Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.

New computational approaches for wrinkled and slack membranes

The static response of thin, wrinkled membranes is studied using both a tension field approximation based on plane stress conditions and a 3D nonlinear elasticityformulation, discretized through 8-noded Cosserat point elements. While the tension field approach only obtains the wrinkled/slack regions and at best a measure of the extent of wrinkliness, the 3D elasticity solution provides, in principle, the deformed shape of a wrinkled/slack membrane. However, since membranes barely resist compression, the discretized and linearized system equations via both the approaches are ill-conditioned and solutions could thus be sensitive to discretizations errors as well as other sources of noises/imperfections. We propose a regularized, pseudo-dynamical recursion scheme that provides a sequence of updates, which are almost insensitive to theregularizing term as well as the time step size used for integrating the pseudo-dynamical form. This is borne out through several numerical examples wherein the relative performance of the proposed recursion scheme vis-a-vis a regularized Newton strategy is compared. The pseudo-time marching strategy, when implemented using 3D Cosserat point elements, also provides a computationally cheaper, numerically accurate and simpler alternative to that using geometrically exact shell theories for computing large deformations of membranes in the presence of wrinkles. (C) 2010 Elsevier Ltd. All rights reserved.

Finite element analysis of shear critical prestressed SFRC beams

This study reports the details of the finite element analysis of eleven shear critical partially prestressed concrete T-beams having steel fibers over partial or full depth. Prestressed concrete T-beams having a shear span to depth ratio of 2.65 and 1.59 and failing in the shear have been analyzed Using 'ANSYS'. The 'ANSYS' model accounts for the nonlinear phenomenon, such as, bond-slip of longitudinal reinforcements, post-cracking tensile stiffness of the concrete, stress transfer across the cracked blocks of the concrete and load sustenance through the bridging of steel fibers at crack interlace. The concrete is modeled using 'SOLID65'-eight-node brick element, which is capable Of simulating the cracking and crushing behavior of brittle materials. The reinforcements such as deformed bars, prestressing wires and steel fibers have been modeled discretely Using 'LINK8' - 3D spar element. The slip between the reinforcement (rebar, fibers) and the concrete has been modeled using a 'COMBIN39'-non-linear spring element connecting the nodes of the 'LINK8' element representing the reinforcement and nodes of the 'SOLID65' elements representing the concrete. The 'ANSYS' model correctly predicted the diagonal tension failure and shear compression failure of prestressed concrete beams observed in the experiment. I-lie capability of the model to capture the critical crack regions, loads and deflections for various types Of shear failures ill prestressed concrete beam has been illustrated.

High temperature deformation processing maps for boron modified Ti-6Al-4V alloys

The alloy, Ti-6Al-4V is an alpha + beta Ti alloy that has large prior beta grain size (similar to 2 mm) in the as cast state. Minor addition of B (about 0.1 wt.%) to it refines the grain size significantly as well as produces in-situ TiB needles. The role played by these microstructural modifications on high temperature deformation processing maps of B-modified Ti64 alloys is examined in this paper.Power dissipation efficiency and instability maps have been generated within the temperature range of 750-1000 degrees C and strain rate range of 10(-3)-10(+1) s(-1). Various deformation mechanisms, which operate in different temperature-strain rate regimes, were identified with the aid of the maps and complementary microstructural analysis of the deformed specimens. Results indicate four distinct deformation domains within the range of experimental conditions examined, with the combination of 900-1000 degrees C and 10(-3)-10(-2) s(-1) being the optimum for hot working. In that zone, dynamic globularization of alpha laths is the principle deformation mechanism. The marked reduction in the prior beta grain size, achieved with the addition of B, does not appear to alter this domain markedly. The other domains, with negative values of instability parameter, show undesirable microstructural features such as extensive kinking/bending of alpha laths and breaking of beta laths for Ti64-0.0B as well as generation of voids and cracks in the matrix and TiB needles in the B-modified alloys. (C) 2010 Elsevier B.V. All rights reserved.

Studies of cryotreatment on the performance of integral diaphragm pressure transducers for space application

The integral diaphragm pressure transducers machined out of precipitation hardened martensite stainless steel (APX4) are widely used for propellant pressure measurements in space applications. These transducers are expected to exhibit dimensional stability and linearity for their entire useful life. These vital factors are very critical for the reliable performance and dependability of the pressure transducers. However, these transducers invariably develop internal stresses during various stages of machining. These stresses have an adverse effect on the performance of the transducers causing deviation from linearity. In order to eliminate these possibilities, it was planned to cryotreat the machined transducers to improve both the long-term linearity and dimensional stability. To study these effects, an experimental cryotreatment unit was designed and developed based on the concept of indirect cooling using the concept of cold nitrogen gas forced closed loop convection currents. The system has the capability of cryotreating large number of samples for varied rates of cooling, soaking and warm-up. After obtaining the initial levels of residual stress and retained austenite using X-ray diffraction techniques, the pressure transducers were cryotreated at 98 K for 36 h. Immediately after cryotreatment, the transducers were tempered at 510 degrees C for 3 h in vacuum furnace. Results after cryo treatment clearly indicated significant reduction in residual stress levels and conversion of retained austenite to martensite. These changes have brought in improvements in long term zero drift and dimensional stability. The cryotreated pressure transducers have been incorporated for actual space applications. (c) 2010 Published by Elsevier Ltd.

Magnetic fabrics indicating Late Quaternary seismicity in the Himalayan foothills

The anisotropy of magnetic susceptibility (AMS) study was performed on soft sediment samples from a trenched fault zone across the Himalayan frontal thrust (HFT), western Himalaya. AMS orientation of K-min axes in the trench sediments is consistent with lateral shortening revealed by geometry of deformed regional structures and recent earthquakes. Well-defined vertical magnetic foliation parallel to the flexure cleavage in which a vertical magnetic lineation is developed, high anisotropy, and triaxial ellipsoids suggest large overprinting of earth-quake- related fabrics. The AMS data suggest a gradual variation from layer parallel shortening (LPS) at a distance from the fault trace to a simple shear fabric close to the fault trace. An abrupt change in the shortening direction (K-min) from NE-SW to E-W suggests a juxtaposition of pre-existing layer parallel shortening fabric, and bending-related flexure associated with an earthquake. Hence the orientation pattern of magnetic susceptibility axes helps in identifying co-seismic structures in Late Holocene surface sediments.

Nanomechanical properties of silicon surfaces nanostructured by excimer laser

Excimer laser irradiation at ambient temperature has been employed to produce nanostructured silicon surfaces. Nanoindentation was used to investigate the nanomechanical properties of the deformed surfaces as a function of laser parameters, such as the angle of incidence and number of laser pulses at a fixed laser fluence of 5 J cm(-2). A single-crystal silicon 311] surface was severely damaged by laser irradiation and became nanocrystalline with an enhanced porosity. The resulting laser-treated surface consisted of nanometer-sized particles. The pore size was controlled by adjusting the angle of incidence and the number of laser pulses, and varied from nanometers to microns. The extent of nanocrystallinity was large for the surfaces irradiated at a small angle of incidence and by a high number of pulses, as confirmed by x-ray diffraction and Raman spectroscopy. The angle of incidence had a stronger effect on the structure and nanomechanical properties than the number of laser pulses.

Influence of microstructure on the wear of grinding media

Owing to the complexity of the wear process, high stress grinding abrasion is quite different from two-body abrasive wear. Reported data on two-body abrasive wear reveal that the wear decreases with an increase in steel hardness. This relationship can be established without having to consider the microstructure of the steel grinding medium. However, it is known that hardness cannot be directly employed to predict the wear of steel balls under three-body grinding abrasion, as occurs during dry grinding of ores in ball mills. The present work suggests that the wear behaviour of grinding balls can be classified according to the microstructural family to which they belong. Thus, in this work on AISI 52100 steel, the separate groups of microstructures were spheroidite—pearlite, bainite, tempered martensite and martensite with retained austenite. It appears that wear behaviour of the first three groups follows the same trend as that observed for two-body wear. The data suggest that an optimum level of retained austenite could improve the wear resistance of microstructures containing martensite.

Stress-strain characteristics of Tress-strain characteristics of reinforcing steel bars under cyclic loading

This paper presents test results for 22 high strength deformed bars and nine mild steel bars subjected to monotonic repeated and reversed axial loading to determine the stress-strain behavior. Equations have been proposed for the stress-strain curves and have been compared with test results. Satisfactory agreement was obtained.

Processing map for hot working of alpha-zirconium

The hot deformation characteristics of alpha-zirconium in the temperature range of 650 °C to 850 °C and in the strain-rate range of 10-3 to 102 s-1 are studied with the help of a power dissipation map developed on the basis of the Dynamic Materials Model.[7,8,9] The processing map describes the variation of the efficiency of power dissipation (η =2m/m + 1) calculated on the basis of the strain-rate sensitivity parameter (m), which partitions power dissipation between thermal and microstructural means. The processing map reveals a domain of dynamic recrystallization in the range of 730 °C to 850 °C and 10−2 to 1−1 with its peak efficiency of 40 pct at 800 °C and 0.1 s-1 which may be considered as optimum hot-working parameters. The characteristics of dynamic recrystallization are similar to those of static recrystallization regarding the sigmoidal variation of grain size (or hardness) with temperature, although the dynamic recrystallization temperature is much higher. When deformed at 650 °C and 10-3 s-1 texture-induced dynamic recovery occurred, while at strain rates higher than 1 s-1, alpha-zirconium exhibits microstructural instabilities in the form of localized shear bands which are to be avoided in processing.

Stress-Strain Characteristics of Reinforcing Steel Bars Under Cyclic Loading

This paper presents test results for 22 high strength deformed bars and nine mild steel bars subjected to monotonic repeated and reversed axial loading to determine the stress-strain behavior. Equations have been proposed for the stress-strain curves and have been compared with test results. Satisfactory agreement was obtained.

On characterization of deformation microstructure in Boron modified Ti-6Al-4V alloy

Addition of boron in small quantities to various titanium alloys have shown significant improvement in mechanical behavior of materials. In the present study, electron back-scatter diffraction (EBSD) techniques have been applied to investigate the deformation microstructure evolution in boron modified two-phase titanium alloy Ti-6Al-4V. The alloy was hot compressed at 750 degrees C up to 50% height reduction at two different strain rates (10(-3) s(-1) and 1 s(-1)). The EBSD analyses indicated significant differences in deformed microstructure of the base alloy and the alloy containing boron. A strong subgrain formation tendency was observed along with inhomogeneous distribution of dislocations inside large a colonies of Ti64. In contrast, a colonies were relatively strain free for Ti64 + B, with more uniform dislocation density distribution. The observed difference is attributed to microstructural modifications viz, grain size refinement and presence of TiB particles at grain boundary produced due to boron addition. (C) 2010 Elsevier B.V. All rights reserved.

Effects of temper level on the dependence of fatigue crack growth threshold and crack closure on the prior austenitic grain size

An attempt has been made to systematically investigate the effects of microstructural parameters, such as the prior austenite grain size (PAGS), in influencing the resistance to fatigue crack growth (FCG) in the near-threshold region under three different temper levels in a quenched and tempered high-strength steel. By austenitizing at various temperatures, the PAGS was varied from about 0.7 to 96 μm. The microstructures with these grain sizes were tempered at 200 °C, 400 °C, and 530 °C and tested for fatigue thresholds and crack closure. It has been found that, in general, three different trends in the dependence of both the total threshold stress intensity range, ΔK th , and the intrinsic threshold stress intensity range, ΔK eff, th , on the PAGS are observable. By considering in detail the factors such as cyclic stress-strain behavior, environmental effects on FCG, and embrittlement during tempering, the present observations could be rationalized. The strong dependence of ΔK th and ΔK eff, th on PAGS in microstructures tempered at 530 °C has been primarily attributed to cyclic softening and thereby the strong interaction of the crack tip deformation field with the grain boundary. On the other hand, a less strong dependence of ΔK th and ΔK eff, th on PAGS is suggested to be caused by the cyclic hardening behavior of lightly tempered microstructures occurring in 200 °C temper. In both microstructures, crack closure influenced near-threshold FCG (NTFCG) to a significant extent, and its magnitude was large at large grain sizes. Microstructures tempered at the intermediate temperatures failed to show a systematic variation of ΔKth and ΔKeff, th with PAGS. The mechanisms of intergranular fracture vary between grain sizes in this temper. A transition from “microstructure-sensitive” to “microstructure-insensitive” crack growth has been found to occur when the zone of cyclic deformation at the crack tip becomes more or less equal to PAGS. Detailed observations on fracture morphology and crack paths corroborate the grain size effects on fatigue thresholds and crack closure.

Microstructural features of flow instability in α-titanium cylinders under high strain rate compression at 25°C to 400°C

Cylindrical specimens of commercial pure titanium have been compressed at strain rates in the range of 0.1 to 100 s-1 and temperatures in the range of 25-degrees-C to 400-degrees-C. At strain rates of 10 and 100 s-1, the specimens exhibited adiabatic shear bands. At lower strain rates, the material deformed in an inhomogeneous fashion. These material-related instabilities are examined in the light of the ''phenomenological model'' and the ''dynamic materials mode.'' It is found that the regime of adiabatic shear band formation is predicted by the phenomenological model, while the dynamic materials model is able to predict the inhomogeneous deformation zone. The criterion based on power partitioning is competent to predict the variations within the inhomogeneous deformation zone.

Processing map for hot working of stainless steel type AISI 316L

Processing and instability maps using a dynamic materials model have been developed for stainless steel type AISI 316L in the temperature range 600-1250-degrees-C and strain rate range 0.001-100 s-1 with a view to optimising its hot workability. Stainless steel type AISI 316L undergoes dynamic recrystallisation, with a peak efficiency of 35% at 1250-degrees-C and 0.05 s-1, which are the optimum parameters for hot working this material. The material undergoes dynamic recovery at 900-degrees-C and 0.001 s-1. The increase in the dynamic recrystallisation and dynamic recovery temperatures in comparison with stainless steel type AISI 304L is attributed to the presence of a backstress caused by the molybdenum additions. These results are in general agreement with those reported elsewhere on stainless steel type 316 deformed in hot extrusion and hot torsion. At temperatures < 850-degrees-C and strain rates > 10 s-1, the material exhibits flow localisation owing to adiabatic shear band formation, whereas at higher temperatures (> 850-degrees-C) and strain rates (> 10 s-1) mechanical twinning and wavy slip bands are observed. (C) 1993 The Institute of Materials.