Effects of crystal orientation and aspect ratio on plastic response of aluminium nanowires under torsion

The plastic response of perfect face-centred cubic single-crystal aluminium (Al) nanowires (NWs) under torsion is studied using molecular dynamics simulations. The Al–Al interaction is described by the many-body tight-binding potential. The effects of the crystal orientation and aspect ratio of the NWs on their deformation are evaluated in terms of atomic trajectories, potential energy, a centrosymmetry parameter and the torque required for deformation. Simulation results clearly show that for NWs, regardless of crystal orientation, dislocations nucleate and propagate on the (1 1 1) close-packed plane. In a NW under torsion, dislocations begin at the surface, extend to the interior along the (1 1 1) close-packed plane and finally diffuse to the middle part. A 〈1 1 0〉-oriented NW has the lowest required torque for deformation due to the occurrence of homogeneous deformation. The mechanism of the plastic response of an Al NW depends on its crystal orientation. For a long NW, geometry instability occurs before material instability (buckling).     

Determination of the tensile strength of superficial passive implant materials]

The crack strength of passivating surface materials or passive layers on electroconductive substrates is determined by the electronic detection of redox reactions at the electrolyte/sample interface. A sudden increase in corrosion current under mechanical tensile loading or bending moments indicates generation or propagation of macro- and micro-cracks in the passivating layer, and exposure of the substrate. A subsequent decrease in the current indicates repassivation. Titanium oxide passivating layers generated by oxygen diffusion hardening (ODH) on titanium show crack formation at a tensile load on the substrate of more than 230 MPa. Repassivating sandwich layers of tantalum and tantalum oxide on steel substrates (AISI 31 6L) generate micro-cracks at more than 300 MPa. The crack formation of the oxide surface materials correlates with the onset of plastic deformation of the substrate.     

Analysis of deformation behaviour of Al–Ni–Co thin film coated aluminium during nano-indentation: a molecular dynamics study

In the present work, molecular dynamics simulations of AlNiCo metallic film deposition on FCC Al substrate and subsequently nano-indentation on the same specimen considering different indenter velocities have been performed using Embedded Atom Method (EAM) potential. The mechanical properties and deformation behaviour of AlNiCo thin film deposited Al substrate is investigated subjected to simulated nano-indentation test. It has been found that indenter velocity significantly influences the calculated hardness of the thin film coated substrate specimen and faster indentation process increases the hardness of the specimen. This finding has been rationalised by correlating with the generation of various full and partial dislocations and their interactions during the nano-indentation process. Sessile dislocations such as stair-rod and Frank partials are found to aid/help the strain hardening phenomena. Furthermore, the effect of indenter velocity on the pile-up formation during the nano-indentation process is also investigated here and it is observed that the amount of pile-up reduces as indenter velocity increases.     

Advanced electron paramagnetic resonance on the catalytic iron–sulfur cluster bound to the CCG domain of heterodisulfide reductase and succinate: quinone reductase

Heterodisulfide reductase (Hdr) is a key enzyme in the energy metabolism of methanogenic archaea. The enzyme catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) to the thiol coenzymes M (CoM-SH) and B (CoB-SH). Cleavage of CoM-S-S-CoB at an unusual FeS cluster reveals unique substrate chemistry. The cluster is fixed by cysteines of two cysteine-rich CCG domain sequence motifs (CX_31–39CCX_35–36CXXC) of subunit HdrB of the Methanothermobacter marburgensis HdrABC complex. We report on Q-band (34 GHz) ⁵⁷Fe electron-nuclear double resonance (ENDOR) spectroscopic measurements on the oxidized form of the cluster found in HdrABC and in two other CCG-domain-containing proteins, recombinant HdrB of Hdr from M. marburgensis and recombinant SdhE of succinate: quinone reductase from Sulfolobus solfataricus P2. The spectra at 34 GHz show clearly improved resolution arising from the absence of proton resonances and polarization effects. Systematic spectral simulations of 34 GHz data combined with previous 9 GHz data allowed the unambiguous assignment of four ⁵⁷Fe hyperfine couplings to the cluster in all three proteins. ¹³C Mims ENDOR spectra of labelled CoM-SH were consistent with the attachment of the substrate to the cluster in HdrABC, whereas in the other two proteins no substrate is present. ⁵⁷Fe resonances in all three systems revealed unusually large ⁵⁷Fe ENDOR hyperfine splitting as compared to known systems. The results infer that the cluster’s unique magnetic properties arise from the CCG binding motif.     

An EPR/HYSCORE, Mössbauer, and resonance Raman study of the hydrogenase maturation enzyme HydF: a model for N-coordination to [4Fe–4S] clusters

The biosynthesis of the organometallic H cluster of [Fe–Fe] hydrogenase requires three accessory proteins, two of which (HydE and HydG) belong to the radical S-adenosylmethionine enzyme superfamily. The third, HydF, is an Fe–S protein with GTPase activity. The [4Fe–4S] cluster of HydF is bound to the polypeptide chain through only the three, conserved, cysteine residues present in the binding sequence motif CysXHisX_(46-53)HisCysXXCys. However, the involvement of the two highly conserved histidines as a fourth ligand for the cluster coordination is controversial. In this study, we set out to characterize further the [4Fe–4S] cluster of HydF using Mössbauer, EPR, hyperfine sublevel correlation (HYSCORE), and resonance Raman spectroscopy in order to investigate the influence of nitrogen ligands on the spectroscopic properties of [4Fe–4S]^2+/+ clusters. Our results show that Mössbauer, resonance Raman, and EPR spectroscopy are not able to readily discriminate between the imidazole-coordinated [4Fe–4S] cluster and the non-imidazole-bound [4Fe–4S] cluster with an exchangeable fourth ligand that is present in wild-type HydF. HYSCORE spectroscopy, on the other hand, detects the presence of an imidazole/histidine ligand on the cluster on the basis of the appearance of a specific spectral pattern in the strongly coupled region, with a coupling constant of approximately 6 MHz. We also discovered that a His-tagged version of HydF, with a hexahistidine tag at the N-terminus, has a [4Fe–4S] cluster coordinated by one histidine from the tag. This observation strongly indicates that care has to be taken in the analysis of data obtained on tagged forms of metalloproteins.     

Grain size effect on the plastic deformation of nanocrystalline silver

The plastic deformation of nanocrystalline Ag, with columnar grains, has been studied by molecular dynamics simulations. The nanocrystalline systems show two types of deformation mechanisms. One is the split of grain boundary that occurs before the activation of the dislocation in nanocrystalline Ag, and almost no dislocation debris and twins are left in the grains. Moreover, split of grain boundary is shown between the grains of nanocrystalline Ag. Another mechanism consists in partial dislocations dominating the process of plastic deformation. Plenty of stacking faults and twins remain in the grains of nanocrystalline Ag. It is revealed that different grain aspect ratios have induced the difference in deformation mechanisms of nanocrystalline Ag. When the grain aspect ratio is less than or equal to 1, the process of plastic deformation is dominated by partial dislocations. Otherwise, the process is dominated by split of grain boundary. The grain aspect ratio is the height in z direction to length in x direction ratio, which was found to noticeably impact yield strength, grain coarsening, indicating that the observed behaviour should have contributed to the plastic deformation significantly.     

Characterization of a modified nitrogenase Fe protein from Klebsiella pneumoniae in which the 4Fe4S cluster has been replaced by a 4Fe4Se cluster

The Azotobacter vinelandii nifS gene product has been used with selenocysteine to reconstitute Klebsiella pneumoniae nitrogenase Fe protein. Chemical analysis and extended X-ray absorption fine structure (EXAFS) spectroscopy show that the 4Fe4S cluster present in the native protein is replaced by a 4Fe4Se cluster. As well, EXAFS spectroscopy shows that the bond lengths to the cysteine thiolate ligands shrink by 0.05 Å (from 2.28 to 2.23 Å) upon reduction, whereas the Fe–Fe distance is essentially unchanged. Thus, the core of the 4Fe4Se cluster remains essentially static on reduction, whilst the external cysteine thiolate ligands are pulled in towards the cluster. Compared with native (S)–Fe protein, the (Se)–Fe protein has a 20-fold increased rate of MgATP-induced Fe chelation, a sixfold decreased specific activity for acetylene reduction, a fivefold decreased rate of MgATP-dependent electron transfer from (Se)–Fe protein to MoFe protein, and a fourfold increase in the ATP to 2e ^? ratio. The high ATP to 2e ^? ratio and decreased specific activity are consistent with a lower rate of dissociation of oxidized (Se)–Fe protein from reduced MoFe protein. Thus, the relatively small adjustments in the Fe protein structure necessary to accommodate the 4Fe4Se cluster are transmitted both to adjacent residues that dock at the surface of the MoFe protein and to the ATP hydrolysis sites located approximately 19 Å away.     

Investigation of asphalt aging behaviour due to oxidation using molecular dynamics simulation

An attempt is made to connect the link between internal chemical and molecular mechanical property change and external physical, rheological and mechanical property change for asphalt before and after oxidative aging using molecular dynamics (MD) simulation. Intermolecular interactions, density, bulk modulus and zero shear viscosity changes of model asphalt systems before and after oxidative aging and mechanical property changes of the asphalt systems under different compressive and tensile stress rates are investigated at room temperature (298 K). Simulation results demonstrate that oxidised functional groups in asphalt molecules increase the strength of intermolecular bonds and the bulk modulus of asphalt, which further contribute to the hardening of the oxidised asphalt. The internal property change is consistent with the external physical and rheological property change after oxidation, which is revealed by the increase of density and viscosity. In addition, both the unoxidised and oxidised asphalts deform more and fail faster with an increase in both compressive and tensile stress rates, especially under tensile stresses. The oxidised asphalt is stiffer than the unoxidised asphalt, which shows less deformation.     

The effect of cement creep and cement fatigue damage on the micromechanics of the cement–bone interface

The cement–bone interface provides fixation for the cement mantle within the bone. The cement–bone interface is affected by fatigue loading in terms of fatigue damage or microcracks and creep, both mostly in the cement. This study investigates how fatigue damage and cement creep separately affect the mechanical response of the cement–bone interface at various load levels in terms of plastic displacement and crack formation. Two FEA models were created, which were based on micro-computed tomography data of two physical cement–bone interface specimens. These models were subjected to tensile fatigue loads with four different magnitudes. Three deformation modes of the cement were considered: ‘only creep’, ‘only damage’ or ‘creep and damage’. The interfacial plastic deformation, the crack reduction as a result of creep and the interfacial stresses in the bone were monitored. The results demonstrate that, although some models failed early, the majority of plastic displacement was caused by fatigue damage, rather than cement creep. However, cement creep does decrease the crack formation in the cement up to 20%. Finally, while cement creep hardly influences the stress levels in the bone, fatigue damage of the cement considerably increases the stress levels in the bone. We conclude that at low load levels the plastic displacement is mainly caused by creep. At moderate to high load levels, however, the plastic displacement is dominated by fatigue damage and is hardly affected by creep, although creep reduced the number of cracks in moderate to high load region.     

Insight into the protein and solvent contributions to the reduction potentials of [4Fe–4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and the homologous Escherichia coli ferredoxin

The crystal structures of the C57A and V13G molecular variants of Allochromatium vinosum 2[4Fe–4S] ferredoxin (AlvinFd) and that of the homologous ferredoxin from Escherichia coli (EcFd) have been determined at 1.05-, 1.48-, and 1.65-Å resolution, respectively. The present structures combined with cyclic voltammetry studies establish clear effects of the degree of exposure of the cluster with the lowest reduction potential (cluster I) towards less negative reduction potentials (E°). This is better illustrated by V13G AlvinFd (high exposure, E° = ?594 mV) and EcFd (low exposure, E° = ?675 mV). In C57A AlvinFd, the movement of the protein backbone, as a result of replacing the noncoordinating Cys57 by Ala, leads to a +50-mV upshift of the potential of the nearby cluster I, by removal of polar interactions involving the thiolate group and adjustment of the hydrogen-bond network involving the cluster atoms. In addition, the present structures and other previously reported accurate structures of this family of ferredoxins indicate that polar interactions of side chains and water molecules with cluster II sulfur atoms, which are absent in the environment of cluster I, are correlated to the approximately 180–250 mV difference between the reduction potentials of clusters I and II. These findings provide insight into the significant effects of subtle structural differences of the protein and solvent environment around the clusters of [4Fe–4S] ferredoxins on their electrochemical properties.     

The effect of polyphosphates and magnesium on the mechanical properties of extracted muscle fibers

Loading of extracted muscle fibers causes a small, sudden lengthening, followed by a slower, plastic extension, which is reversed only by active contraction. Polyphosphates in the presence of Mg strongly accelerate plastic extension, but elastic changes in length remain the same as during rigor. The modulus of elasticity on the average is about 6.2 x 10⁷ dynes per cm.² This value is about 40 times larger than that of rubber, if compared on a water-free basis. Extension of muscle, therefore, is almost entirely due to plastic deformation. Mg is essential for the softening action of adenosinetriphosphate (ATP) and can produce partial relaxation in the absence of a relaxation factor. After partial removal of bound Mg, ATP causes strong contraction, but only slight softening. The same condition is produced by very low concentrations of ATP in the presence of phosphocreatine. These observations show that during contraction passive mechanical properties may remain essentially like those during rigor. The constancy of elastic extensibility distinguishes contraction produced by ATP from contraction induced by non-specific agents in various fibrous structures and caused by an increase in configurational entropy.     

Dependence of the mechanical properties of a pullulan film on the preparation temperature

The mechanical properties of pullulan films prepared at various temperatures were investigated. The films prepared at high temperatures (40 degrees C and 60 degrees C; H-films) did not show any clear plastic deformation in tensile test, indicating that they were brittle. In contrast, those prepared at low temperatures (4 degrees C, 13 degrees C, and 25 degrees C; L-films) showed such deformation. The latter films had higher values for both tensile strength and elastic modulus than the former, indicating that the L-films were stiffer and more flexible than the H-films. Stretching the L-films clearly showed a shear deformation band inclined at 45 degrees to the stretching direction, indicating that they were amorphous.     

Direct Compression Behavior of Low- and High-Methoxylated Pectins

The objective of this study was to evaluate possible usefulness of pectins for direct compression of tablets. The deformation behavior of pectin grades of different degree of methoxylation (DM), namely, 5%, 10%, 25%, 35%, 40%, 50%, and 60% were, examined in terms of yield pressures (YP) derived from Heckel profiles for both compression and decompression and measurements of elastic recovery after ejection. All pectin grades showed a high degree of elastic recovery. DM 60% exhibited most plastic deformation (YP 70.4 MPa) whereas DM 5% (104.6 MPa) and DM 10% (114.7 MPa) least. However, DM 60% gave no coherent tablets, whereas tablet tensile strengths for DM 5% and DM 10% were comparable to Starch 1500^®. Also, Heckel profiles were similar to Starch 1500^®. For sieved fractions (180–250 and 90–125 μm) of DM 25% and DM 40% originating from the very same batch, YPs were alike, indicating minor effects of particle size. These facts indicate that DM is important for the compaction behavior, and batch-to-batch variability should also be considered. Therefore, pectins of low degree of methoxylation may have a potential as direct compression excipients.     

HdrC2 from Acidithiobacillus ferrooxidans Owns Two Iron–Sulfur Binding Motifs But Binds Only One Variable Cluster Between [4Fe–4S] and [3Fe–4S]

The heterodisulfide reductase complex HdrABC from Acidithiobacillus ferrooxidans was suggested to own novel features that act in reverse to convert the sulfane sulfur of GS _n H species (n > 1) into sulfite in sulfur oxidation. The HdrC subunit is potentially encoded by two different highly upregulated genes sharing only 29 % identity in A. ferrooxidans grown in sulfur-containing medium, which were named as HdrC1 and HdrC2, respectively and had been confirmed to contain iron–sulfur cluster by expression and characterization, especially the HdrC1 which had been showed to bind only one [4Fe–4S] cluster by mutations. However, the mutations of the HdrC2 remain to be done and the detailed binding information of it is still unclear. Here, we report the expression, mutations, and molecular modeling of the HdrC2 from A. ferrooxidans. This HdrC2 had two identical motifs (Cx₂Cx₂Cx₃C) containing total of eight cysteine residues potentially for iron–sulfur cluster binding. This purified HdrC2 was exhibited to contain one variable cluster converted between [4Fe–4S] and [3Fe–4S] according to different conditions by the UV-scanning and EPR spectra. The site-directed mutagenesis results of these eight residues further confirmed that the HdrC2 in reduction with Fe²⁺ condition loaded only one [4Fe–4S]⁺ with spin S = 1/2 ligated by the residues of Cys73, Cys109, Cys112, and Cys115; the HdrC2 in natural aeration condition lost the Fe atom ligated by the residue of Cys73 and loaded only one [3Fe–4S]⁰ with spin S = 0; the HdrC2 in oxidation condition loaded only one [3Fe–4S]⁺ with spin S = 1/2. Molecular modeling results were also in line with the experiment results.     

Structural evolution and dislocation behaviour study during nanoindentation of Mo20W20Co20Ta20Zr20 high entropy alloy coated Ni single crystal using molecular dynamic simulation

In this present study, deformation behaviour of Mo₂₀W₂₀Co₂₀Ta₂₀Zr₂₀ high entropy alloy (HEA) coated single crystal (SC) nickel (Ni) subjected to nanoindentation test have been investigated to study the mechanical properties and underlying mechanism during nanoindentation test using molecular dynamics (MD) simulation with embedded atom method (EAM) potential. Centro-Symmetry Parameter (CSP) Analysis and Radial Distribution Function (RDF) plots are obtained to get insight of structural evolution during nanoindentation and thereby determine the underlying physics of deformation. During nanoindention test Stacking faults (SFs) formation, dislocation generation, dislocation loops, Lomer–Cottrell (LC) lock and Hirth lock formation due to dislocation-dislocation interaction are observed. At higher indentation depth, formation of dislocation loops is augmented, which indicates nanoindentation deformation is found to be Stacking Fault dominated deformation. The accumulation and relaxation of shear stress near indenter tip at the time of deformation process under nanoindentation test causes the variation of dislocation density, strain hardening, and plastic deformation, which is influenced by the formation of dislocation barriers (LC and Hirth locks) and dislocation loops (shear and prismatic loops).     

A model for predicting growth responses in plants to changes in external water potential: Zea mays primary roots

In response to osmotic step changes, three distinct phases have been noted in the growth response of Zea mays primary roots. They are cessation or slowing of growth over a period of 15–20 minutes, tissue contraction, and a damped oscillatory return to nearly normal growth rate, all within a period of about one hour. A system model of the tissue response is presented to explain such behavior and to serve in a predictive capacity to govern future experiments.It is supposed that for turgor pressure in excess of a cell wall yield threshold, plastic flow is the major component of wall deformation, and that when turgor falls below yield threshold, elastic deformation is dominant. The equations of the model describe growth rate as a function of time in terms of the following properties; plastic flow, elastic deformation, permeability to water, and solute uptake. They are derived from basic equations of feedback interactions between internal osmotic pressure and growth rate, and between wall softening, turgor and growth rate.The model predicts oscillatory growth rate regulation, and phase and amplitude relationships between turgor pressure and growth rate. The simplest model which accounts for all observations is that of biphasic deformation, two modes of wall softening, and a dual feedback system involving osmotic and yield threshold control of growth rate.It should be noted that to predict the time course of turgor pressure, osmotic pressure, yield pressure, and growth rate, two initial conditions and six system parameter values are sufficient. So far only the initial values of growth rate and its derivative can be obtained for Zea mays primary roots. However, values for wall softening and hardening coefficients (including the strain and turgor independent component), plastic extensibility, water permeability and dilution rate coefficients have not been obtained as yet for Zea roots. Values for some of these parameters have been obtained for other roots, coleoptiles, and giant algal cells.Lest the reader despair, it should be pointed out that experimental observations coupled with simulation studies will help establish restricted ranges of values that the system parameters might assume. These can then be compared with known values in the literature and values experimentally obtained in the future.     

Single-crystal Al–Cu50Zr50 metallic glass cold welds: tensile and creep behaviour

ABSTRACT

Tensile and creep properties of dissimilar cold weld joints (Al (metal)–Cu₅₀Zr₅₀ (metallic glass)) are investigated using molecular dynamics simulations. Embedded atom method potential is used to model the interactions between Al–Cu–Zr atoms. Cold welding is carried out at three different velocities (20, 30 and 40?m/s) and for three interferences (0.4, 1.3 and 2.3?nm). The strength of the welded joints is measured using the tensile test carried out at a strain rate of 1.5 × 10⁹/s. Structure studies by radial distribution function analysis indicate amorphisation of Al in the weld regions. Tensile studies show that the maximum strength is obtained in the sample that is welded for 1.3?nm interference. Creep studies carried out over range of stresses (200–350?MPa) and temperatures (200–500?K) show very short primary creep and significant steady-state creep. The stress exponent n has two values; at lower stress, n?=?1.2, and at higher stress, n?=?4.06, respectively. The deformation mechanisms are observed to be slip by Shockley partial dislocation and by twinning in Al region. The icosahedral cluster population in metallic glass decreases as the temperature increases and contributes to large plastic strain.     

Biologically related iron-sulfur clusters as reaction centers. Reduction of acetylene to ethylene in systems based on [Fe4S4(SR)4]3-

The possibility that clusters containing the Fe4S4 core unit found in a wide variety of proteins can effect reductive transformations of Fe-S enzyme substrates has been investigated using the reduced synthetic clusters [Fe4S4(SPh)4]3- and acetylene, an alternate nitrogenase substrate. The system [Fe4S4(SPh)4]3-/acetic acid/acetic anhydride in N-methylpyrollidinone at approximately 25 degrees was found to reduce acetylene homogeneously to ethylene, and in the presence of a deuterium source to afford as the principal stereochemical product cis-1,2-C2H2D2. No appreciable reduction was found using the oxidized cluster [Fe4S4(SPh)4]2-. The system is not catalytic and departs from the strict stoichiometry of the reaction, 2[Fe4S4(SPh)4]3- + C2H2 + 2H+ leads to 2 [Fe4S4(SPh)4]2- + C2H4, primarily because of a competing cluster oxidation reaction which could not be eliminated. Based on this reaction ca. 60% conversion of acetylene to ethylene was achieved. A reaction sequence based on absorption and 1H nmr spectral observations and product stereo-chemistry is suggested. The results demonstrate that biologically related, reduced Fe4S4 clusters can effect reduction of at least one Fe-S enzyme substrate, and raise the general possibility of substrate transformation with such clusters as reaction sites in biological systems.     

Larval crowding in Drosophila melanogaster induces Hsp70 expression,and leads to increased adult longevity and adult thermal stress resistance

In this study we show for the first time that moderate high larval density induces Hsp70 expression in Drosophila melanogaster larvae. Larval crowding led to both increased mean and maximal longevity in adults of both sexes. Two different measures of heat-stress resistance increased in adult flies developed at high density compared to flies developed at low density. The hardening-like effect of high larval density carried over to the adult life stage. The hardening memory (the period of increased resistance after hardening) was long compared to hardening of adult flies, and possibly lasts throughout life. The increase in resistance in adults following development at high larval density seemed not to be connected to Hsp70 itself, since Hsp70 expression level in adult flies after hardening was independent of whether larvae developed at low or high densities. More likely, Hsp70 may be one of many components of the stress response resulting in hardening.     

Thermal-stability and tensile properties of two single-walled Si–H nanotubes

The Molecular dynamics (MD) method was used to predict the thermal-stability and tensile properties of two single-walled Si nanotubes that are hydrogenated outside and both inside and outside respectively, i.e. the Si_o–H and Si_io–H nanotubes. Further, the axial-tensile properties of the two Si–H nanotubes were discussed by comparison with one (14,14) carbon nanotube. The obtained results show that: (1) the two Si–H nanotubes both have the Si skeletons with the structure similar to the {110} planes of single-crystal silicon, and they can stably exist only at the temperature lower than 200 and 125 K respectively and (2) the Si_o–H and Si_io–H nanotubes, respectively, have the tensile strength of 4.0 and 1.2 GPa as well as the fracture strain of 0.35 and 0.32; both their tensile strength and fracture strain are much lower than the corresponding ones of the (14,14) carbon-tube.