Anisotropic swelling of anisotropic elastic panels.

While isotropic in-plane swelling problems for thin elastic sheets have been studied extensively in recent years, many shape-programmable materials, including nematic solids and 3D-printed structures, are anisotropic, as are most industrial sheet materials. In this theoretical work, we consider central swelling and shrinkage of plates of aspect ratio and material properties relevant to the manufacture of engineered wood composite panels in which both in-plane swelling and material stiffness are highly orthotropic, leading to multiple separations in energy scales. With transverse swelling in the soft direction, and gradients in the stiff direction, the warped plates adopt two distinct types of configurations, axisymmetric and twisted, which we illustrate with toy models. We employ a two-parameter family of isometries to embed the metric programmed by the swelling, thus reducing the problem to one of minimizing bending energy alone. A simple argument is seen to closely predict averaged axisymmetric curvatures. While purely cylindrical shapes are unobtainable by pure in-plane swelling, they can be closely approximated in a highly anisotropic system. However, anisotropy can favor twisting, and breaks a degenerate soft deformation mode associated with minimal surfaces in isotropic materials. Bifurcations from axisymmetric to twisted shapes can be induced by anisotropy or by certain attributes of a central shrinkage profile. Finally, we note how our findings indicate practical limitations on the diagnosis of moisture inhomogeneities in manufactured panels by observation of warped conformations, due to the sensitivity of the qualitative response to specifics of the profile.

Contrasting bending energies from bulk elastic theories.

The choice of elastic energies for thin plates and shells is an unsettled issue with consequences for much recent modeling of soft matter. Through consideration of simple deformations of a thin body in the plane, we demonstrate that four bulk isotropic quadratic elastic theories have fundamentally different predictions with regard to bending behavior. At finite thickness, these qualitative effects persist near the limit of mid-surface isometry, and not all theories predict an isometric ground state. We discuss how certain kinematic measures that arose in early studies of rod mechanics lead to coherent definitions of stretching and bending, and promote the adoption of these quantities in the development of a covariant theory based on stretches rather than metrics.

Preliminary crystallographic data and quaternary structural implications of the central subunit of the multi-subunit complex transcarboxylase.

The hexameric central subunit (Mr = 360,000) of the multi-subunit complex transcarboxylase has been crystallized by bulk dialysis against 250 mM-sodium acetate (pH 5.5). The crystals are cubic, a = 193.1 A, space group P4(1)32 or enantiomorph. The number of molecules per unit cell is four and was deduced from the density of the crystals (1.10 g cm-3) and the mother liquor (1.01 g cm-3) and the specific volume of the protein calculated from molecular dimensions obtained from electron microscopy studies. Four molecules per cell requires the central subunits to lie on 3-fold axes, which are perpendicular to 2-fold rotation axes, so that the molecules satisfy 32 symmetry giving one subunit as the asymmetric unit. Of the four possible models that have been considered for the quaternary structure of transcarboxylase, only that with antiparallel subunits, two sets of isologous binding sites and D3 symmetry is in agreement with the symmetry requirements of the cubic crystals.

Primary structure of the 5 S subunit of transcarboxylase as deduced from the genomic DNA sequence.

Transcarboxylase from Propionibacterium shermanii is a complex biotin-containing enzyme composed of 30 polypeptides of three different types. It is composed of six dimeric outer subunits associated with a central cylindrical hexameric subunit through 12 biotinyl subunits; three outer subunits on each face of the central hexamer. Each outer dimer is termed a 5 S subunit which associates with two biotinyl subunits. The enzyme catalyzes a two-step reaction in which methylmalonyl-CoA and pyruvate form propionyl-CoA and oxalacetate, the 5 S subunit specifically catalyzing one of these reactions. We report here the cloning, sequencing and expression of the monomer of the 5 S subunit. The gene was identified by matching amino acid sequences derived from isolated authentic 5 S peptides with the deduced sequence of an open reading frame present on a cloned P. shermanii genomic fragment known to contain the gene encoding the 1.3 S biotinyl subunit. The cloned 5 S gene encodes a protein of 519 amino acids, M(r) 57,793. The deduced sequence shows regions of extensive homology with that of pyruvate carboxylase and oxalacetate decarboxylase, two enzymes which catalyze the same or reverse reaction. A fragment was subcloned into pUC19 in an orientation such that the 5 S open reading frame could be expressed from the lac promoter of the vector. Crude extracts prepared from these cells contained an immunoreactive band on Western blots which co-migrated with authentic 5 S and were fully active in catalyzing the 5 S partial reaction. We conclude that we have cloned, sequenced and expressed the monomer of the 5 S subunit and that the expressed product is catalytically active.

Role of carbon monoxide dehydrogenase in acetate synthesis by the acetogenic bacterium, Acetobacterium woodii.

Carbon monoxide dehydrogenase (CODH) plays a key role in acetate synthesis by the acetogenic bacterium, Clostridium thermoaceticum. Acetobacterium woodii, like C. thermoaceticum contains high levels of CODH. In this work we show that crude extracts of A. woodii synthesize acetate from methyl tetrahydrofolate or methyl iodide, carbon monoxide and coenzyme A (CoA). The purified CODH from A. woodii catalyzes an exchange reaction between CO and the carbonyl group of acetyl-CoA even faster than the C. thermoaceticum enzyme, indicating the CODH of A. woodii, like that of C. thermoaceticum is an acetyl-CoA synthetase. Fluorescence and EPR studies further support this postulate by demonstrating that CODH binds CoA near the CO binding site involving a tryptophan residue. The UV absorption spectra and the amino acid compositions of A. woodii and C. thermoaceticum CODHs are very similar. Evidence is presented using purified enzymes from A. woodii that the synthesis of acetyl-CoA occurs by a pathway similar to that utilized by C. thermoaceticum.

Particle image velocimetry measurements of blood velocity in a continuous flow ventricular assist device.

The third prototype of a continuous flow ventricular assist device (CFVAD3) is being developed and tested for implantation in humans. The blood in the pump flows through a fully shrouded four-bladed impeller (supported by magnetic bearings) and through small clearance regions on either side of the impeller. Measurements of velocities using particle image velocimetry of a fluid with the same viscosity as blood have been made in one of these clearance regions. Particle image velocimetry is a technique that measures the instantaneous velocity field within an illuminated plane of the fluid field by scattering light from particles added to the fluid. These measurements have been used to improve understanding of the fluid dynamics within these critical regions, which are possible locations of both high shear and stagnation, both of which are to be avoided in a blood pump. Computational models of the pump exist and these models are currently being used to aid in the design of future prototypes. Among other things, these models are used to predict the potential for hemolysis and thrombosis. Measurements of steady flow at two operating speeds and flow rates are presented. The measurements are compared with the computed solutions to validate and refine, where necessary, the existing computational models.

Numerical studies of blood shear and washing in a continuous flow ventricular assist device.

The third prototype of a continuous flow ventricular assist device (CF3) is being developed and tested for implantation in humans. The blood in the pump flows through a fully shrouded four bladed impeller (supported by magnetic bearings) and through small clearance regions on either side of the impeller. Computational fluid dynamics (CFD) solutions for this flow have been obtained by using TascFlow, a software package available from AEA Technology, UK. These flow solutions have been used to estimate the shear stresses on the blood in the pump and, hence, to minimize hemolysis. In addition, the solutions are informative for achieving a design that will provide good washing of the blood to minimize the possibility of stagnation points that can lead to thrombosis. This study presents numerical studies of these phenomena in the CF3. The calculated shear rate results are compared with values published in the open literature. The comparisons indicate that hemolysis will not be a problem with CF3, which is in agreement with preliminary experimental measurements. Flow studies are being conducted to determine the optimal size of the clearance regions.

Numerical solution for blood flow in a centrifugal ventricular assist device.

A very small centrifugal pump, fully supported by magnetic bearings, is being developed for use as a ventricular assist device to be implanted in humans. In this paper, we apply computational fluid dynamics to model the blood flow to aid in the design of the ventricular assist device. The flow of blood through the pump has been modeled using computational fluid dynamics (CFD) software that is commercially available from AEA Technology, UK. The flow regions modeled in version 3 of the Continuous Flow Ventricular Assist Device (CF3) are the fully shrouded four bladed impeller and the two clearance regions around the impeller that are bounded by the pump hub and shroud. This paper describes the geometry and computational grids developed for the flow regions, and the equations of motion for the blood flow are developed. The overall numerically-evaluated flow rates and head rise have similar trends to the flow parameters experimentally measured, indicating that future pump designs can be effectively modeled numerically before being constructed and tested. Numerical solutions are presented and compared with experimentally-obtained overall pump performance results. These solutions are used to predict shear stress levels to be experienced by the blood flowing through the pump, and it is predicted that hemolysis will be insignificant. The solutions also indicate no regions of flow stagnation that can be a source of thrombosis in pumps. The calculations provide a viable design method to achieve improved efficiency in future versions of this pump.

Design of a continuous flow centrifugal pediatric ventricular assist device.

Thousands of pediatric patients suffering from cardiomyopathy or single ventricular physiologies secondary to debilitating heart defects may benefit from long-term mechanical circulatory support due to the limited number of donor hearts available. This article presents the initial design of a fully implantable centrifugal pediatric ventricular assist device (PVAD) for 2 to 12 year olds. Conventional pump design equations, including a nondimensional scaling approach, enabled performance estimations of smaller scale versions (25 mm and 35 mm impeller diameters) of our adult support VAD. Based on this estimated performance, a computational model of the PVAD with a 35 mm impeller diameter was generated. Employing computational fluid dynamics (CFD) software, the flow paths through the PVAD and overall performance were analyzed for steady state flow conditions. The numerical simulations involved flow rates of 2 to 5 LPM for rotational speeds of 2750 to 3250 RPM and incorporated a k-epsilon fluid turbulence model with a logarithmic wall function to characterize near-wall flow conditions. The CFD results indicated best efficiency points ranging from 25% to 28%, which correlate well with typical values of blood pumps. The results further demonstrated that the pump could deliver 2 to 5 LPM at 70 to 95 mmHg for desired physiologic conditions in resting 2 to 12 year olds. Scalar stress levels remained below 300 Pa, thereby signifying potentially low levels of hemolysis. Several flow regions in the pump exhibited signs of vortices, retrograde flow, and stagnation points, which require optimization and further study. This CFD model represents a reasonable starting point for future model enhancements, leading to prototype manufacturing and experimental validation.

Life with CO or CO2 and H2 as a source of carbon and energy.

An account is presented of the recent discovery of a pathway of growth by bacteria in which CO or CO2 and H2 are sources of carbon and energy. The Calvin cycle and subsequently other cycles were discovered in the 1950s, and in each the initial reaction of CO2 involved adding CO2 to an organic compound formed during the cyclic pathway (for example, CO2 and ribulose diphosphate). Studies were initiated in the 1950s with the thermophylic anaerobic organism Clostridium thermoaceticum, which Barker and Kamen had found fixed CO2 in both carbons of acetate during fermentation of glucose. The pathway of acetyl-CoA biosynthesis differs from all others in that two CO2 are combined with coenzyme A (CoASH) forming acetyl CoA, which then serves as the source of carbon for growth. This mechanism is designated the acetyl CoA pathway and some have called it the Wood pathway. A unique feature is the role of the enzyme carbon monoxide dehydrogenase (CODH), which catalyzes the conversion of CoASH, CO, and a methyl group to acetyl CoA, the final step of the pathway. The pathway involves the reduction of CO2 to formate, which then combines with tetrahydrofolate (THF) to form formyl THF. It in turn is reduced to CH3-THF. The methyl is then transferred to the cobalt on a corrinoid-containing enzyme. From there the methyl is transferred to CODH, and CO and CoASH bind with the enzyme at separate sites. Acetyl CoA is then synthesized. CODH would more properly be called carbon monoxide dehydrogenase-acetyl CoA synthase as it catalyzes oxidation of CO to CO2 and the synthesis of acetyl CoA. The solution of the mechanism of this pathway required more than 30 years, in part because the intermediate compounds are bound to enzymes, the enzymes are extremely sensitive to O2 and must be isolated under strictly anerobic conditions, and the role of a corrinoid and CODH was unprecedented. It is now apparent that this pathway occurs (perhaps with some modification) in many bacteria including the methane and sulfur bacteria. In some humans this pathway is catalyzed by the bacteria of the gut and acetate is produced rather than methane; it is calculated that 2.3 x 10(6) metric tons of acetate are formed daily from CO2. A similar synthesis occurs in the hind gut of termites. It is becoming apparent that the acetyl CoA pathway plays a significant role in the carbon cycle.(ABSTRACT TRUNCATED AT 400 WORDS)

The anatomy of transcarboxylase and the role of its subunits.

Biotin enzymes in general catalyze the fixation of CO2 and in a few instances decarboxylations yielding CO2. Transcarboxylase is an exception; it catalyzes the transfer of a carboxyl group from one compound to another and CO2 is not involved. This enzyme plays an essential role in the formation of propionic acid by propionibacteria and its structure and catalytic mechanism have been extensively investigated including studies of the quaternary structure by electron microscopy. The structure is complex, consisting of three types of subunits: (1) a central hexameric subunit, (2) six dimeric outside subunits, and (3) twelve biotinyl subunits which bind the outside subunits to the central subunit. There are 12 substrate sites on the central subunit (2 per polypeptide) and 2 substrate sites on each of the dimeric outside subunits. The carboxyl is transferred between these sites via the biotin of the biotinyl subunit. The biotinyl subunit (approximately 123 residues) has been completely sequenced and it has been shown that the first 42 residues serve in binding the outside subunits to the central subunit and the remainder of the sequence is involved in placing the biotin between the subunits so that it may serve as the carboxyl carrier between the substrate sites on the central and outside subunits. It is proposed that the dual sites on the polypeptides of the central subunit have arisen as a consequence of gene duplication and fusion. An intriguing question is why such a complicated structure is required for catalysis of a rather simple reaction.

Purification of the subunits of transcarboxylase by affinity chromatography on avidin-sepharose.

Transcarboxylase consists of a central 12 SH subunits each of which is linked to the central subunit by two similar to 1.3 SE biotin carboxyl carrier proteins. The subunits from dissociated transcarboxylase have been difficult to isolate because conditions which stabilize them also promote their reassociation to the intact enzyme. In this paper, we describe the use of avidin-Sepharose to adsorb the enzyme from crude extracts or partially purified transcarboxylase of propionibacteria. After removing impurities by washing the column with phosphate buffer at pH 6.5, in which the transcarboxylase is stable, the enzyme is dissociated first by elution at pH 8 yielding a fraction containing mostly 12 SH subunit which can be rapidly stabilized against dissociation to 6 SH without the problem of reconstitution because the 1.3 SE and most of the 5 SE subunits are not eluted. The second elution is at pH 9 which yields the 5 SE subunit by dissociation from the 1.3 SE biotin subunit and the 1.3 SE subunit remains bound to the avidin. The 12 SH and 5 SE subunits are further purified by glycerol density gradient centrifugation or by chromatography on Bio-Gel. Very active enzyme can be reconstituted from these subunits upon the addition of the 1.3 SE subunit.

Purification of the "corrinoid" enzyme involved in the synthesis of acetate by Clostridium thermoaceticum.

A corrinoid enzyme has been purified to approximately 80% homogeneity from Clostridium thermoaceticum. It catalyzes the formation of acetate from N5-methyltetrahydrofolate and pyruvate in combination with the required supplementary enzymes which are supplied by an extract that has been treated with propyl iodide. The enzyme was purified by chromatography on a folate affinity column and a DEAE-Bio-Gel column and by ultrafiltration. The molecular weight as determined by sedimentation equilibrium is 158,000 and the sedimentation coefficient is 10.5 S. By gel electrophoresis in sodium dodecyl sulfate, the subunit molecular weight was found to be 40,000, thus, the enzyme may be a tetramer of four similar subunits. The results of electron microscopy confirmed the tetrameric structure. In the absence of sodium dodecyl sulfate, two bands of similar intensity were observed by electrophoresis, but both yielded the 40,000 molecular weight subunit in the presence of sodium dodecyl sulfate. These results indicate the two bands represent either two different molecular weight forms of the enzyme or two differently charged isoenzymes. The enzyme is quite labile being sensitive to dilution, aerobic conditions, and light. Dithiothreitol and glycerol were found to stabilize the enzyme. The cofactor requirements for acetate synthesis have been determined. ATP, thiamin pyrophosphate, S-adenosylmethionine, and Fe2+ were found to be required for maximum activity and the Km values were determined. High concentrations of methyltetrahydrofolate, pyruvate, and S-adenosylmethionine were found to inhibit the synthesis of acetate.

Mechanism of acetate synthesis from CO2 by Clostridium acidiurici.

Total synthesis of acetate from CO2 by Clostridium acidiurici during fermentations of hypoxanthine has been shown to involve synthesis of glycine from methylenetetrahydrofolate, CO2, and NH3. The glycine is converted to serine by the addition of methylenetetrahydrofolate, and the resulting serine is converted to pyruvate, which is decarboxylated to form acetate. Since CO2 is converted to methylenetetrahydrofolate, both carbons of the acetate are derived from CO2. The evidence supporting this pathway is based on (i) the demonstration that glycine decarboxylase is present in C. acidiurici, (ii) the fact that glycine is synthesized by crude extracts at a rate which is rapid enough to account for the in vivo synthesis of acetate from CO2, (iii) the fact that methylenetetrahydrofolate is an intermediate in the formation of both carbons of acetate from CO2, and (iv) the fact that the alpha carbon of glycine is the source of the carboxyl group of acetate. Evidence is presented that this synthesis of acetate does not involve carboxylation of a methyl corrinoid enzyme such as occurs in Clostridium thermoaceticum and Clostridium formicoaceticum. Thus, there are two different mechanisms for the total synthesis of acetate from CO2 by clostridia.