Large Changes In Geometry Research Articles

Topologies of Complexes Containing O6-Alkylguanine–DNA Alkyltransferase and DNA

The mutagenic and cytotoxic effects of many alkylating agents are reduced by O6-alkylguanine–DNA alkyltransferase (AGT). In humans, this protein not only protects the integrity of the genome, but also contributes to the resistance of tumors to DNA-alkylating chemotherapeutic agents. Here we describe and test models for cooperative multiprotein complexes of AGT with single-stranded and duplex DNAs that are based on in vitro binding data and the crystal structure of a 1:1 AGT–DNA complex. These models predict that cooperative assemblies contain a three-start helical array of proteins with dominant protein–protein interactions between the amino-terminal face of protein n and the carboxy-terminal face of protein n+3, and they predict that binding duplex DNA does not require large changes in B-form DNA geometry. Experimental tests using protein cross-linking analyzed by mass spectrometry, electrophoretic and analytical ultracentrifugation binding assays, and topological analyses with closed circular DNA show that the properties of multiprotein AGT–DNA complexes are consistent with these predictions.

Comparison of numerical and ultrasonic techniques for quantifying interference fit pressures

Press fits are commonly used in manufactured assemblies, components, and machines. For example railway wheels are press or shrink fitted onto axles. Railway axles occasionally fail by fatigue resulting from the alternating rotating bending loading. The site of the fatigue crack initiation is commonly at the location of the press fit. Therefore, a good understanding is needed of the press-fit region, particularly where stress-raising effects are caused by, for example, large changes in geometry. Analytical techniques are unable to predict stresses in these areas. In this work, an ultrasonic technique was used to measure the contact stresses in a real shaft—sleeve contact. The results were compared with finite-element models of the same components. The results from the two techniques compared well both in the centre of the fit and around the edges where the stresses were raised. Both showed good correlation with the analytical Lamé solution away from the edges. The two techniques could therefore be combined in a design tool to help remove problems with edge effects that could lead to mechanical failures.

Myosin filament assembly in an ever-changing myofilament lattice of smooth muscle

A major development in smooth muscle research in recent years is the recognition that the myofilament lattice of the muscle is malleable. The malleability appears to stem from plastic rearrangement of contractile and cytoskeletal filaments in response to stress and strain exerted on the muscle cell, and it allows the muscle to adapt to a wide range of cell lengths and maintain optimal contractility. Although much is still poorly understood, we have begun to comprehend some of the basic mechanisms underlying the assembly and disassembly of contractile and cytoskeletal filaments in smooth muscle during the process of adaptation to large changes in cell geometry. One factor that likely facilitates the plastic length adaptation is the ability of myosin filaments to form and dissolve at the right place and the right time within the myofilament lattice. It is proposed herein that formation of myosin filaments in vivo is aided by the various filament-stabilizing proteins, such as caldesmon, and that the thick filament length is determined by the dimension of the actin filament lattice. It is still an open question as to how the dimension of the dynamic filament lattice is regulated. In light of the new perspective of malleable myofilament lattice in smooth muscle, the roles of many smooth muscle proteins could be assigned or reassigned in the context of plastic reorganization of the contractile apparatus and cytoskeleton.

Electric-field-induced flame speed modification

The effects of pulsed and continuous DC electric fields on the reaction zones of premixed propane–air flames have been investigated using several types of experimental measurements. All observed effects on the flame are dependent on the applied voltage polarity, indicating that negatively charged flame species do not play a role in the perturbation of the reaction zone. Experiments designed to characterize the electric-field-induced modifications of the shape and size of the inner cone, and the concomitant changes in the temperature profiles of flames with equivalence ratios between 0.8 and 1.7, are also reported. High-speed two-dimensional imaging of the flame response to a pulsed DC voltage shows that the unperturbed conical flame front (laminar flow) is driven into a wrinkled laminar flamelet (cellular) geometry on a time scale of the order of 5 ms. Temperature distributions derived from thin filament pyrometry (TFP) measurements in flames perturbed by continuous DC fields show similar large changes in the reaction zone geometry, with no change in maximum flame temperature. All measurements are consistent with the observed flame perturbations being a fluid mechanical response to the applied field brought about by forcing positive flame ions counter to the flow. The resulting electric pressure decreases Lewis numbers of the ionic species and drives the effective flame Lewis number below unity. The observed increases in flame speed and the flame fronts trend toward turbulence can be described in terms of the flame front wrinkling and concomitant increase in reaction sheet area. This effect is a potentially attractive means of controlling flame fluid mechanical characteristics. The observed effects require minimal input electrical power (<1 W for a 1 kW burner) due to the much better electric field coupling achieved in the present experiments compared to the previous studies.

Shape adaptation of long bone structures using a contour based approach†

In this work, an approach for mechanically driven shape adaptation of long bone structures is presented which utilizes contour descriptions to track morphological changes at different bone cross sections. A script-based procedure is used to iteratively generate a solid geometry and finite element (FE) model from these contours, perform a stress analysis, and then update the contour shapes using the results of the stress analysis using a prescribed remodeling rule. Because a remeshing operation is performed at each timestep the method is able to effectively simulate large changes in geometry. Several examples of shape adaptation of idealized and geometrically accurate long-bone structures are presented using a variety of remodeling signals and parameters.

SIFT: a method to verify the IMRT fluence delivered during patient treatment using an electronic portal imaging device.

Radiotherapy patients are increasingly treated with intensity-modulated radiotherapy (IMRT) and high tumor doses. As part of our quality control program to ensure accurate dose delivery, a new method was investigated that enables the verification of the IMRT fluence delivered during patient treatment using an electronic portal imaging device (EPID), irrespective of changes in patient geometry. Each IMRT treatment field is split into a static field and a modulated field, which are delivered in sequence. Images are acquired for both fields using an EPID. The portal dose image obtained for the static field is used to determine changes in patient geometry between the planning CT scan and the time of treatment delivery. With knowledge of these changes, the delivered IMRT fluence can be verified using the portal dose image of the modulated field. This method, called split IMRT field technique (SIFT), was validated first for several phantom geometries, followed by clinical implementation for a number of patients treated with IMRT. The split IMRT field technique allows for an accurate verification of the delivered IMRT fluence (generally within 1% [standard deviation]), even if large interfraction changes in patient geometry occur. For interfraction radiological path length changes of 10 cm, deliberately introduced errors in the delivered fluence could still be detected to within 1% accuracy. Application of SIFT requires only a minor increase in treatment time relative to the standard IMRT delivery. A new technique to verify the delivered IMRT fluence from EPID images, which is independent of changes in the patient geometry, has been developed. SIFT has been clinically implemented for daily verification of IMRT treatment delivery.

ADJUSTMENT OF STREAM CHANNEL CAPACITY FOLLOWING DAM CLOSURE, YEGUA CREEK, TEXAS1

ABSTRACT: In Yegua Creek, a principal tributary of the Brazos River in Texas, surveys of a 19 km channel reach downstream of Somerville Dam show that channel capacity decreased by an average of 65 percent in a 34 year period following dam closure. The decrease corresponds with an approximately 85 percent reduction in annual flood peaks. Channel depth has changed the most, decreasing by an average of 61 percent. Channel width remained stable with an average decrease of only 9 percent, reflecting cohesive bank materials along with the growth of riparian vegetation resulting from increased low flows during dry summer months. Although large changes in stream channel geometry are not uncommon downstream of dams, such pronounced reductions in channel capacity could have long‐term implications for sediment delivery through the system.

Theoretical study of the excited state intramolecular proton transfer in barbituric acid

AM1 calculations on the tautomers of barbituric acid have been carried out for the singlet and triplet states of these molecules. The results show that the triketo form, which is most stable for the ground state, gets destabilized on excitation, as the cleavage of a carbon–nitrogen bond occurs. Large changes in geometry on excitation are confined mainly to the urea portion of the molecule and the carbonyl groups. This has been explained from an analysis of the highest occupied and lowest unoccupied molecular orbitals. The absorption and fluorescence spectra have also been calculated, and these indicate that absorption takes the ground state triketo form of the molecule to its (ππ ∗) excited state, which may easily isomerize to the 4-hydroxy form, which has a more stable singlet excited state. Fluorescence then occurs from this state. This is especially likely since the proton transfer barrier reduces substantially for the excited state.

Some acoustics of the shakuhachi—and of the shakuhachi player’s face

The shakuhachi is an end-blown Japanese flute. Like other flutes, it is open at the place of excitation, so it operates at minima of the acoustic impedance. The jet interacts with both the bore impedance and the radiation impedance, which is baffled by the player’s face. Large changes in the relative geometry of the instrument and the face contribute to the flexibility in pitch and timbre that are important elements of the traditional playing style, and which gives the instrument much of the expressiveness for which it is renowned. We report measurements of the impedance spectra Z(f) of the bore, and of the baffled radiation load imposed on the jet. Z(f) of the instrument differs from that of the Western flute family because the shakuhachi has neither the narrow chimney of the Western flute, nor the short resonator upstream of the jet. These influence the overall form of Z(f) for the instrument. Other features of Z(f) are explained by the tone hole position and geometry. The Z(f) of the radiation field varies for different playing positions, which has important effects on the tuning of the minima and on the spectral response.

Simple shearing flow of dry soap foams with tetrahedrally close-packed structure

The microrheology of dry soap foams subjected to quasistatic, simple shearing flow is analyzed. Two different monodisperse foams with tetrahedrally close-packed (TCP) structure are examined: Weaire-Phelan (A15) and Friauf-Laves (C15). The elastic–plastic response is evaluated by using the Surface Evolver to calculate foam structures that minimize total surface area at each value of strain. The foam geometry and macroscopic stress are piecewise continuous functions of strain. The stress scales as T/V1/3, where T is surface tension and V is cell volume. Each discontinuity corresponds to large changes in foam geometry and topology that restore equilibrium to unstable configurations that violate Plateau’s laws. The instabilities occur when the length of an edge on a polyhedral foam cell vanishes. The length can tend to zero smoothly or abruptly with strain. The abrupt case occurs when a small increase in strain changes the energy profile in the neighborhood of a foam structure from a local minimum to a saddle...

The role of residues outside the active site: structural basis for function of C191 mutants of Escherichia coli aspartate aminotransferase.

In previous kinetic studies of Escherichia coli aspartate aminotransferase, it was determined that some substitutions of conserved cysteine 191, which is located outside of the active site, altered the kinetic parameters of the enzyme (Gloss,L.M., Spencer,D. E. and Kirsch,J.F., 1996, Protein Struct. Funct. Genet., 24, 195-208). The mutations resulted in an alkaline shift of 0.6-0.8 pH units for the pK(a) of the internal aldimine between the PLP cofactor and Lys258. The change in the pK(a) affected the pH dependence of the k(cat)/K(m) (aspartate) values for the mutant enzymes. To help to understand these observations, crystal structures of five mutant forms of E.coli aspartate aminotransferase (the maleate complexes of C191S, C191F, C191Y and C191W, and C191S without maleate) were determined at about 2 A resolution in the presence of the pyridoxal phosphate cofactor. The overall three-dimensional fold of each mutant enzyme is the same as that of the wild-type protein, but there is a rotation of the mutated side chain around its C(alpha)-C(beta) bond. This side chain rotation results in a change in the pattern of hydrogen bonding connecting the mutant residue and the protonated Schiff base of the cofactor, which could account for the altered pK(a) of the Schiff base imine nitrogen that was reported previously. These results demonstrate how residues outside the active site can be important in helping determine the subtleties of the active site amino acid geometries and interactions and how mutations outside the active site can have effects on catalysis. In addition, these results help explain the surprising result previously reported that, for some mutant proteins, replacement of a buried cysteine with an aromatic side chain did not destabilize the protein fold. Instead, rotation around the C(alpha)-C(beta) bond allowed each large aromatic side chain to become buried in a nearby pocket without large changes in the enzyme's backbone geometry.

Floodplain sedimentation along extended river reaches

Large scale changes in floodplain geometry, as contemplated for the Rhine River as part of combined renaturalisation and flood control projects in The Netherlands, will change the rate of floodplain sedimentation. To investigate the seriousness of the anticipated increase, a modelling approach was developed to simulate floodplain sedimentation along extended river reaches with a series of floodplains alternatingly located on both sides of the main channel. The floodplains are schematised as sedimentation basins, which function as sinks for the suspended sediment, which is conveyed to the floodplains during floods via convective transport from the main channel. To assess the deposition of fine sediments in a floodplain, the method of Chen (1975) is used. Via the repetitive use of the continuity equation for fine sediments, a longitudinal reduction in sediment concentration is found. The modelling approach was verified using suspended load data from the IJssel River, one of the distributaries of the Rhine River in The Netherlands, during flood. Using the developed approach the local and the downstream effect of e.g. lowering the floodplain levels with several meters could be determined.

A study of the perforation of aluminium laminate targets

Experiments are described in which laminated aluminium alloy targets, of a variety of configurations, are perforated by flat-ended and conical penetrators. Target ballistic limit velocities are determined and the results are used to evaluate energy absorption mechanisms and to compare deformation and failure modes. It is demonstrated by modelling that increasing the numbers of layers in multi-layer targets increases the tensile stretching work in perforation. However, since this is accompanied by reductions in other work terms, only small changes are found in total energy absorption, despite large changes in failure geometry. The propensity to stretch and bend or to shear a plug is affected by target exit-side layer thickness relative to projectile diameter, with thick layers tending to favour plugging by a shear mechanism. In targets with thin exit-side layers tensile, rather than shear, mechanisms are apparent in failure and plug separation. A model is developed which treats the perforation of laminates as a two-stage process of indentation on the impact side, and either shear or dishing failure on the exit side, depending on target configuration. For the cases examined the model gives good predictions of the ballistic limit, including distinguishing between differently configured laminates, and correctly accounts for the effect of projectile nose shape. As part of this process, the estimation of dishing energies is improved by accounting for the effect of tangential curvature. In spite of its success in predicting ballistic limits, the model involves some simplifications which do not mirror experimental observations. A notable example is its neglect of the detailed geometric features of deformation. Nevertheless, the model can be used to elucidate design features for laminated targets.

Elastic energy of curvature-driven bump formation on red blood cell membrane

Model calculations were performed to explore quantitative aspects of the discocyte-echinocyte shape transformation in red blood cells. The shape transformation was assumed to be driven by changes in the preferred curvature of the membrane bilayer and opposed by the elastic shear rigidity of the membrane skeleton. The energy required for echinocyte bump formation was calculated for a range of bump shapes for different preferred curvatures. Energy minima corresponding to nonzero bump heights were found when the stress-free area difference between the membrane leaflets or the spontaneous curvature of the membrane became sufficiently large, but the calculations predict that the membrane can tolerate significant differences in the resting areas of the inner and outer leaflets or significant spontaneous curvature without visible changes in shape. Thus, if the cell is near the threshold for bump formation, the calculations predict that small changes in membrane properties would produce large changes in cellular geometry. These results provide a rational framework for interpreting observations of shape transformations in red cells and for understanding the mechanism by which small changes in membrane elastic properties might lead to significant changes in geometry.

Reduction in phosphoribulokinase activity by antisense RNA in transgenic tobacco: effect on CO2 assimilation and growth in low irradiance

SummaryTo quantify the importance of the Calvin cycle enzyme phosphoribulokinase (PRK) in photosynthesis and to perturb photosynthesis without large direct reductions in leaf protein content, tobacco plants (Nicotiana tabacum L.) were transformed with an inverted cDNA encoding tobacco PRK. A population of plants expressing antisense RNA and a range of PRK activities from wild‐type to less than 5% of wild‐type were obtained. CO2 assimilation under the growing conditions (330 µmol photons m−2 sec−1, 350 µbar CO2, 25°C) was not inhibited until more than 85% of PRK activity had been removed. With reduction in PRK activity of between 85 and 95%, assimilation rates and amounts of chlorophyll compared with wild‐type were reduced by up to half. Decreased absorption of light by leaves with less chlorophyll accounte0d for only a small part of the reduction in assimilation rate. When PRK activity was below 15% of wild‐type, amounts of ribulose‐5‐phosphate, ribose‐5‐phosphate, ATP and fructose‐6‐phosphate were 1.5‐ to fivefold higher and levels of ribulose‐1,5‐bisphosphate, 3‐phosphoglyceric acid and ADP 1.5‐ to fourfold lower than in wild‐type. It is estimated that these changes maintained flux through PRK to realise the assimilation rates observed. A possible shift of control within the Calvin cycle towards fructose‐1,6‐bisphosphatase in plants with low PRK is discussed. Amounts of hexoses and starch in particular were reduced in plants expressing the lowest PRK activities; amounts of sucrose were little affected. Lower CO2 assimilation in plants with low PRK activity correlated with reduced relative growth rate of shoots and delayed flowering, but there was no effect on specific leaf area. It is concluded that (i) in wild‐type plants grown in constant low light, PRK has a flux‐control coefficient for CO2 assimilation of zero, and that even when amounts of PRK are reduced 20‐fold relative to wild‐type, altered amounts of metabolites compensate for much of the reduction in PRK protein; (ii) in plants where there is a 95% reduction in amounts of PRK, photosynthesis was reduced twofold without large changes in leaf protein content or leaf geometry.

FEM simulation of the static and dynamic forming of circular plates

A commercially available finite-element package (ABAQUS) has been used to analyse the forming of a circular plate subjected to simultaneous stretching and bending processes. The method is used to study the plate response under both static and dynamic loading conditions, retaining the non-linearities involved in the large changes in geometry, the continuous change in contact surface conditions and the isotropic material work-hardening characteristics. An axisymmetric model is studied and discussed in detail. For the dynamic case, the plate is assumed to be deformed by the impact of a cylindrical projectile. In the dynamic analysis response the material strain-rate dependence via the Cowper-Symonds power law is included in the analysis. An algorithm to deal with the contact between the cylindrical projectile and plate has been developed by means of the penalty approach. The interaction of the sliding surfaces is modelled with a modified Coulomb friction law. A qualitative comparison betwee the computed results and experiments is referred to in the text.

Lattice relaxation of zeolites

Quantum-chemical cluster calculations as well as solid-state chemical lattice-calculations indicate that zeolitic SiO2- and AlPO4-structures are flexible structures. The structures reflect the subtle balance of electrostatic and covalent interactions. The different electrostatic interactions lower the symmetry of layered AlPO4-structures compared to that of the corresponding SiO2-compounds. The result is a smaller zeolite-channel dimension for the AlPO4-structure compared to that of the corresponding SiO2-network. Deprotonation of the zeolite-lattice leads to large local changes in geometry that changes acidity compared to that predicted for a non-flexible lattice. Changes in lattice vibrational frequencies are consistent with the theoretically predicted relaxation of the zeolite-lattice.

An iterative franck-condon analysis procedure for the determination of ionic geometries for H 2O and H 2S

The pattern search optimization procedure is applied to a Franck-Condon analysis method with the use of the formulation proposed by Kupka and Cribb for evaluating vibrational overlap integrals [H. Kupka and P.H. Cribb, J. Chem. Phys., 85 (1986) 1303; H. Kupka and G. Olbrich, J. Chem. Phys., 80 (1985) 3163]. The method was applied to three different ionization processes accompanied by small to large changes in molecular geometry. It was found that ionic geometries thus deduced for transitions with small structural changes agree well with observation. However, the agreement is poor for transitions with large geometric changes although the method can still account for the observed vibrational intensity distributions to a certain extent. In addition, properties of the pattern search method as well as Kupka and Cribb's formulation for Franck-Condon analyses are discussed.

A design method for two‐dimensional cascades of turbomachinery blades

AbstractA design method for two‐dimensional cascades of turbomachinery blades is presented. A finite element potential flow program is extended to allow fluid to transpire through the blade surface, the displaced surface streamline defining a new blade geometry. The potential changes are related linearly to the transpired flow rates. New surface velocities may then be specified as a function of surface distance, in accordance with boundary layer considerations. Closure and smoothness of the new blade are successfully achieved, while large changes in the blade geometry are possible.

NEAR-EDGE STRUCTURE OF OXYGEN IN INORGANIC OXIDES : EFFECT OF LOCAL GEOMETRY AND CATION TYPE

NEXAFS measurements at the oxygen K-edge have been carried out on a variety of crystalline oxide samples to examine the effects of differences in local coordination environment of oxygen on near-edge structure. All spectra display an intense white line at about 543 eV and a strong shape resonance about 20 eV above the edge. The white line shifts to higher energies with increasing oxygen coordination number, although differences in nearest-neighbor type can affect this correlation. In addition, the Ca and transition-metal contain- ing oxides display features 6-10 eV below and 6-9 eV above the white line. The intensities of these features vary inversely with the number of 3d-electrons but their energies are independent of cation oxidation state. Large changes in coordination number and geometry affect edge structure less than variations in types of nearest- neighbor cations. The inverse distance-energy relationship is poorly obeyed in these compounds when oxygen- cation bond lengths are compared with the position of the strongest shape resonance for a given structure type. The near-edge structure is qualitatively interpreted using the results of recent Xa multiple scattered-wave calcu- lations.