Kryoelektronenmikroskopie von Proteinen: 3D-Struktur (12 A) des Hämocyanins der Schnecke Haliotis

Zusammenfassung:Die Quartärstruktur des respiratorischen Proteins Hämocyanin (Isoform HtH1) aus der marinen Schnecke Haliotis tuberculata wurde vermittels Kryoelektronen-mikroskopie und 3D-Rekonstruktion untersucht. Das Molekül ist zylinderförmig, hat einen Durchmesser von ca. 35 nm und besteht aus einer Zylinderwand und einem internen Kragenkomplex. Dieser wiederum besteht aus einem Collar und einem Arc.Die kryoelektronenmikroskopischen Aufnahmen von in glasartigem Eis fixierten HtH1-Molekülen brachte eine enorme Verbesserung der Anzahl der zur Verfügung stehenden Ansichtswinkel gegenüber den negativkontrastierten Molekülen, die auf Karbonfilm präpariert waren.Die 3D-Rekonstruktion des HtH1 mittels Aufnahmen bei drei verschiedenen Defo-kuswerten verbesserte die Auflösung noch einmal deutlich gegenüber den Rekon-struktionen, die aus Aufnahmen bei einem festen Defokuswert gemacht wurden, und zwar auf 12 Å. Das Molekül besitzt eine D5-Symmetrie.Aus dieser bisher genausten Rekonstruktion eines Molluskenhämocyanins aus EM-Bildern ließen sich folgende neue Strukturdetails ableiten:· Ein Untereinheitendimer konnte als Repeating Unit im Dekamer des HtH1 beschrieben werden.· Das Untereinheitendimer konnte aus der 3D-Dichtekarte isoliert werden. Es be-steht eindeutig aus 16 Massen, die funktionellen Domänen entsprechen. Zwei dieser Massen bilden den Collar, zwei den Arc und 12 das Wandsegment.· Die gegenläufige Anordnung der beiden Untereinheiten innerhalb dieses Unte-reinheitendimers konnten bestätigt und auf zwei Möglichkeiten eingeschränkt werden.· Die Zahl der alternativen Anordnungen der 16 funktionellen Domänen (HtH1-a bis HtH1-h) im Untereinheitendimer konnten von 80 auf 2 eingeengt werden.· Es konnte über molekulares Modellieren mithilfe einer publizierten Kristallstruk-tur eine 3D-Struktur fastatomarer Auflösung der funktionellen Domäne HtH1-g berechnet werden.· Die funktionelle Domäne HtH1-g konnte als Domänenpaar plausibel in die 3D?Dichtekarte des Untereinheitendimers eingepasst werden, und zwar in die beiden Massen des Arc.Aus der elektronenmikroskopisch gewonnenen Dichtekarte wurde mit Hilfe des

Mapping the elastic response of epithelial apical cell membranes suspended across porous array

As the elastic response of cell membranes to mechanical stimuli plays a key role in various cellular processes, novel biophysical strategies to quantify the elasticity of native membranes under physiological conditions at a nanometer scale are gaining interest. In order to investigate the elastic response of apical membranes, elasticity maps of native membrane sheets, isolated from MDCK II (Madine Darby Canine kidney strain II) epithelial cells, were recorded by local indentation with an Atomic Force Microscope (AFM). To exclude the underlying substrate effect on membrane indentation, a highly ordered gold coated porous array with a pore diameter of 1.2 μm was used to support apical membranes. Overlays of fluorescence and AFM images show that intact apical membrane sheets are attached to poly-D-lysine coated porous substrate. Force indentation measurements reveal an extremely soft elastic membrane response if it is indented at the center of the pore in comparison to a hard repulsion on the adjacent rim used to define the exact contact point. A linear dependency of force versus indentation (-dF/dh) up to 100 nm penetration depth enabled us to define an apparent membrane spring constant (kapp) as the slope of a linear fit with a stiffness value of for native apical membrane in PBS. A correlation between fluorescence intensity and kapp is also reported. Time dependent hysteresis observed with native membranes is explained by a viscoelastic solid model of a spring connected to a Kelvin-Voight solid with a time constant of 0.04 s. No hysteresis was reported with chemically fixated membranes. A combined linear and non linear elastic response is suggested to relate the experimental data of force indentation curves to the elastic modulus and the membrane thickness. Membrane bending is the dominant contributor to linear elastic indentation at low loads, whereas stretching is the dominant contributor for non linear elastic response at higher loads. The membrane elastic response was controlled either by stiffening with chemical fixatives or by softening with F-actin disrupters. Overall, the presented setup is ideally suitable to study the interactions of the apical membrane with the underlying cytoskeleton by means of force indentation elasticity maps combined with fluorescence imaging.

Computer-aided operation planning and 3-dimensional osteotomy guidance for alveolar distraction

Objectives: In alveolar distraction, in cases of severe atrophy in particular, it is often difficult to perform osteotomies in order to make a transport segment in optimal size and shape. Moreover care must be taken, not to damage the closely locating anato- mical structures such as the maxillary sinus, the inferior alveolar nerve, and the roots of the neighboring teeth. For setting ideal osteotomy lines exactly, we have developed a CT-based preoperative planning tool. Methods: 3-dimensional visual reconstruction of the jaw is created from the preoperative CT scans (1.0-mm slice thick- ness). Using the image-processing software Mimics (Materialise, Yokohama, Japan), various procedures of virtual cutting are simulated first to determine optimal osteotomy lines and to design an ideal transport segment. After the computer planning, data from the virtual solid model are transferred to a rapid prototype model, and a guiding splint is made to transfer the planned surgical simulation to the actual surgery. Results: The method was used in a case of severe atrophy of the anterior maxilla. The patient had a large maxillary sinus requir- ing a precise osteotomy in this critical area. Using the splint allowing a 3-dimensional guidance, alveolar osteotomies were easily done to achieve a transport segment in sufficient dimen- sion as planned, and any perforation of the maxillary sinus could be avoided. Finally the alveolar distraction of 10mm has suc- cessfully been performed. Conclusion: The preoperative planning method and the guiding splint described here are useful in problematic cases requiring an extremely precise osteotomy due to lack of bony space.

Determinação analítica da correção de hélice em um par engrenado devido ao efeito da flexo-torção.

O foco do presente trabalho é estudar a intensificação da pressão de contato entre os dentes de duas engrenagens cilíndricas de dentes retos, que ocorre por causa do deslocamento dos componentes de um redutor de velocidades. Essa intensificação ocorre inclusive em um redutor fabricado sem quaisquer erros de usinagem ou de montagem. A correção de hélice é uma usinagem realizada na superfície do dente da engrenagem que compensa os deslocamentos dos eixos e engrenagens, devido à flexão e à torção, e os deslocamentos dos dentes das engrenagens, devido à flexão e à pressão de contato. Foram estudados efeitos importantes para essa correção de hélice em um redutor de velocidades. Com isso, foi desenvolvido um modelo analítico que calcula a correção necessária para diminuir esse intensificador de pressão de contato em função dos deslocamentos citados acima. Esse modelo analítico foi comparado com um modelo analítico da literatura e com o software comercial RIKOR®. Os resultados de correção de hélice propostos são similares aos da literatura e do RIKOR® com exceção das bordas das engrenagens, aonde existem algumas divergências. Posteriormente, foi desenvolvido um modelo sólido de engrenagem com o perfil evolvente e com as correções de hélice calculadas analiticamente. Este modelo tridimensional (3D) foi elaborado usando os softwares SolidWorks® e Inventor® e simulado por elementos finitos por meio do software ANSYS®. Verificou-se que as três correções de hélice - a proposta, a da literatura e a do RIKOR® - realmente diminuem a intensificação de pressão de contato no flanco do dente da engrenagem. Por fim, foi possível visualizar que a correção proposta nesta dissertação é 3% mais efetiva que a proposta pela literatura e pelo RIKOR® para o caso analisado.

ACcESS: Australia's contribution to the iSERVO Institute's development

The new Australian Computational Earth Systems Simulator research facility provides a virtual laboratory for studying the solid earth and its complex system behavior. The facility's capabilities complement those developed by overseas groups, thereby creating the infrastructure for an international computational solid earth research virtual observatory.

Dynamic rupture in a 3-D particle-based simulation of a rough planar fault

An appreciation of the physical mechanisms which cause observed seismicity complexity is fundamental to the understanding of the temporal behaviour of faults and single slip events. Numerical simulation of fault slip can provide insights into fault processes by allowing exploration of parameter spaces which influence microscopic and macroscopic physics of processes which may lead towards an answer to those questions. Particle-based models such as the Lattice Solid Model have been used previously for the simulation of stick-slip dynamics of faults, although mainly in two dimensions. Recent increases in the power of computers and the ability to use the power of parallel computer systems have made it possible to extend particle-based fault simulations to three dimensions. In this paper a particle-based numerical model of a rough planar fault embedded between two elastic blocks in three dimensions is presented. A very simple friction law without any rate dependency and no spatial heterogeneity in the intrinsic coefficient of friction is used in the model. To simulate earthquake dynamics the model is sheared in a direction parallel to the fault plane with a constant velocity at the driving edges. Spontaneous slip occurs on the fault when the shear stress is large enough to overcome the frictional forces on the fault. Slip events with a wide range of event sizes are observed. Investigation of the temporal evolution and spatial distribution of slip during each event shows a high degree of variability between the events. In some of the larger events highly complex slip patterns are observed.

Use of computational fluid dynamics in the design of bubble column reactors

Investigations into the modelling techniques that depict the transport of discrete phases (gas bubbles or solid particles) and model biochemical reactions in a bubble column reactor are discussed here. The mixture model was used to calculate gas-liquid, solid-liquid and gasliquid-solid interactions. Multiphase flow is a difficult phenomenon to capture, particularly in bubble columns where the major driving force is caused by the injection of gas bubbles. The gas bubbles cause a large density difference to occur that results in transient multi-dimensional fluid motion. Standard design procedures do not account for the transient motion, due to the simplifying assumptions of steady plug flow. Computational fluid dynamics (CFD) can assist in expanding the understanding of complex flows in bubble columns by characterising the flow phenomena for many geometrical configurations. Therefore, CFD has a role in the education of chemical and biochemical engineers, providing the examples of flow phenomena that many engineers may not experience, even through experimentation. The performance of the mixture model was investigated for three domains (plane, rectangular and cylindrical) and three flow models (laminar, k-e turbulence and the Reynolds stresses). mThis investigation raised many questions about how gas-liquid interactions are captured numerically. To answer some of these questions the analogy between thermal convection in a cavity and gas-liquid flow in bubble columns was invoked. This involved modelling the buoyant motion of air in a narrow cavity for a number of turbulence schemes. The difference in density was caused by a temperature gradient that acted across the width of the cavity. Multiple vortices were obtained when the Reynolds stresses were utilised with the addition of a basic flow profile after each time step. To implement the three-phase models an alternative mixture model was developed and compared against a commercially available mixture model for three turbulence schemes. The scheme where just the Reynolds stresses model was employed, predicted the transient motion of the fluids quite well for both mixture models. Solid-liquid and then alternative formulations of gas-liquid-solid model were compared against one another. The alternative form of the mixture model was found to perform particularly well for both gas and solid phase transport when calculating two and three-phase flow. The improvement in the solutions obtained was a result of the inclusion of the Reynolds stresses model and differences in the mixture models employed. The differences between the alternative mixture models were found in the volume fraction equation (flux and deviatoric stress tensor terms) and the viscosity formulation for the mixture phase.

A Raman spectroscopic study of the different vanadate-groups in solid-state compounds, model case : mineral phases vésigniéite, BaCu3(VO4)2(OH)2, and volborthite, Cu3V2O7(OH)2•2H2O

Raman spectroscopy has been used to study vanadates in the solid state. The molecular structure of the vanadate minerals vésigniéite [BaCu3(VO4)2(OH)2] and volborthite [Cu3V2O7(OH)2·2H2O] have been studied by Raman spectroscopy and infrared spectroscopy. The spectra are related to the structure of the two minerals. The Raman spectrum of vésigniéite is characterized by two intense bands at 821 and 856 cm−1 assigned to ν1 (VO4)3− symmetric stretching modes. A series of infrared bands at 755, 787 and 899 cm−1 are assigned to the ν3 (VO4)3− antisymmetric stretching vibrational mode. Raman bands at 307 and 332 cm−1 and at 466 and 511 cm−1 are assigned to the ν2 and ν4 (VO4)3− bending modes. The Raman spectrum of volborthite is characterized by the strong band at 888 cm−1, assigned to the ν1 (VO3) symmetric stretching vibrations. Raman bands at 858 and 749 cm−1 are assigned to the ν3 (VO3) antisymmetric stretching vibrations; those at 814 cm−1 to the ν3 (VOV) antisymmetric vibrations; that at 508 cm−1 to the ν1 (VOV) symmetric stretching vibration and those at 442 and 476 cm−1 and 347 and 308 cm−1 to the ν4 (VO3) and ν2 (VO3) bending vibrations, respectively. The spectra of vésigniéite and volborthite are similar, especially in the region of skeletal vibrations, even though their crystal structures differ.

A coupled SPH-DEM model for fluid and solid mechanics of apple parenchyma cells during drying

A coupled SPH-DEM based two-dimensional (2-D) micro-scale single cell model is developed to predict basic cell-level shrinkage effects of apple parenchyma cells during air drying. In this newly developed drying model, Smoothed Particle Hydrodynamics (SPH) is used to model the low Reynolds Number fluid motions of the cell protoplasm, and a Discrete Element Method (DEM) is employed to simulate the polymer-like cell wall. Simulations results reasonably agree with published experimental drying results on cellular shrinkage properties such as cellular area, diameter and perimeter. These preliminary results indicate that the model is effective for the modelling and simulation of apple parenchyma cells during air drying.

Constitutive model for municipal solid waste incorporating mechanical creep and biodegradation-induced compression

A constitutive model is proposed to describe the stress-strain behavior of municipal solid waste (MSW) under loading using the critical state soil mechanics framework. The modified cam clay model is extended to incorporate the effects of mechanical creep and time dependent biodegradation to calculate total compression under loading. Model parameters are evaluated based on one-dimensional compression and triaxial consolidated undrained test series conducted on three types of MSW: (a) fresh MSW obtained from working phase of a landfill, (b) landfilled waste retrieved from a landfill after 1.5 years of degradation, and (c) synthetic MSW with controlled composition. The model captures the stress-strain and pore water pressure response of these three types of MSW adequately. The model is useful for assessing the deformation and stability of landfills and any post-closure development structures located on landfills.

Prediction of solid block masonry prism compressive strength using FE model

Masonry strength is dependent upon characteristics of the masonry unit,the mortar and the bond between them. Empirical formulae as well as analytical and finite element (FE) models have been developed to predict structural behaviour of masonry. This paper is focused on developing a three dimensional non-linear FE model based on micro-modelling approach to predict masonry prism compressive strength and crack pattern. The proposed FE model uses multi-linear stress-strain relationships to model the non-linear behaviour of solid masonry unit and the mortar. Willam-Warnke's five parameter failure theory developed for modelling the tri-axial behaviour of concrete has been adopted to model the failure of masonry materials. The post failure regime has been modelled by applying orthotropic constitutive equations based on the smeared crack approach. Compressive strength of the masonry prism predicted by the proposed FE model has been compared with experimental values as well as the values predicted by other failure theories and Eurocode formula. The crack pattern predicted by the FE model shows vertical splitting cracks in the prism. The FE model predicts the ultimate failure compressive stress close to 85 of the mean experimental compressive strength value.

Spectral asymptotics of the Helmholtz model in fluid-solid structures

A model representing the vibrations of a coupled fluid-solid structure is considered. This structure consists of a tube bundle immersed in a slightly compressible fluid. Assuming periodic distribution of tubes, this article describes the asymptotic nature of the vibration frequencies when the number of tubes is large. Our investigation shows that classical homogenization of the problem is not sufficient for this purpose. Indeed, our end result proves that the limit spectrum consists of three parts: the macro-part which comes from homogenization, the micro-part and the boundary layer part. The last two components are new. We describe in detail both macro- and micro-parts using the so-called Bloch wave homogenization method. Copyright (C) 1999 John Wiley & Sons, Ltd.

A nonlinear spectral finite element model for analysis of wave propagation in solid with internal friction and dissipation

A geometrically non-linear Spectral Finite Flement Model (SFEM) including hysteresis, internal friction and viscous dissipation in the material is developed and is used to study non-linear dissipative wave propagation in elementary rod under high amplitude pulse loading. The solution to non-linear dispersive dissipative equation constitutes one of the most difficult problems in contemporary mathematical physics. Although intensive research towards analytical developments are on, a general purpose cumputational discretization technique for complex applications, such as finite element, but with all the features of travelling wave (TW) solutions is not available. The present effort is aimed towards development of such computational framework. Fast Fourier Transform (FFT) is used for transformation between temporal and frequency domain. SFEM for the associated linear system is used as initial state for vector iteration. General purpose procedure involving matrix computation and frequency domain convolution operators are used and implemented in a finite element code. Convergnence of the spectral residual force vector ensures the solution accuracy. Important conclusions are drawn from the numerical simulations. Future course of developments are highlighted.

A numerical model of a liquid-feed solid polymer electrolyte DMFC and its experimental validation

A one-dimensional, biphasic, multicomponent steady-state model based on phenomenological transport equations for the catalyst layer, diffusion layer, and polymeric electrolyte membrane has been developed for a liquid-feed solid polymer electrolyte direct methanol fuel cell (SPE- DMFC). The model employs three important requisites: (i) implementation of analytical treatment of nonlinear terms to obtain a faster numerical solution as also to render the iterative scheme easier to converge, (ii) an appropriate description of two-phase transport phenomena in the diffusive region of the cell to account for flooding and water condensation/evaporation effects, and (iii) treatment of polarization effects due to methanol crossover. An improved numerical solution has been achieved by coupling analytical integration of kinetics and transport equations in the reaction layer, which explicitly include the effect of concentration and pressure gradient on cell polarization within the bulk catalyst layer. In particular, the integrated kinetic treatment explicitly accounts for the nonhomogeneous porous structure of the catalyst layer and the diffusion of reactants within and between the pores in the cathode. At the anode, the analytical integration of electrode kinetics has been obtained within the assumption of macrohomogeneous electrode porous structure, because methanol transport in a liquid-feed SPE- DMFC is essentially a single-phase process because of the high miscibility of methanol with water and its higher concentration in relation to gaseous reactants. A simple empirical model accounts for the effect of capillary forces on liquid-phase saturation in the diffusion layer. Consequently, diffusive and convective flow equations, comprising Nernst-Plank relation for solutes, Darcy law for liquid water, and Stefan-Maxwell equation for gaseous species, have been modified to include the capillary flow contribution to transport. To understand fully the role of model parameters in simulating the performance of the DMCF, we have carried out its parametric study. An experimental validation of model has also been carried out. (C) 2003 The Electrochemical Society.