Atomistic modelling of interface structure and deformation mechanisms in the Al/GaN multilayer under compression

The properties of ohmic contact and thermal boundary conductance between Al and GaN have been studied extensively, but the interface structures and deformation mechanisms in the Al/GaN multilayer can be rarely found in literatures. By molecular dynamics (MD) simulations, we systematically studied the interface structures and structural deformations in the Al/GaN multilayer. Two kinds of interface structures are identified according to the different terminal surfaces of GaN; glide-set terminal interface and shuffle-set terminal interface. Further analysis shows that interface has the maximum stress and misfit lines have the maximum stress values, which serve as the dislocation sources in the Al layer due to the larger stress in the interface. The mechanical responses of the Al/GaN multilayer exhibit a minor stage and some distinctive drops in the stress–strain curve. The first stage is associated with the dislocation nucleation from the interface. Upon further compression, more slip systems appear in the Al layer and dislocation nucleation in GaN could induce drops in curves. Meanwhile, the multiplications of dislocations cause strain hardening behaviours.     

Shearing in a Biomimetic Apatite-Protein Composite: Molecular Dynamics of Slip Zone Formation,Plastic Flow and Backcreep Mechanisms

We report molecular dynamics simulations of shear in a biomimetic hydroxyapatite-collagen composite. Our model exhibits elastic properties fully dominated by the inorganic component. However, beyond the elastic regime the biomolecules along with the hierarchical nature of the composite account for the formation of structure-inherent slip zones. These accommodate shear without compromising the overall structure and lead to the sliding of intrinsically defined rods at roughly constant restoring force. Upon releasing load, rod displacement is reversible and backcreep is observed as gradual ionic rearrangement in the slip zone, subjected to an activation barrier.     

Mechanical properties of collagen fibrils

The formation of collagen fibers from staggered subfibrils still lacks a universally accepted model. Determining the mechanical properties of single collagen fibrils (diameter 50-200 nm) provides new insights into collagen structure. In this work, the reduced modulus of collagen was measured by nanoindentation using atomic force microscopy. For individual type 1 collagen fibrils from rat tail, the modulus was found to be in the range from 5 GPa to 11.5 GPa (in air and at room temperature). The hypothesis that collagen anisotropy is due to the subfibrils being aligned along the fibril axis is supported by nonuniform surface imprints performed by high load nanoindentation.     

Molecular motors: how to make models that can be used to convey the concept of molecular ratchets and thermal capture

A wide variety of cellular processes use molecular motors, including processive motors that move along some form of track (e.g., myosin with actin, kinesin or dynein with tubulin) and polymerases that move along a template (e.g., DNA and RNA polymerases, ribosomes). In trying to understand how these molecular motors actually move, many apply their understanding of how man-made motors work: the latter use some form of energy to exert a force or torque on its load. However, quite a different mechanism has been proposed to possibly account for the movement of molecular motors. Rather than hydrolyzing ATP to push or pull their load, they might use their own thermal vibrational energy as well as that of their load and their environment to move the load, capturing those movements that occur along a desired vector or axis and resisting others; ATP hydrolysis is required to make backward movements impossible. This intriguing thermal capture or Brownian ratchet model is relatively more difficult to convey to students. In this report, we describe several teaching aids that are very easily constructed using widely available household materials to convey the concept of a molecular ratchet.     

Growth of Collagen Fibril Seeds from Embryonic Tendon: Fractured Fibril Ends Nucleate New Tip Growth

Collagen fibrils are the principal tensile element of vertebrate tissues where they occur in the extracellular matrix as spatially organised arrays. A major challenge is to understand how the mechanisms of nucleation, growth and remodelling yield fibrils of tissue-specific diameter and length. Here we have developed a seeding system whereby collagen fibrils were isolated from avian embryonic tendon and added to purified collagen solution, in order to characterise fibril surface nucleation and growth mechanisms. Fragmentation of tendon in liquid nitrogen followed by Dounce homogenisation generated fibril length fragments. Most (> 94%) of the fractured ends of fibrils, which show an abrupt square profile, were found to act as nucleation sites for further growth by molecular accretion. The mechanism of this nucleation and growth process was investigated by transmission electron microscopy, atomic force microscopy and scanning transmission electron microscopy mass mapping. Typically, a single growth spur occurred on the N-terminal end of seed fibrils whilst twin spurs frequently formed on the C-terminal end before merging into a single tip projection. The surface nucleation and growth process generated a smoothly tapered tip that achieved maximum diameter when the axial extension reached ∼ 13 μm. Lateral growth also occurred along the entire length of all seed fibrils that contained tip projections. The data support a model of collagen fibril growth in which the broken ends of fibrils are nucleation sites for propagation in opposite axial directions. The observed fibril growth behaviour has direct relevance to tendon matrix remodelling and repair processes that might involve rupture of collagen fibrils.     

Modeling the effects of particles,interstitials, vacancies and tip geometry on indentation-induced plasticity

In this work, which is a follow-up of an earlier work by the authors in this journal, we discuss the effects of particles, interstitials, vacancies and indenter-tip geometry on indentation-induced plasticity. A nano-indentation model based on a close-packed array of straws was used. Upon indentation with a cylindrical indenter, the results observed in situ, match qualitatively computer atomistic and finite-element simulation models. This model helps explain the phenomenon and physical reasons for annihilation of vacancies. It also shows the strong effect of interstitials on the inception of plasticity at their sites. It shows that a rigid particle acts as a stress concentrator even away from the indenter. On indentation with a flat indenter, curling of atoms at the indenter edges was observed, along with slip lines reported in the literature.     

Mechanical property determination of bone through nano- and micro-indentation testing and finite element simulation

Measurement of the mechanical properties of bone is important for estimating the stresses and strains exerted at the cellular level due to loading experienced on a macro-scale. Nano- and micro-mechanical properties of bone are also of interest to the pharmaceutical industry when drug therapies have intentional or non-intentional effects on bone mineral content and strength. The interactions that can occur between nano- and micro-indentation creep test condition parameters were considered in this study, and average hardness and elastic modulus were obtained as a function of indentation testing conditions (maximum load, load/unload rate, load-holding time, and indenter shape). The results suggest that bone reveals different mechanical properties when loading increases from the nano- to the micro-scale range (microN to N), which were measured using low- and high-load indentation testing systems. A four-parameter visco-elastic/plastic constitutive model was then applied to simulate the indentation load vs. depth response over both load ranges. Good agreement between the experimental data and finite element model was obtained when simulating the visco-elastic/plastic response of bone. The results highlight the complexity of bone as a biological tissue and the need to understand the impact of testing conditions on the measured results.     

Age-related changes in mouse bone permeability

The determination of lacunar-canalicular permeability is essential for understanding local fluid flow in bone, which may indicate how bone senses changes in the mechanical environment to regulate mechano-adaptation. The estimates of lacunar-canalicular permeability found in the literature vary by up to eight orders of magnitude, and age-related permeability changes have not been measured in non-osteonal mouse bone. The objective of this study is to use a poroelastic approach based on nanoindentation data to characterize lacunar-canalicular permeability in murine bone as a function of age. Nine wild type C57BL/6 mice of different ages (2, 7 and 12 months) were used. Three tibiae from each age group were embedded in epoxy resin, cut in half and indented in the longitudinal direction in the mid-cortex using two spherical fluid indenter tips (R=238 μm and 500 μm). Results suggest that the lacunar-canalicular intrinsic permeability of mouse bone decreases from 2 to 7 months, with no significant changes from 7 to 12 months. The large indenter tip imposed larger contact sizes and sampled larger ranges of permeabilities, particularly for the old bone. This age-related difference in the distribution was not seen for indents with the smaller radius tip. We conclude that the small tip effectively measured lacunar-canalicular permeability, while larger tip indents were influenced by vascular permeability. Exploring the age-related changes in permeability of bone measured by nanoindentation will lead to a better understanding of the role of fluid flow in mechano-transduction. This understanding may help indicate alterations in bone adaptation and remodeling.     

Motor mechanisms of balance during quiet standing.

The purpose of this paper is to highlight the motor mechanisms involved in balance as the human, as a biped, continuously defends against gravitational and internal forces to maintain a safe posture. The search for these mechanisms needs precise and valid 3D measurements including both limbs plus valid biomechanical models. The literature shows the need for two force platforms to separate the mechanisms at the ankle and hip (load/unload mechanism). Also, precise measures ( approximately 0.03 mm) of markers on a multi-segment 3D bilateral model are required to record the minute trajectories of all segments and joints. The controlled variable, center-of-mass, is seen to be virtually in phase with the controlling variable, the center-of-pressure, which suggests a 0th order system where a simple series elastic spring could maintain balance. The first model involves a mass/spring/damper of medial/lateral balance: the stiffness was varied with stance width and the predicted sway from a spring controlled inverted pendulum closely matched the experimentally measured stiffness and sway. The second was a non-linear model of the plantarflexor series elastic elements which resulted in three closely validated predictions of anterior/posterior balance: the locus of the gravitational load line, the predicted ankle moment and the ankle stiffness at the operating point.     

The nanoindentation responses of nickel surfaces with different crystal orientations

Molecular dynamics (MD) simulations are applied to elucidate the anisotropic characteristics in the material responses for crystallographic nickel substrates with (100), (110) and (111) surface orientations during nanoindentation, compensating for the experimental limitation of nanoindentation—particularly for pure nickel substrates of three crystallographic orientations. This study examines several factors under indentation: three-dimensional phases of plastic deformation which correspond to atomic stress distributions, pile-up patterns at maximum indentation depth, and extracted material properties at different crystallographic orientations. The present results reveal that the strain energy of the substrate exerted by the tip is stored by the formation of the homogeneous nucleation, and is dissipated by the dislocation sliding of the {111} plane. The steep variations of the indentation curve from the local peak to the local minimums are affected by the numbers of slip angle of {111} sliding plane. The pile-up patterns of the three nickel substrates prove that the crystalline nickel materials demonstrate the pile-up phenomenon from nanoindentation on the nano-scale. The three crystallographic nickel substrates exhibit differing amounts of pile-up dislocation spreading at different crystallographic orientations. Finally, the effects of surface orientation in material properties of FCC nickel material on the nano-scale are observable through the slip angle numbers of {111} sliding planes which influence hardness values, as well as the cohesive energy of different crystallographic surfaces that indicate Young's modulus.     

Hydrodynamic and Thermal Slip Effect on Double-Diffusive Free Convective Boundary Layer Flow of a Nanofluid Past a Flat Vertical Plate in the Moving Free Stream

The effects of hydrodynamic and thermal slip boundary conditions on the double-diffusive free convective flow of a nanofluid along a semi-infinite flat solid vertical plate are investigated numerically. It is assumed that free stream is moving. The governing boundary layer equations are non-dimensionalized and transformed into a system of nonlinear, coupled similarity equations. The effects of the controlling parameters on the dimensionless velocity, temperature, solute and nanofluid concentration as well as on the reduced Nusselt number, reduced Sherwood number and the reduced nanoparticle Sherwood number are investigated and presented graphically. To the best of our knowledge, the effects of hydrodynamic and thermal slip boundary conditions have not been investigated yet. It is found that the reduced local Nusselt, local solute and the local nanofluid Sherwood numbers increase with hydrodynamic slip and decrease with thermal slip parameters.     

Finite element estimates of interface stress in the trans-tibial prosthesis using gap elements are different from those using automated contact

When compared with automated contact methods of finite element (FE) analyses, gap elements have certain inherent disadvantages in simulating large slip of compliant materials on stiff surfaces. However, automated contact has found limited use in the biomechanical literature. A non-linear, three-dimensional, geometrically accurate, FE analysis of the trans-tibial limb-socket prosthetic system was used to compare an automated contact interface model with a gap element model, and to evaluate the sensitivity of automated contact to interfacial coefficient of friction (COF). Peak normal stresses and resultant shear stresses were higher in the gap element model than in the automated contact model, while the maximum axial slip was less. Under proximally directed load, compared with automated contact, gap elements predicted larger areas of stress concentration that were located more distally. Gap elements did not predict any relative slip at the distal end, and also transmitted a larger proportion of axial load as shear stress. Both models demonstrated non -linear sensitivity to COF, with larger variation at lower magnitudes of COF. By imposing physical connections between interface surfaces, gap elements distort the interface stress distributions under large slip. Automated contact methods offer an attractive alternative in applications such as prosthetic FE modeling, where the initial position of the limb in the socket is not known, where local geometric features have high design significance, and where large slip occurs under load.     

Recovering from Laboratory-Induced slips and trips causes high levels of lumbar muscle activity and spine loading

Slips, trips, and falls are some of the most substantial and prevalent causes of occupational injuries and fatalities, and these events may contribute to low-back problems. We quantified lumbar kinematics (i.e., lumbar angles relative to pelvis) and kinetics during unexpected slip and trip perturbations, and during normal walking, among 12 participants (6F, 6 M). Individual anthropometry, lumbar muscle geometry, and lumbar angles, along with electromyography from 14 lumbar muscles were used as input to a 3D, dynamic, EMG-based model of the lumbar spine. Results indicated that, in comparison with values during normal walking, lumbar range of motion, lumbosacral (L5/S1) loads, and lumbar muscle activations were all significantly higher during the slip and trip events. Maximum L5/S1 compression forces exceeded 2700 N during slip and trip events, compared with ∼ 1100 N during normal walking. Mean values of L5/S1 anteroposterior (930 N), and lateral (800 N) shear forces were also substantially larger than the shear force during the normal walking (230 N). These observed levels of L5/S1 reaction forces, along with high levels of bilateral lumbar muscle activities, suggest the potential for overexertion injuries and tissue damage during unexpected slip and trip events, which could contribute to low back injuries. Outcomes of this study may facilitate the identification and control of specific mechanisms involved with low back disorders consequent to slips or trips.     

A modified active Brownian dynamics model using asymmetric energy conversion and its application to the molecular motor system

We consider a modified energy depot model in the overdamped limit using an asymmetric energy conversion rate, which consists of linear and quadratic terms in an active particle’s velocity. In order to analyze our model, we adopt a system of molecular motors on a microtubule and employ a flashing ratchet potential synchronized to a stochastic energy supply. By performing an active Brownian dynamics simulation, we investigate effects of the active force, thermal noise, external load, and energy-supply rate. Our model yields the stepping and stalling behaviors of the conventional molecular motor. The active force is found to facilitate the forwardly processive stepping motion, while the thermal noise reduces the stall force by enhancing relatively the backward stepping motion under external loads. The stall force in our model decreases as the energy-supply rate is decreased. Hence, assuming the Michaelis–Menten relation between the energy-supply rate and the an ATP concentration, our model describes ATP-dependent stall force in contrast to kinesin-1.     

Protein retention and localization in the endoplasmic reticulum and the golgi apparatus.

Protein transport along the secretory pathway is supported by a noria of vesicles that bud and fuse, load and unload their cargo from one compartment into the other. However, despite this constant flow-through of proteins and lipids the various compartments of the secretory pathway are able to maintain their own specific composition. Here, we discuss recent insights into mechanisms of protein retention and localization that are necessary for the maintenance of endoplasmic reticulum (ER)- and Golgi-associated typical functions such as protein folding and glycosylation in plant cells.     

Intra-abdominal pressure mechanism for stabilizing the lumbar spine

Currently, intra-abdominal pressure (IAP) is thought to provide stability to the lumbar spine but the exact principles have yet to be specified. A simplified physical model was constructed and theoretical calculations performed to illustrate a possible intra-abdominal pressure mechanism for stabilizing the spine. The model consisted of an inverted pendulum with linear springs representing abdominal and erector spinae muscle groups. The IAP force was simulated with a pneumatic piston activated with compressed air. The critical load of the model was calculated theoretically based on the minimum potential energy principle and obtained experimentally by increasing weight on the model until the point of buckling. Two distinct mechanisms were simulated separately and in combination. One was antagonistic flexor extensor muscle coactivation and the second was abdominal muscle activation along with generation of IAP. Both mechanisms were effective in stabilizing the model of a lumbar spine. The critical load and therefore the stability of the spine model increased with either increased antagonistic muscle coactivation forces or increased IAP along with increased abdominal spring force. Both mechanisms were also effective in providing mechanical stability to the spine model when activated simultaneously. Theoretical calculation of the critical load agreed very well with experimental results (95.5% average error). The IAP mechanism for stabilizing the lumbar spine appears preferable in tasks that demand trunk extensor moment such as lifting or jumping. This mechanism can increase spine stability without the additional coactivation of erector spinae muscles.     

Overexpression of RCN1 and RCN2, rice TERMINAL FLOWER 1/CENTRORADIALIS homologs,confers delay of phase transition and altered panicle morphology in rice

TERMINAL FLOWER 1 (TFL1)/CENTRORADIALIS (CEN)-like genes play important roles in determining plant architecture, mainly by controlling the timing of phase transition. To investigate the possibility of similar mechanisms operating in the control of inflorescence architecture in rice, we analysed the functions of RCN1 and RCN2, rice TFL1/CEN homologs. Constitutive overexpression of RCN1 or RCN2 in Arabidopsis caused a late-flowering and highly branching phenotype, indicating that they possess conserved biochemical functions as TFL1. In 35S::RCN1 and 35S::RCN2 transgenic rice plants, the delay of transition to the reproductive phase was observed. The transgenic rice plants exhibited a more branched, denser panicle morphology. Detailed observation of the panicle structure revealed that the phase change from the branch shoot to the floral meristem state was also delayed, leading to the generation of higher-order panicle branches. These results suggest rice has a pathway that can respond to the overexpressed TFL1/CEN-like functions, and the molecular mechanisms controlling the phase transition of meristems are conserved between grass and dicot species, at least to some extent.     

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).     

The influence of grafted polymer architecture and fluid hydrodynamics on protein separation by entropic interaction chromatography

Entropic interaction chromatography (EIC) provides efficient size-based separation of protein mixtures through the entropy change associated with solute partitioning into a layer of hydrophilic homopolymer that has been end-grafted within the pores of a macroporous chromatography support. In this work, surface-initiated atom-transfer radical polymerization (ATRP) is used to prepare a library of EIC stationary phases covering a wide range of grafted-chain densities and molecular weights. Exhaustive chain cleavage and analysis by saponification and GPC-MALLS, respectively, show that the new ATRP synthesis procedure allows for excellent control over graft molecular weight and polydispersity. The method is used to prepare high-density grafts (up to 0.164 +/- 0.005 chains/nm(2)) that extend the range of EIC applications to include efficient buffer-exchange and desalting of protein preparations. Reducing the graft density allows for greater partitioning of high molecular weight solutes, extending the linear range of the selectivity curve. Increasing graft molecular weight also alters selectivity, but more directly affects column capacity by increasing the volume of the grafted layer. Protein partitioning in high-density EIC columns is found to decrease with mobile-phase velocity (u). Although solute mass transfer resistances leading to an increase in plate height can explain this effect, pressure drop data across the column are indicative of weak convective flow through at least a fraction of the grafted architecture. Modeling of the grafted brush properties in the presence of solvent flow by subjecting a self-consistent-field theory representation of the brush to a viscous shear force predicts that the grafted chains will tilt and elongate in the direction of flow. The shear force may therefore act to reduce the number of conformations available to chains, increasing their rigidity without significantly altering the thickness of the grafted layer. A reduction in protein partitioning is then predicted when the dependence on u of the solute entropy loss is stronger than that of the grafted polymer, a condition met at high graft densities.     

Nucleation and growth of macrofibrils in trichocyte (hard-alpha) keratins

The intermediate filaments (IF) in trichocyte (hard-alpha) keratin form ordered aggregates that are infiltrated by sulfur-rich and tyrosine-rich proteins during fiber development to give a filament-matrix texture, which is stabilized in the later stages by the formation of disulfide linkages. Two polymorphic forms of macrofibril are found in the cortical cells of fine Merino wool. In the first the packing of the IF in the macrofibril is quasi-hexagonal whilst in the second the IF are packed in cylindrical sheets around a central core. In hairs the second type generally predominate. In the present contribution specific models for the mechanisms of nucleation and growth are developed for the two types of macrofibril and their applicability tested by analyzing transmission electron micrographs of wool and hair. Evidence is presented which supports the idea that sheet formation plays an important role in both types of macrofibril assembly and it is suggested that differing intersheet interactions are responsible for the differences between the ortho- and para-types. It is shown that the increase in IF tilt with radius in the ortho-type can be related to the surface lattice of the IF as determined from X-ray diffraction studies. Two possible types of intersheet interaction in the ortho-type are discussed, the first leading to an increase of around 0.5 degrees in IF tilt per layer and the second leading to a much larger tilt of 9.4 degrees per layer. A crude estimate based on the decrease in visibility of the IF with increasing radius in cross-section yielded a value of 0.35 degrees -0.7 degrees.