Strain rate dependency of dislocation plasticity.
Ontology highlight
ABSTRACT:
SUBMITTER: Fan H
PROVIDER: S-EPMC7988163 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The plastic behaviour of individual Cu crystallites under nanoextrusion is studied by molecular dynamics simulations. Single-crystal Cu fcc nanoparticles are embedded in a spherical force field mimicking the effect of a contracting carbon shell, inducing pressure on the system in the range of gigapascals. The material is extruded from a hole of 1.1-1.6 nm radius under athermal conditions. Simultaneous nucleation of partial dislocations at the extrusion orifice leads to the formation of dislocation dendrites in the particle causing strain hardening and high flow stress of the material. As the extrusion orifice radius is reduced below 1.3 Å we observe a transition from displacive plasticity to solid-state amorphisation.
| S-EPMC3628289 | biostudies-literature
Project description:Probing the mechanisms of defect-defect interactions at strain rates lower than 10(6) s(-1) is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation-defect interactions at virtually any strain rate, exemplified within 10(-7) to 10(7) s(-1). We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation-relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate-dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 10(5) to 10(7) s(-1). Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed.
| S-EPMC3816434 | biostudies-literature
Project description:IntroductionSaccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints in oxygen transfer and cooling capacities, have to be operated at low specific growth rates. Because intracellular levels of key metabolites are growth-rate dependent, slow growth can significantly affect biomass-specific productivity. Using an engineered Saccharomyces cerevisiae strain expressing a heterologous pathway for resveratrol production as a model energy-requiring product, the impact of specific growth rate on yeast physiology and productivity was investigated in aerobic, glucose-limited chemostat cultures.ResultsStoichiometric analysis revealed that de novo resveratrol production from glucose requires 13 moles of ATP per mole of produced resveratrol. The biomass-specific production rate of resveratrol showed a strong positive correlation with the specific growth rate. At low growth rates a substantial fraction of the carbon source was invested in cellular maintenance-energy requirements (e.g. 27 % at 0.03 h(-1)). This distribution of resources was unaffected by resveratrol production. Formation of the by-products coumaric, phloretic and cinnamic acid had no detectable effect on maintenance energy requirement and yeast physiology in chemostat. Expression of the heterologous pathway led to marked differences in transcript levels in the resveratrol-producing strain, including increased expression levels of genes involved in pathways for precursor supply (e.g. ARO7 and ARO9 involved in phenylalanine biosynthesis). The observed strong differential expression of many glucose-responsive genes in the resveratrol producer as compared to a congenic reference strain could be explained from higher residual glucose concentrations and higher relative growth rates in cultures of the resveratrol producer.ConclusionsDe novo resveratrol production by engineered S. cerevisiae is an energy demanding process. Resveratrol production by an engineered strain exhibited a strong correlation with specific growth rate. Since industrial production in fed-batch reactors typically involves low specific growth rates, this study emphasizes the need for uncoupling growth and product formation via energy-requiring pathways.
| S-EPMC4570684 | biostudies-literature
Project description:Size-affected dislocation-mediated plasticity is important in a wide range of materials and technologies. Here we develop a generalized size-dependent dislocation-based model that predicts strength as a function of crystal/grain size and the dislocation density. Three-dimensional (3D) discrete dislocation dynamics (DDD) simulations reveal the existence of a well-defined relationship between strength and dislocation microstructure at all length scales for both single crystals and polycrystalline materials. The results predict a transition from dislocation-source strengthening to forest-dominated strengthening at a size-dependent critical dislocation density. It is also shown that the Hall-Petch relationship can be physically interpreted by coupling with an appropriate kinetic equation of the evolution of the dislocation density in polycrystals. The model is shown to be in remarkable agreement with experiments. This work presents a micro-mechanistic framework to predict and interpret strength size-scale effects, and provides an avenue towards performing multiscale simulations without ad hoc assumptions.
| S-EPMC4354076 | biostudies-literature
Project description:Dislocation nucleation is essential to our understanding of plastic deformation, ductility, and mechanical strength of crystalline materials. Molecular dynamics simulation has played an important role in uncovering the fundamental mechanisms of dislocation nucleation, but its limited timescale remains a significant challenge for studying nucleation at experimentally relevant conditions. Here we show that dislocation nucleation rates can be accurately predicted over a wide range of conditions by determining the activation free energy from umbrella sampling. Our data reveal very large activation entropies, which contribute a multiplicative factor of many orders of magnitude to the nucleation rate. The activation entropy at constant strain is caused by thermal expansion, with negligible contribution from the vibrational entropy. The activation entropy at constant stress is significantly larger than that at constant strain, as a result of thermal softening. The large activation entropies are caused by anharmonic effects, showing the limitations of the harmonic approximation widely used for rate estimation in solids. Similar behaviors are expected to occur in other nucleation processes in solids.
| S-EPMC3069194 | biostudies-literature
Project description:Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints in oxygen transfer and cooling capacities, have to be operated at low specific growth rates. Because intracellular levels of key metabolites and cellular energy status are growth-rate dependent, slow growth can significantly affect biomass-specific productivity. Using an engineered Saccharomyces cerevisiae strain expressing a heterologous pathway for resveratrol production as a model energy-requiring product, the impact of specific growth rate on yeast physiology and productivity was investigated in aerobic, glucose-limited chemostat cultures. Stoichiometric analysis revealed that de novo resveratrol production from glucose requires a net input of 2 moles of ATP per mole of produced resveratrol. The biomass-specific production rate of resveratrol showed a strong positive correlation with the specific growth rate. At low growth rates, a substantial fraction of the carbon source was invested in cellular maintenance-energy requirements (e.g., 27% at 0.03 h-1). This distribution of resources was unaffected by resveratrol production. Formation of the by-products coumaric, phloretic and cinnamic acid had no detectable effect on maintenance energy requirement and yeast physiology in the chemostats. Expression of the heterologous pathway led to marked differences in transcript levels in the resveratrol-producing strain, including increased expression levels of genes involved in pathways for precursor supply (e.g., ARO7 and ARO9 involved in phenylalanine biosynthesis). The observed strong differential expression of many glucose-responsive genes in the resveratrol producer as compared to a congenic reference strain could be explained from higher residual glucose concentrations and higher relative growth rates in cultures of the resveratrol producer. De novo resveratrol production by engineered S. cerevisiae is an energy demanding process. Resveratrol production by an engineered strain exhibited a strong correlation with specific growth rate. Since industrial production in fed-batch reactors typically involves low specific growth rates, this study emphasizes the need for uncoupling growth and product formation via energy-requiring pathways. The goal of the present study is to investigate the impact of specific growth rate on biomass-specific productivity, product yield, by-product formation and host strain physiology of an S. cerevisiae strain that was previously engineered for de novo production of resveratrol from glucose. To this end, (by)product formation, physiology and transcriptome were analysed in steady-state, glucose-limited chemostat cultures grown at different dilution rates.
2015-12-22 | E-GEOD-65942 | biostudies-arrayexpress
Project description:Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints in oxygen transfer and cooling capacities, have to be operated at low specific growth rates. Because intracellular levels of key metabolites and cellular energy status are growth-rate dependent, slow growth can significantly affect biomass-specific productivity. Using an engineered Saccharomyces cerevisiae strain expressing a heterologous pathway for resveratrol production as a model energy-requiring product, the impact of specific growth rate on yeast physiology and productivity was investigated in aerobic, glucose-limited chemostat cultures. Stoichiometric analysis revealed that de novo resveratrol production from glucose requires a net input of 2 moles of ATP per mole of produced resveratrol. The biomass-specific production rate of resveratrol showed a strong positive correlation with the specific growth rate. At low growth rates, a substantial fraction of the carbon source was invested in cellular maintenance-energy requirements (e.g., 27% at 0.03 h-1). This distribution of resources was unaffected by resveratrol production. Formation of the by-products coumaric, phloretic and cinnamic acid had no detectable effect on maintenance energy requirement and yeast physiology in the chemostats. Expression of the heterologous pathway led to marked differences in transcript levels in the resveratrol-producing strain, including increased expression levels of genes involved in pathways for precursor supply (e.g., ARO7 and ARO9 involved in phenylalanine biosynthesis). The observed strong differential expression of many glucose-responsive genes in the resveratrol producer as compared to a congenic reference strain could be explained from higher residual glucose concentrations and higher relative growth rates in cultures of the resveratrol producer. De novo resveratrol production by engineered S. cerevisiae is an energy demanding process. Resveratrol production by an engineered strain exhibited a strong correlation with specific growth rate. Since industrial production in fed-batch reactors typically involves low specific growth rates, this study emphasizes the need for uncoupling growth and product formation via energy-requiring pathways.
2015-12-22 | GSE65942 | GEO
Project description:Understanding deformation mechanisms in silicon is critical for reliable design of miniaturized devices operating at high temperatures. Bulk silicon is brittle, but it becomes ductile at about 540 °C. It creeps (deforms plastically with time) at high temperatures (?800 °C). However, the effect of small size on ductility and creep of silicon remains elusive. Here, we report that silicon at small scales may deform plastically with time at lower temperatures (400 °C) above a threshold stress. We achieve this stress by bending single-crystal silicon microbeams using an in situ thermomechanical testing stage. Small size, together with bending, localize high stress near the surface of the beam close to the anchor. This localization offers flaw tolerance, allowing ductility to win over fracture. Our combined scanning, transmission electron microscopy, and atomic force microscopy analysis reveals that as the threshold stress is approached, multiple dislocation nucleation sites appear simultaneously from the high-stressed surface of the beam with a uniform spacing of about 200 nm between them. Dislocations then emanate from these sites with time, lowering the stress while bending the beam plastically. This process continues until the effective shear stress drops and dislocation activities stop. A simple mechanistic model is presented to relate dislocation nucleation with plasticity in silicon.
| S-EPMC7382262 | biostudies-literature
Project description:Understanding the coordinated deformation of multiple phases under applied stress is crucial for the structural design of dual-phase or multiphase advanced alloys. In this study, in-situ transmission electron microscope tensile tests were performed to investigate the dislocation behaviors and the transportation of dislocation plasticity during the deformation of a dual-phase Ti-10(wt.%) Mo alloy having hexagonal close-packed α phase and body-centered cubic β phase. We demonstrated that the dislocation plasticity preferred to transmit from alpha to alpha phase along the longitudinal axis of each plate, regardless of where dislocations were formed. The intersections of different α plates provided local stress concentration that facilitated the initiation of dislocation activities from there. Dislocations then migrated along the longitudinal axis of α plates and carried dislocation plasticity from one plate to another through these intersections as well. Since the α plates distributed in various orientations, dislocation slips occurred in multiple directions, which is beneficial for uniform plastic deformation of the material. Our micropillar mechanical testing further quantitatively demonstrated that the distribution of α plates and the α–α plates’ intersections plays important role in tuning the mechanical properties of the material.
| S-EPMC9938182 | biostudies-literature
Project description:BACKGROUND:It appears that substitution rate estimates co-vary very strongly with their timescale of measurement; the shorter the timescale, the higher the estimated value. Foamy viruses have a long history of co-speciation with their hosts, and one of the lowest estimated rates of evolution among viruses. However, when their rate of evolution is estimated over short timescales, it is more reminiscent of the rapid rates seen in other RNA viruses. This discrepancy between their short-term and long-term rates could be explained by the time-dependency of substitution rate estimates. Several empirical models have been proposed and used to correct for the time-dependent rate phenomenon (TDRP), such as a vertically-translated exponential rate decay model and a power-law rate decay model. Nevertheless, at present, it is still unclear which model best describes the rate dynamics. Here, we use foamy viruses as a case study to empirically describe the phenomenon and to determine how to correct rate estimates for its effects. Four empirical models were investigated: (i) a vertically-translated exponential rate decay model, (ii) a simple exponential rate decay model, (iii) a vertically-translated power-law rate decay model, and (iv) a simple power-law rate decay model. RESULTS:Our results suggest that the TDRP is likely responsible for the large discrepancy observed in foamy virus short-term and long-term rate estimates, and the simple power-law rate decay model is the best model for inferring evolutionary timescales. Furthermore, we demonstrated that, within the Bayesian phylogenetic framework, currently available molecular clocks can severely bias evolutionary date estimates, indicating that they are inadequate for correcting for the TDRP. Our analyses also suggest that different viral lineages may have different TDRP dynamics, and this may bias date estimates if it is unaccounted for. CONCLUSIONS:As evolutionary rate estimates are dependent on their measurement timescales, their values must be used and interpreted under the context of the timescale of rate estimation. Extrapolating rate estimates across large timescales for evolutionary inferences can severely bias the outcomes. Given that the TDRP is widespread in nature but has been noted only recently the estimated timescales of many viruses may need to be reconsidered and re-estimated. Our models could be used as a guideline to further improve current phylogenetic inference tools.
| S-EPMC4480597 | biostudies-other