Analysis of deformation and contraction in cylindrical crystals due to dispirations or dislocations.

Cylindrical crystal structures are common in biology. The shape changes and movements of cylindrical crystals are basic to the understanding of the contractile mechanisms in biological systems such as tobacco mosaic viruses and the tail sheath of T-even bacteriophages. It has been suggested that the concept of defects in crystal physics can be applied to study these contractile mechanisms. The defect believed to be responsible for the shape changes of cylindrical crystals is known as a dispiration. Dispirations are characterized by the shear displacement on the slip plane through a screw symmetry operation. The elastic field of a dispiration can be decomposed into its translational (dislocation) and rotational (disclination) components. The magnitude of the translational and rotational displacements in a cylindrical crystal has been related to the crystal structural parameters. The passage of a dispiration along a helical plane in a cylindrical crystal can induce one of two types of shape changes. In one type, only the disclination component of the dispiration contributes to contraction, whereas in the other type, both the disclination and dislocation components are responsible for the shape change. Estimates of the magnitude of contraction are made in terms of the dimensional and structural parameters of the cylindrical crystal. The reversal of the direction of helical slip results in extension instead of contraction of the cylindrical crystal. The local elastic deformation of a dispiration dipole situated on the helical plane of a cylindrical crystal is examined. It has been shown that, for the first type of deformation mentioned above, closed form solutions of the stress field can be obtained by superposing the stress fields of two dispiration dipoles with slip planes parallel and normal to the cylinder axis, respectively. The approximations of shallow shell theory are adopted in the analysis. Future problems of biological interests are identified.     

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.     

Strain Field Mapping of Dislocations in a Ge/Si Heterostructure

Ge/Si heterostructure with fully strain-relaxed Ge film was grown on a Si (001) substrate by using a two-step process by ultra-high vacuum chemical vapor deposition. The dislocations in the Ge/Si heterostructure were experimentally investigated by high-resolution transmission electron microscopy (HRTEM). The dislocations at the Ge/Si interface were identified to be 90° full-edge dislocations, which are the most efficient way for obtaining a fully relaxed Ge film. The only defect found in the Ge epitaxial film was a 60° dislocation. The nanoscale strain field of the dislocations was mapped by geometric phase analysis technique from the HRTEM image. The strain field around the edge component of the 60° dislocation core was compared with those of the Peierls–Nabarro and Foreman dislocation models. Comparison results show that the Foreman model with a = 1.5 can describe appropriately the strain field around the edge component of a 60° dislocation core in a relaxed Ge film on a Si substrate.     

Plastic deformation behaviours of CuZr amorphous/crystalline nanolaminate: a molecular dynamics study

Abstract

The plastic deformation behaviours of Cu₅₀Zr₅₀/B2 CuZr amorphous/crystalline nanolaminate were studied at the atomic scale using molecular dynamics simulations. For pure metallic glass, the highly localised shear banding leads to the overall shear failure. And the plastic deformation of B2 CuZr crystal is mainly determined by the martensitic phase transformation. The composite material, nanolaminate, achieves great improvement of plastic deformation compared with the pure metallic glass and the pure crystal. This plasticity enhancement is attributed to two mechanisms: the suppression effect of the nucleation and propagation of the shear band and the regulating effect of the distribution of the shear transformation zones and phase transformation zones. The shear transformation zones can be induced by the interaction between phase transformation zones and interface. The immature shear band or shear transformations zones and phase transformation zones form a network to transmit the strain jointly within the entire sample. Amorphous/crystalline interface connects different layers and transmits the strain within the nanolaminate. Interfaces also plays the roles of source and sink of the shear transformation zones, shear band and phase transformation zones. On the basis of this plastic deformation mechanism, the present study provides a route for controlling the plasticity properties of amorphous/crystalline nanolaminate.     

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.     

Molecular dynamics study on deformation and mechanics of nanoscale Au/Cu multilayers under indentation

The effects of individual layer thickness, indentation velocity, and temperature on the mechanical properties and mechanics of nanoscale Au/Cu multilayers under indentation were studied using molecular dynamics simulations based on the many-body embedded-atom potential. The simulation results show that layer interfaces act as strong barriers that resist the propagation of dislocations, even at an extremely small individual layer thickness of 3 nm. The number of dislocations increases significantly and the growth of dislocations decreases with decreasing individual layer thickness. There is no clear relationship between the magnitude of the required indentation force and the number of film layers; however, the average required indentation force increases with increasing indentation velocity and decreasing temperature. During indentation at a relatively low velocity, dislocation propagation is more significant; the number of disordered atoms significantly increases at a relatively high indentation velocity.     

A computational study of the aerodynamic performance of a dragonfly wing section in gliding flight

A comprehensive computational fluid-dynamics-based study of a pleated wing section based on the wing of Aeshna cyanea has been performed at ultra-low Reynolds numbers corresponding to the gliding flight of these dragonflies. In addition to the pleated wing, simulations have also been carried out for its smoothed counterpart (called the 'profiled' airfoil) and a flat plate in order to better understand the aerodynamic performance of the pleated wing. The simulations employ a sharp interface Cartesian-grid-based immersed boundary method, and a detailed critical assessment of the computed results was performed giving a high measure of confidence in the fidelity of the current simulations. The simulations demonstrate that the pleated airfoil produces comparable and at times higher lift than the profiled airfoil, with a drag comparable to that of its profiled counterpart. The higher lift and moderate drag associated with the pleated airfoil lead to an aerodynamic performance that is at least equivalent to and sometimes better than the profiled airfoil. The primary cause for the reduction in the overall drag of the pleated airfoil is the negative shear drag produced by the recirculation zones which form within the pleats. The current numerical simulations therefore clearly demonstrate that the pleated wing is an ingenious design of nature, which at times surpasses the aerodynamic performance of a more conventional smooth airfoil as well as that of a flat plate. For this reason, the pleated airfoil is an excellent candidate for a fixed wing micro-aerial vehicle design.     

Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure

Cyanobacteria form a very large and diverse phylum of prokaryotes that perform oxygenic photosynthesis. Many species of cyanobacteria live colonially in long trichomes of hundreds to thousands of cells. Of the filamentous species, many are also motile, gliding along their long axis, and display photomovement, by which a trichome modulates its gliding according to the incident light. The latter has been found to play an important role in guiding the trichomes to optimal lighting conditions, which can either inhibit the cells if the incident light is too weak, or damage the cells if too strong. We have developed a computational model for gliding filamentous photophobic cyanobacteria that allows us to perform simulations on the scale of a Petri dish using over 10(5) individual trichomes. Using the model, we quantify the effectiveness of one commonly observed photomovement strategy--photophobic responses--in distributing large populations of trichomes optimally over a light field. The model predicts that the typical observed length and gliding speeds of filamentous cyanobacteria are optimal for the photophobic strategy. Therefore, our results suggest that not just photomovement but also the trichome shape itself improves the ability of the cyanobacteria to optimize their light exposure.     

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).     

Adhesive dynamics simulations of the shear threshold effect for leukocytes

Many experiments have measured the effect of force on the dissociation of single selectin bonds, but it is not yet clear how the force dependence of molecular dissociation can influence the rolling of cells expressing selectin molecules. Recent experiments using constant-force atomic force microscopy or high-resolution microscopic observations of pause-time distributions of cells in a flow chamber show that for some bonds, the dissociation rate is high at low force and initially decreases with force, indicating a catch bond. As the force continues to increase, the dissociation rate increases again, like a slip bond. It has been proposed that this catch-slip bond leads to the shear threshold effect, in which a certain level of shear rate is required to achieve rolling. We have incorporated a catch-slip dissociation rate into adhesive dynamics simulations of cell rolling. Using a relatively simple model for the shear-controlled association rate for selectin bonds, we were able to recreate characteristics of the shear threshold effect seen most prominently for rolling through L-selectin. The rolling velocity as a function of shear rate showed a minimum near 100 s-1. Furthermore, cells were observed to roll at a shear rate near the threshold, but detach and move more quickly when the shear rate was dropped below the threshold. Finally, using adhesive dynamics, we were able to determine ranges of parameters necessary to see the shear threshold effect in the rolling velocity. In summary, we found through simulation that the catch-slip behavior of selectin bonds can be responsible for the shear threshold effect.     

State Based Model of Long-Term Potentiation and Synaptic Tagging and Capture

Recent data indicate that plasticity protocols have not only synapse-specific but also more widespread effects. In particular, in synaptic tagging and capture (STC), tagged synapses can capture plasticity-related proteins, synthesized in response to strong stimulation of other synapses. This leads to long-lasting modification of only weakly stimulated synapses. Here we present a biophysical model of synaptic plasticity in the hippocampus that incorporates several key results from experiments on STC. The model specifies a set of physical states in which a synapse can exist, together with transition rates that are affected by high- and low-frequency stimulation protocols. In contrast to most standard plasticity models, the model exhibits both early- and late-phase LTP/D, de-potentiation, and STC. As such, it provides a useful starting point for further theoretical work on the role of STC in learning and memory.     

Intermonolayer friction and surface shear viscosity of lipid bilayer membranes

The flow behavior of lipid bilayer membranes is characterized by a surface viscosity for in-plane shear deformations, and an intermonolayer friction coefficient for slip between the two leaflets of the bilayer. Both properties have been studied for a variety of coarse-grained double-tailed model lipids, using equilibrium and nonequilibrium molecular dynamics simulations. For lipids with two identical tails, the surface shear viscosity rises rapidly with tail length, while the intermonolayer friction coefficient is less sensitive to the tail length. Interdigitation of lipid tails across the bilayer midsurface, as observed for lipids with two distinct tails, strongly enhances the intermonolayer friction coefficient, but hardly affects the surface shear viscosity. The simulation results are compared against the available experimental data.     

An experimental and computational investigation of the post-yield behaviour of trabecular bone during vertebral device subsidence

Interbody fusion device subsidence has been reported clinically. An enhanced understanding of the mechanical behaviour of the surrounding bone would allow for accurate predictions of vertebral subsidence. The multiaxial inelastic behaviour of trabecular bone is investigated at a microscale and macroscale level. The post-yield behaviour of trabecular bone under hydrostatic and confined compression is investigated using microcomputed tomography-derived microstructural models, elucidating a mechanism of pressure-dependent yielding at the macroscopic level. Specifically, microstructural trabecular simulations predict a distinctive yield point in the apparent stress–strain curve under uniaxial, confined and hydrostatic compression. Such distinctive apparent stress–strain behaviour results from localised stress concentrations and material yielding in the trabecular microstructure. This phenomenon is shown to be independent of the plasticity formulation employed at a trabecular level. The distinctive response can be accurately captured by a continuum model using a crushable foam plasticity formulation in which pressure-dependent yielding occurs. Vertebral device subsidence experiments are also performed, providing measurements of the trabecular plastic zone. It is demonstrated that a pressure-dependent plasticity formulation must be used for continuum level macroscale models of trabecular bone in order to replicate the experimental observations, further supporting the microscale investigations. Using a crushable foam plasticity formulation in the simulation of vertebral subsidence, it is shown that the predicted subsidence force and plastic zone size correspond closely with the experimental measurements. In contrast, the use of von Mises, Drucker–Prager and Hill plasticity formulations for continuum trabecular bone models lead to over prediction of the subsidence force and plastic zone.     

Brownian dynamics simulations of molecular recognition in an antibody-antigen system.

The crystal structure for an antibody-antigen system, that of the anti-hen egg lysozyme monoclonal antibody HyHEL-5 complexed to lysozyme, is used as the starting point for computer simulations of diffusional encounters between the two proteins. The investigation consists of two parts: first, the linearized Poisson-Boltzmann equation is solved to determine the long-range electrostatic forces between antibody and antigen, and then, the relative motion as influenced by these forces is modeled within Brownian motion theory. The effects of various point mutations on the calculated reaction rate are considered. It is found that charged residues close to the binding site exert the greatest influence in steering the proteins into a configuration favorable for their binding, while more distant mutations are qualitatively described by the Smoluchowski model for the mutual diffusion of two uniformly charged spheres. The antibody residues involved in forming salt links with the lysozyme, Glu-H35 and Glu-H50, appear to be particularly important in electrostatic steering, as neutralization of both of them yields reaction rates that are two to three orders of magnitude below those of wild-type rates. The relative rates obtained from the simulations can be tested through kinetic measurements on mutant protein complexes. Kinetically efficient partners can also be designed and constructed through directed mutagenesis.     

Shear-Induced Extensional Response Behaviors of Tethered von Willebrand Factor

We perform single-molecule flow experiments using confocal microscopy and a microfluidic device for shear rates up to 20,000 s⁻¹ and present results for the shear-induced unraveling and elongation of tethered von Willebrand factor (VWF) multimers. Further, we employ companion Brownian dynamics simulations to help explain details of our experimental observations using a parameterized coarse-grained model of VWF. We show that global conformational changes of tethered VWF can be accurately captured using a relatively simple mechanical model. Good agreement is found between experimental results and computational predictions for the threshold shear rate of extension, existence of nonhomogenous fluorescence distributions along unraveled multimer contours, and large variations in extensional response behaviors. Brownian dynamics simulations reveal the strong influence of varying chain length, tethering point location, and number of tethering locations on the underlying unraveling response. Through a complex molecule like VWF that naturally adopts a wide distribution of molecular size and has multiple binding sites within each molecule, this work demonstrates the power of tandem experiment and simulation for understanding flow-induced changes in biomechanical state and global conformation of macromolecules.     

Interferometric Studies of Growth Kinetics and Surface Morphology in Macromolecular Crystal Growth: Canavalin, Thaumatin, and Turnip Yellow Mosaic Virus

In situ laser Michelson interferometry was utilized to investigate mechanisms of growth and surface morphology in protein and virus crystallization, These included plant proteins canavalin and thaumatin and turnip yellow mosaic virus. The experimental apparatus allowed us to obtain interferometric patterns and investigate growth kinetics from growing macromolecular crystals as small as 20 μm. For the crystallization of canavalin, dislocations are the sources of growth steps on the surfaces. Supersaturation and time dependencies of the normal growth rates, tangential growth step velocities, and the slopes of the dislocation hillocks were measured. The kinetic coefficient β (rate of incorporation of protein molecules into the growing crystal) was estimated for canavalin to be 9 × 10^-4 cm/sec. This is among the first estimates of such fundamental kinetic parameters for macromolecular crystallization. The change in the activities of dislocation sources under different growth conditions was also analyzed. Michelson interferometry was clearly demonstrated to be a useful tool for quantitative studies of macromolecular crystal growth.     

Correlation between sagging and shear elasticity in pectin, gelatin and polyacrylamide gels

The relationship between the height of gels determined by a sag test and their elastic shear modulus (G′) has been both investigated experimentally and simulated using a finite element analysis for the inhomogeneous deformation of gels due to gravity. It was assumed in the simulations that gels can be modeled as incompressible linear elastic materials. General relationships between the sag of gels and their elastic modulus were obtained from the simulations for slip and no-slip conditions. The relationships were tested experimentally on pectin, gelatin and polyacrylamide gels with a range of concentrations and rigidities. The good agreement between the predictions and the results shows that these gels can be modeled accurately as incompressible elastic materials. A standard 150° SAG pectin gel, which sags 23.5% in the SAG test, has G′ moduli of 429 and 379 Pa under slip and no-slip conditions, respectively.     

von Willebrand factor unfolding mediates platelet deposition in a model of high-shear thrombosis

Thrombosis under high-shear conditions is mediated by the mechanosensitive blood glycoprotein von Willebrand factor (vWF). vWF unfolds in response to strong flow gradients and facilitates rapid recruitment of platelets in flowing blood. While the thrombogenic effect of vWF is well recognized, its conformational response in complex flows has largely been omitted from numerical models of thrombosis. We recently presented a continuum model for the unfolding of vWF, where we represented vWF transport and its flow-induced conformational change using convection-diffusion-reaction equations. Here, we incorporate the vWF component into our multi-constituent model of thrombosis, where the local concentration of stretched vWF amplifies the deposition rate of free-flowing platelets and reduces the shear cleaning of deposited platelets. We validate the model using three benchmarks: in vitro model of atherothrombosis, a stagnation point flow, and the PFA-100, a clinical blood test commonly used for screening for von Willebrand disease (vWD). The simulations reproduced the key aspects of vWF-mediated thrombosis observed in these experiments, such as the thrombus location, thrombus growth dynamics, and the effect of blocking platelet-vWF interactions. The PFA-100 simulations closely matched the reported occlusion times for normal blood and several hemostatic deficiencies, namely, thrombocytopenia, vWD type 1, and vWD type 3. Overall, this multi-constituent model of thrombosis enables macro-scale 3D simulations of thrombus formation in complex geometries over a wide range of shear rates and accounts for qualitative and quantitative hemostatic deficiencies in patient blood.     

The bacterial flagellum as an imperfect cylindrical crystal: flagellar geometry, movement and polymorphism, and the role of partial dislocations

A pairing attraction between helical turns of subunits in a cylindrical crystal, like that in the dahlemense strain of tobacco mosaic virus, can cause the axis of the rod or crystal to become helical. This is true only if the number of helices is odd. The shape of a bacterial flagellum can be accounted for then if, as Caspar &; Holmes and Klug have suggested, rows of its subunits exhibit such a pairing interaction. Klug's thoughts on bacterial flagella are developed and extended into a model that accounts qualitatively for geometry, movement and polymorphism of flagella. If the number of helices between which there is a pairing interaction is odd, then the crystal is an imperfect cylindrical crystal. The geometry of such crystals is described. They contain a line defect, termed here an antiphase boundary, across which the pairing interaction is reversed. The boundary is a line of expansion on the convex side of a curved filament. Movement of flagella is explained by circumferential displacement of the antiphase boundary. One polymorphic form can convert to another if a dislocation passes along it. Straight flagella are perfect cylindrical crystals with no antiphase boundary.     

莫桑鼻给非鲫滤泡闭锁中卵黄溶致液晶的缺陷

采用冰冻蚀刻电镜术揭示了莫桑鼻给非鲫滤泡闭锁过程中卵黄溶致液晶(YLLC)的缺陷.缺陷主要类型为共焦域、壁、位错(螺旋平动位错和刃位错)、向错、Grandjiean台阶和箍缩.讨论了生物体内YLLC缺陷产生的可能原因以及生物体内溶致液晶对生物膜性结构的形成和细胞内外物质运输的作用.