Mechanical Failure Mode of Metal Nanowires: Global Deformation versus Local Deformation.
Ontology highlight
ABSTRACT:
SUBMITTER: Ho DT
PROVIDER: S-EPMC4471887 | biostudies-other | 2015
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Crystal deformation mechanisms and mechanical behaviors in semiconductor nanowires (NWs), in particular ZnSe NWs, exhibit a strong orientation dependence. However, very little is known about tensile deformation mechanisms for different crystal orientations. Here, the dependence of crystal orientations on mechanical properties and deformation mechanisms of zinc-blende ZnSe NWs are explored using molecular dynamics simulations. We find that the fracture strength of [111]-oriented ZnSe NWs shows a higher value than that of [110] and [100]-oriented ZnSe NWs. Square shape ZnSe NWs show greater value in terms of fracture strength and elastic modulus compared to a hexagonal shape at all considered diameters. With increasing temperature, the fracture stress and elastic modulus exhibit a sharp decrease. It is observed that the {111} planes are the deformation planes at lower temperatures for the [100] orientation; conversely, when the temperature is increased, the {100} plane is activated and contributes as the second principal cleavage plane. Most importantly, the [110]-directed ZnSe NWs show the highest strain rate sensitivity compared to the other orientations due to the formation of many different cleavage planes with increasing strain rates. The calculated radial distribution function and potential energy per atom further validates the obtained results. This study is very important for the future development of efficient and reliable ZnSe NWs-based nanodevices and nanomechanical systems.
| S-EPMC9981763 | biostudies-literature
Project description:MotivationNetwork alignment (NA) aims to find regions of similarities between species' molecular networks. There exist two NA categories: local (LNA) and global (GNA). LNA finds small highly conserved network regions and produces a many-to-many node mapping. GNA finds large conserved regions and produces a one-to-one node mapping. Given the different outputs of LNA and GNA, when a new NA method is proposed, it is compared against existing methods from the same category. However, both NA categories have the same goal: to allow for transferring functional knowledge from well- to poorly-studied species between conserved network regions. So, which one to choose, LNA or GNA? To answer this, we introduce the first systematic evaluation of the two NA categories.ResultsWe introduce new measures of alignment quality that allow for fair comparison of the different LNA and GNA outputs, as such measures do not exist. We provide user-friendly software for efficient alignment evaluation that implements the new and existing measures. We evaluate prominent LNA and GNA methods on synthetic and real-world biological networks. We study the effect on alignment quality of using different interaction types and confidence levels. We find that the superiority of one NA category over the other is context-dependent. Further, when we contrast LNA and GNA in the application of learning novel protein functional knowledge, the two produce very different predictions, indicating their complementarity. Our results and software provide guidelines for future NA method development and evaluation.Availability and implementationSoftware: http://www.nd.edu/~cone/LNA_GNA CONTACT: : tmilenko@nd.eduSupplementary information: Supplementary data are available at Bioinformatics online.
| S-EPMC5048063 | biostudies-literature
Project description:Growing experimental evidence suggests that mechanical tension plays a significant role in determining the growth, guidance, and function of neurons. Mechanical tension in axons contributes to neurotransmitter clustering at the Drosophila neuromuscular junction (NMJ) and is actively regulated by neurons both in vitro and in vivo. In this work, we applied mechanical strain on in vivo Drosophila neurons and in vitro Aplysia neurons and studied their vesicle dynamics by live-imaging. Our experiments show that mechanical stretch modulates the dynamics of vesicles in two different model systems: (1) The global accumulation of synaptic vesicles (SV) at the Drosophila NMJ and (2) the local motion of individual large dense core vesicles (LDCV) in Aplysia neurites. Specifically, a sustained stretch results in enhanced SV accumulation in the Drosophila NMJ. This increased SV accumulation occurs in the absence of extracellular Ca(2+), plateaus after approximately 50 min, and persists for at least 30 min after stretch is reduced. On the other hand, mechanical compression in Aplysia neurites immediately disrupts LDCV motion, leading to decreased range and processivity. This impairment of LDCV motion persists for at least 15 min after tension is restored. These results show that mechanical stretch modulates both local and global vesicle dynamics and strengthens the notion that tension serves a role in regulating neuronal function.
| S-EPMC3445628 | biostudies-literature
Project description:A hallmark of tissue ageing is the irreversible oxidative modification of its proteins. We show that single proteins, kept unfolded and extended by a mechanical force, undergo accelerated ageing in times scales of minutes to days. A protein forced to be continuously unfolded completely loses its ability to contract by folding, becoming a labile polymer. Ageing rates vary among different proteins, but in all cases they lose their mechanical integrity. Random oxidative modification of cryptic side chains exposed by mechanical unfolding can be slowed by the addition of antioxidants such as ascorbic acid, or accelerated by oxidants. By contrast, proteins kept in the folded state and probed over week-long experiments show greatly reduced rates of ageing. We demonstrate a novel approach whereby protein ageing can be greatly accelerated: the constant unfolding of a protein for hours to days is equivalent to decades of exposure to free radicals under physiological conditions.
| S-EPMC5540753 | biostudies-literature
Project description:Coiled coils are important structural motifs formed by two or more amphipathic ?-helices that twist into a supercoil. These motifs are found in a wide range of proteins, including motor proteins and structural proteins, that are known to transmit mechanical loads. We analyze atomically detailed simulations of coiled-coil cracking under load with Milestoning. Milestoning is an approach that captures the main features of the process in a network, quantifying kinetics and thermodynamics. A 112-residue segment of the ?-myosin S2 domain was subjected to constant-magnitude (0-200 pN) and constant-direction tensile forces in molecular dynamics simulations. Twenty 20 ns straightforward simulations at several load levels revealed that initial single-residue cracking events (? > 90°) at loads <100 pN were accompanied by rapid refolding without either intra- or interhelix unfolding propagation. Only initial unfolding events at the highest load (200 pN) regularly propagated along and between helices. Analysis of hydrophobic interactions and of interhelix hydrogen bonds did not show significant variation as a function of load. Unfolding events were overwhelmingly located in the vicinity of E929, a charged residue in a hydrophobic position of the heptad repeat. Milestoning network analysis of E929 cracking determined that the mean first-passage time ranges from 20 ns (200 pN) to 80 ns (50 pN), which is ?20 times the mean first-passage time of an isolated helix with the same sequence.
| S-EPMC3752098 | biostudies-literature
Project description:Silicon nanowires of various diameters were irradiated with 100 keV and 300 keV Ar(+) ions on a rotatable and heatable stage. Irradiation at elevated temperatures above 300 °C retains the geometry of the nanostructure and sputtering can be gauged accurately. The diameter dependence of the sputtering shows a maximum if the ion range matches the nanowire diameter, which is in good agreement with Monte Carlo simulations based on binary collisions. Nanowires irradiated at room temperature, however, amorphize and deform plastically. So far, plastic deformation has not been observed in bulk silicon at such low ion energies. The magnitude and direction of the deformation is independent of the ion-beam direction and cannot be explained with mass-transport in a binary collision cascade but only by collective movement of atoms in the collision cascade with the given boundary conditions of a high surface to volume ratio.
| S-EPMC4463547 | biostudies-literature
Project description:?(v)?(3) integrin-mediated cell adhesion is crucially influenced by how far ligands are spaced apart. To evaluate the impact of local ligand density versus global ligand density of a given surface, we used synthetic micronanostructured cell environments with user-defined ligand spacing and patterns to investigate cellular adhesion. The development of stable focal adhesions, their number, and size as well as the cellular adhesion strength proved to be influenced by local more than global ligand density.
| S-EPMC3806292 | biostudies-literature
Project description:Ion channels turn diverse types of inputs, ranging from neurotransmitters to physical forces, into electrical signals. Channel responses to ligands generally rely on binding to discrete sensor domains that are coupled to the portion of the channel responsible for ion permeation. By contrast, sensing physical cues such as voltage, pressure, and temperature arises from more varied mechanisms. Voltage is commonly sensed by a local, domain-based strategy, whereas the predominant paradigm for pressure sensing employs a global response in channel structure to membrane tension changes. Temperature sensing has been the most challenging response to understand and whether discrete sensor domains exist for pressure and temperature has been the subject of much investigation and debate. Recent exciting advances have uncovered discrete sensor modules for pressure and temperature in force-sensitive and thermal-sensitive ion channels, respectively. In particular, characterization of bacterial voltage-gated sodium channel (BacNaV) thermal responses has identified a coiled-coil thermosensor that controls channel function through a temperature-dependent unfolding event. This coiled-coil thermosensor blueprint recurs in other temperature sensitive ion channels and thermosensitive proteins. Together with the identification of ion channel pressure sensing domains, these examples demonstrate that "local" domain-based solutions for sensing force and temperature exist and highlight the diversity of both global and local strategies that channels use to sense physical inputs. The modular nature of these newly discovered physical signal sensors provides opportunities to engineer novel pressure-sensitive and thermosensitive proteins and raises new questions about how such modular sensors may have evolved and empowered ion channel pores with new sensibilities.
| S-EPMC5945320 | biostudies-literature
Project description:During knee movement, femoral cartilage articulates against cartilage from the tibial plateau, and the resulting mechanical behavior is yet to be fully characterized. The objectives of this study were to determine (1) the overall and depth-varying axial and shear strains and (2) the associated moduli, of femoral and tibial cartilages during the compression and shearing of apposing tibial and femoral samples. Osteochondral blocks from human femoral condyles (FCs) characterized as normal and donor-matched lateral tibial plateau (TP) were apposed, compressed 13%, and subjected to relative lateral motion. When surfaces began to slide, axial (-E(zz)) and shear (E(xz)) strains and compressive (E) and shear (G) moduli, overall and as a function of depth, were determined for femoral and tibial cartilages. Tibial -E(zz) was approximately 2-fold greater than FC -E(zz) near the surface (0.38 versus 0.22) and overall (0.16 versus 0.07). Near the surface, E(xz) of TP was 8-fold higher than that of FC (0.41 versus 0.05), while overall E(xz) was 4-fold higher (0.09 versus 0.02). For TP and FC, -E(zz) and E(xz) were greatest near the surface and decreased monotonically with depth. E for FC was 1.7-fold greater than TP, both near the surface (0.40 versus 0.24MPa) and overall (0.76 versus 0.47MPa). Similarly, G was 7-fold greater for FC (0.22MPa) than TP near the surface (0.03MPa) and 3-fold higher for FC (0.38MPa) than TP (0.13MPa) overall. These results indicate that tibial cartilage deforms and strains more axially and in shear than the apposing femoral cartilage during tibial-femoral articulation, reflecting their respective moduli.
| S-EPMC2882527 | biostudies-literature
Project description:The measurement of Poisson's ratio of nanomaterials is extremely challenging. Here we report a lateral atomic force microscope experimental method to electromechanically measure the Poisson's ratio and gauge factor of individual nanowires. Under elastic loading conditions we monitor the four-point resistance of individual metallic nanowires as a function of strain and different levels of electrical stress. We determine the gauge factor of individual wires and directly measure the Poisson's ratio using a model that is independently validated for macroscopic wires. For macroscopic wires and nickel nanowires we find Poisson's ratios that closely correspond to bulk values, whereas for silver nanowires significant deviations from the bulk silver value are observed. Moreover, repeated measurements on individual silver nanowires at different levels of mechanical and electrical stress yield a small spread in Poisson ratio, with a range of mean values for different wires, all of which are distinct from the bulk value.
| S-EPMC4102115 | biostudies-literature