated co-localization of the chaperone with aggregates of thermally denatured proteins. We generated random amino acid substitutions in the C-terminal 199 amino acid residues of a GFP-Hsp104 fusion protein, and we used a visual screen to identify mutants that remained diffusely distributed immediately after heat shock. Multiple amino acid substitutions were required for loss of heat-inducible redistribution, and this correlated with complete loss of nucleotide-dependent oligomerization. Based on the multiply substituted proteins, several single amino acid substitutions were generated by site-directed mutagenesis. The singly substituted proteins retained the ability to oligomerize and detect substrates. Intriguingly, some derivatives of Hsp104 functioned well in prion propagation and multiple stress tolerance but failed to protect yeast from extreme thermal stress. We demonstrate that these proteins co-aggregate in the presence of other thermolabile proteins during heat treatment both in vitro and in vivo suggesting a novel mechanism for uncoupling the function of Hsp104 in acute severe heat shock from its functions at moderate temperatures.

Adenosine Triphosphatases↗
PubMed1995

The spinal loop dialysis catheter: characterization of use in the unanesthetized rat.

To permit long-term measurement of time-dependent changes in levels of dialyzable drugs and transmitters in the spinal intrathecal (i.t.) space of the unanesthetized rat, we developed a dialysis catheter for chronic placement. This was accomplished by constructing a loop probe 9 cm in length from 0.3-mm-diameter dialysis tubing that was made impermeable except for the distal loop. This loop catheter was readily inserted though an incision in the cisternal membrane and passed to the lumbar enlargement. The ends of the catheter were then externalized on the top of the head. To permit i.t. injections, an additional i.t. catheter could also be inserted simultaneously by the same route. For dialysis, an external end of the loop catheter was connected to a syringe pump and perfused with artificial CSF (10 microliters/min) and the out flow collected. A series of studies were performed to demonstrate the characteristics and utility of this technique. (1) Stability of resting release: glutamate and glucose concentrations in spinal dialysate showed no significant changes from 3 to 10 days after implantation. (2) Spinal cord ischemia: ischemia induced by aortic occlusion or cardiac arrest evoked a time dependent increase in retrieved glutamate. (3) Spinal cord compression caused a time-dependent glutamate, aspartate and PGE2 increase. (4) Noxious afferent stimulation induced by the injection of formalin into the hindpaw resulted in a rapid and transient increase in dialysate glutamate concentration. (5) Direct activation of spinal excitatory amino acids receptors by i.t. injection of kainic acid (1 microgram) evoked a significant increase in aspartate and taurine. (6) Continuous delivery of spinal opiate (alfentanil) via dialysis resulted in a maintained, concentration dependent elevation in the thermal escape latencies in the unanesthetized rat. The loop dialysis catheter provides a robust experimental tool for studying time dependent changes in the concentration of diffusible substances in spinal CSF over an extended post-implantation interval and allows comparison of these changes with concurrently assessed behavioral indices.

Alfentanil↗
PubMed2002

Physical stability and solubility of the thermotropic mesophase of fenoprofen calcium as pure drug and in a tablet formulation.

The aim of this study was to investigate and compare the physical stability and solubility of the liquid crystalline form of fenoprofen calcium as pure drug and in a proprietary tablet formulation (Nalfon), and to investigate if a simple heat treatment of a proprietary tablet containing fenoprofen calcium may lead to a physically stable formulation with enhanced dissolution rate and apparent solubility. The liquid crystalline form of fenoprofen calcium (thermotropic mesophase) was prepared by heating the crystalline drug to 125 degrees C to remove the water of crystallisation. Differential scanning calorimetry investigation revealed an endothermic peak at 89 degrees C upon heating (liquid crystal formation) attributable to water loss from the crystalline dihydrate. The liquid crystalline order was maintained upon cooling. No interference of tablet excipients with the thermal behaviour of the drug in the tablet formulation was observed. The crystalline dihydrate and liquid crystalline forms of fenoprofen calcium could be differentiated by diffuse reflectance infra-red spectroscopy and X-ray powder diffraction, both as pure drug and in tablet formulation. The supercooled liquid crystal (thermotropic reversed hexagonal phase) alone and in preheated and ground tablets was physically stable when stored in a dry environment or at 33% relative humidities (RH) at both 20 and 40 degrees C for 2 months. At 40 degrees C and 75% RH the supercooled mesophase extensively converted to the crystalline dihydrate within 6 days. Liquid crystalline fenoprofen calcium stored at 20 degrees C and 75% RH showed only partial dihydrate conversion after 2 months of storage. The solubility of the crystalline dihydrate alone and from the tablet formulation was 2.8+/-0.2 mg/ml and 3.0+/-0.2 mg/ml (mean+/-s.d.), respectively, (not significantly different), whereas the maximum solubility of the liquid crystal was 5.0+/-0.3 mg/ml (mean+/-s.d.) and 6.9+/-0.6 mg/ml (mean+/-s.d.), respectively (significantly different). The difference in maximum solubility between the crystalline dihydrate form of fenoprofen calcium and the fenoprofen calcium mesophase was highly significant, for both the pure drugs and the tablet formulations. The dissolution rate of the liquid crystalline fenoprofen calcium in preheated, intact tablets was significantly lower than that of the crystalline form in non-preheated tablets. Gross visual changes and scanning electron microscopy indicated that the disintegration properties of the tablet may be detrimentally effected by heating the tablet to 125 degrees C, diminishing the beneficial effect of improved solubility of the liquid crystal. The study has shown that conversion of the crystalline form of fenoprofen calcium to the liquid crystal can enhance the apparent solubility of the pure drug and the drug in presence of tablet excipients, but that the conversion should be performed before tablet formulation in order to increase dissolution of this poorly water-soluble drug.

Chemistry, Pharmaceutical↗
PubMed2000

Fabrication, characterization, and enzymatic activity of encapsulated fungal protease--fatty lipid biocomposite films.

Encapsulation of an aspartic protease from the fungus Aspergillus saitoi (F-prot) in thermally evaporated fatty acid films by a simple beaker-based immersion technique under enzyme-friendly conditions is described. The approach is based on diffusion of the enzyme from aqueous solution, driven primarily by attractive electrostatic interaction between charged groups on the enzyme surface and ionized lipid molecules in the film. The encapsulated enzyme molecules could be "pumped out" of the biocomposite film into solution by modulating the electrostatic interaction between the enzyme and fatty acid molecules via solution pH variation. The kinetics of F-prot diffusion into the acid films was followed using quartz crystal microgravimetry measurements while the secondary and tertiary structure of the enzyme in the lipid matrix was studied using Fourier transform infrared (FT-IR) and fluorescence spectroscopies. FT-IR and fluorescence measurements indicated little perturbation to the native structure of the enzyme. A chemical analysis of the F-prot-fatty acid biocomposite film was also performed using X-ray photoelectron spectroscopy. The encapsulated F-prot molecules showed catalytic activity (as estimated by reaction with hemoglobin) comparable to free enzyme molecules in solution, indicating facile access of biological analytes/reactants in solution to the enzyme molecules. The advantages/disadvantages of this approach vis-à-vis methods currently used for encapsulation of biomolecules are briefly discussed.

Aspergillus↗
PubMed1981

Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.

Genome regulatory proteins (e.g., repressors or polymerases) that function by binding to specific chromosomal target base pair sequences (e.g., operators or promoters) can appear to arrive at their targets at faster than diffusion-controlled rates. These proteins also exhibit appreciable affinity for nonspecific DNA, and thus this apparently facilitated binding rate must be interpreted in terms of a two-step binding mechanism. The first step involves free diffusion to any nonspecific binding site on the DNA, and the second step comprises a series of protein translocation events that are also driven by thermal fluctuations. Because of nonspecific binding, the search process in the second step is of reduced dimensionality (or volume); this results in an accelerated apparent rate of target location. In this paper we define four types of processes that may be involved in these protein translocation events between DNA sites. These are (i) "macroscopic" dissociation--reassociation processes within the domain of the DNA molecule, (ii) "microscopic" dissociation--reassociation events between closely spaced sites in the DNA molecule, (iii) "intersegment transfer" (via "ring-closure") processes between different segments of the DNA molecule, and (iv) "sliding" along the DNA molecule. We present mathematical and physical descriptions of each of these processes, and the consequences of each for the overall rate of target location are worked out as a function of both the nonspecific binding affinity between protein and DNA and the length of the DNA molecule containing the target sequence. The theory is developed in terms of the Escherichia coli lac repressor--operator interaction since data for testing these approaches are available for this system [Barkley, M. (1981) Biochemistry 20, 3833; Winter, R. B., & von Hippel, P. H. (1981) Biochemistry (second paper of three in this issue); Winter, R. B., Berg, O. G., & von Hippel, P. H. (1981) Biochemistry (third paper of three in this issue)]. However, we emphasize that this approach is general for the analysis of mechanisms of biological target location involving facilitated transfer processes via nonspecific binding to the general system of which the target forms a small part.

Binding Sites↗
PubMed2005

In situ reactivity and FTIR study of the wet and dry photooxidation of propane on anatase TiO2.

The photocatalytic oxidation (PCO) of trace amounts of propane (500 ppm) on nanocrystalline anatase TiO2 has been investigated in situ as a function of temperature (T = 318-473 K), humidity (C(H2O) = 0-4%), and time by means of mass spectrometry and diffuse reflectance Fourier transform infrared spectroscopy (DRIFT). Propane adsorbs associatively on TiO2 at 318 K in dry air, while at 473 K small amounts of thermal dissociation products appear on the surface. In agreement with previous studies, propane is found primarily to be converted to acetone by reactions with photogenerated oxygen radicals. Various successive reaction paths exist, where the branching depends on the temperature and hydroxylation state of the surface. Under dry conditions at 318 K, acetone oxidation is initially kinetically hindered, while, above 400 K, acetone readily decomposes. The thermally assisted reaction channel leads to detrimental bonding of surface species and inhibition of the catalytic activity. It is manifested by a coloration of the sample and suggested to be coupled to surface reduction. Under humidified conditions, there is an optimum of the PCO in C(H2O) and T space, which is estimated to correspond to an equilibrium coverage of one monolayer of H2O (or bilayer). The latter reaction condition also corresponds to sustained high propane conversion and is characterized by rapid establishment of steady state rates. The optimum PCO is discussed in terms of a balance between (i) sustaining enough of a photoactive water monolayer to avoid detrimental bonding of surface species, (ii) allowing reactants to adsorb and access bulk TiO2 photoexcitations, and at the same time (iii) maximizing the thermally assisted decomposition of intermediates.

Journal Article↗
PubMed2006

Photogeneration of distant radical pairs in aqueous pyruvic acid glasses.

The lambda > 300 nm photolysis of h4- or d4-pyruvic acid aqueous glasses at 77 K yields identical electron magnetic resonance (EMR) spectra arising from distant (r greater or similar 0.5 nm) triplet radical pairs. Spectra comprise: (1) well-resolved quartets, X, at g approximately ge, that closely match the powder spectra of spin pairs interacting across r approximately 1.0 nm with D approximately 3.0 mT, E approximately 0 mT zero field splittings (ZFS), and (2) broad signals, Y, centered at g approximately 2.07 that display marked g-anisotropy and g-strain, exclude D greater or similar 20.0 mT values (i.e., r less or similar 0.5 spin nm separations), and track the temperature dependence of related g approximately 4 features. These results imply that the n-pi excitation of pyruvic acid, PA, induces long-range electron transfer from the promoted carbonyl chromophore into neighboring carbonyl acceptors, rather than homolysis into contact radical pairs or concerted decarboxylation into a carbene. Since PA is associated into hydrogen-bonded dimers prior to vitrification, X signals arise from radical pairs ensuing intradimer electron transfer to a locked acceptor, while Y signals involve carbonyl groups attached to randomly arranged, disjoint monomers. The ultrafast decarboxylation of primary radical ion pairs, 3[PA+* PA-*], accounts for the release of CO2 under cryogenic conditions, the lack of thermal hysteresis displayed by magnetic signals between 10 and 160 K, and averted charge retrotransfer. All EMR signals disappear irreversibly above the onset of ice diffusivity at approximately 190 K.

Journal Article↗
PubMed2005

Parallels between the dynamics at the noise-perturbed onset of chaos in logistic maps and the dynamics of glass formation.

We develop the characterization of the dynamics at the noise-perturbed edge of chaos in logistic maps in terms of the quantities normally used to describe glassy properties in structural glass formers. Following the recognition [Phys. Lett. A 328, 467 (2004)] that the dynamics at this critical attractor exhibits analogies with that observed in thermal systems close to vitrification, we determine the modifications that take place with decreasing noise amplitude in ensemble- and time-averaged correlations and in diffusivity. We corroborate explicitly the occurrence of two-step relaxation, aging with its characteristic scaling property, and subdiffusion and arrest for this system. We also discuss features that appear to be specific to the map.

Journal Article↗
PubMed1992

Photoacoustic detection of triplet state and singlet oxygen in highly absorbing samples.

A photoacoustic (PA) effect theory taking into account two heat sources corresponding to the radiationless relaxation processes of two states of different lifetimes and to the heat diffusion across the sample is herewith presented. Results obtained demonstrate that the amplitude and the phase of the PA signal depend on the sample's thermal properties, on its optical absorption coefficient, on the lifetime of the long-lived excited state, and on the ratio of the two heat sources. This ratio can be expressed as a function of the product of the energy of the excited state times the quantum yield of its production. Simulations of PA amplitude and phase variations vs light modulation frequency exhibit new features of the PA signal:phase inversion and fast decrease of the amplitude. Experimental verifications were carried out on solutions and gels. Fitting of the amplitude and phase variations allow us to measure the lifetime and conversion yield of the intermediate state which can be a triplet state or singlet oxygen, O2(1 delta g). The addition of an acceptor, specific to O2(1 delta g), induces changes in the amplitude of the PA signal which can be used to study the production and deactivation of this excited form of oxygen. This work demonstrates the usefulness of PA in the detection of metastable excited states such as the triplet state and singlet oxygen and in their quantitative analysis.

Coloring Agents↗
PubMed2005

A finite element method model to simulate laser interstitial thermo therapy in anatomical inhomogeneous regions.

BACKGROUND: Laser Interstitial ThermoTherapy (LITT) is a well established surgical method. The use of LITT is so far limited to homogeneous tissues, e.g. the liver. One of the reasons is the limited capability of existing treatment planning models to calculate accurately the damage zone. The treatment planning in inhomogeneous tissues, especially of regions near main vessels, poses still a challenge. In order to extend the application of LITT to a wider range of anatomical regions new simulation methods are needed. The model described with this article enables efficient simulation for predicting damaged tissue as a basis for a future laser-surgical planning system. Previously we described the dependency of the model on geometry. With the presented paper including two video files we focus on the methodological, physical and mathematical background of the model. METHODS: In contrast to previous simulation attempts, our model is based on finite element method (FEM). We propose the use of LITT, in sensitive areas such as the neck region to treat tumours in lymph node with dimensions of 0.5 cm - 2 cm in diameter near the carotid artery. Our model is based on calculations describing the light distribution using the diffusion approximation of the transport theory; the temperature rise using the bioheat equation, including the effect of microperfusion in tissue to determine the extent of thermal damage; and the dependency of thermal and optical properties on the temperature and the injury. Injury is estimated using a damage integral. To check our model we performed a first in vitro experiment on porcine muscle tissue. RESULTS: We performed the derivation of the geometry from 3D ultrasound data and show for this proposed geometry the energy distribution, the heat elevation, and the damage zone. Further on, we perform a comparison with the in-vitro experiment. The calculation shows an error of 5% in the x-axis parallel to the blood vessel. CONCLUSIONS: The FEM technique proposed can overcome limitations of other methods and enables an efficient simulation for predicting the damage zone induced using LITT. Our calculations show clearly that major vessels would not be damaged. The area/volume of the damaged zone calculated from both simulation and in-vitro experiment fits well and the deviation is small. One of the main reasons for the deviation is the lack of accurate values of the tissue optical properties. In further experiments this needs to be validated.

Animals↗
PubMed1989

Microstructure and mechanical properties of Ti-Ta/alumina and Ti-Nb/alumina joints for dental implants.

The microstructure of Ti-Ta and Ti-Nb alloys diffusion bonded to a 99.7 wt% Al2O3 ceremic for dental implants is subdivided into a reaction double layer containing the phases TiAl and Ti3Al, a transition region of coarse alpha-Ti plates in beta-Ti, and the unaffected bulk metal, the alpha-Ti/beta-Ti structure of which can be refined by annealing at 800 degrees C for 1 hour after bonding. Optimized joints fabricated by diffusion bonding in a high vacuum at 1,200 degrees C from a 99.7 wt% Al2O3 ceramic and Ti-Ta alloys fitted in their thermal contraction behavior to that of the ceramic by the addition of 30 to 40 wt% Ta showed a fracture resistance of 2.3 MN/m3/2. Approximately 80% of the bend test specimens notched at the Ti-Ta/alumina interface failed by crack extension parallel to the interface within the ceramic, which is typical for a metal-ceramic bond of high to medium interfacial strength.

Aluminum Oxide↗