ADI schemes for heat equations with irregular boundaries and interfaces in 3D with applications

In this paper, efficient alternating direction implicit (ADI) schemes are proposed to solve three-dimensional heat equations with irregular boundaries and interfaces. Starting from the well-known Douglas-Gunn ADI scheme, a modified ADI scheme is constructed to mitigate the issue of accuracy loss in solving problems with time-dependent boundary conditions. The unconditional stability of the new ADI scheme is also rigorously proven with the Fourier analysis. Then, by combining the ADI schemes with a 1D kernel-free boundary integral (KFBI) method, KFBI-ADI schemes are developed to solve the heat equation with irregular boundaries. In 1D sub-problems of the KFBI-ADI schemes, the KFBI discretization takes advantage of the Cartesian grid and preserves the structure of the coefficient matrix so that the fast Thomas algorithm can be applied to solve the linear system efficiently. Second-order accuracy and unconditional stability of the KFBI-ADI schemes are verified through several numerical tests for both the heat equation and a reaction-diffusion equation. For the Stefan problem, which is a free boundary problem of the heat equation, a level set method is incorporated into the ADI method to capture the time-dependent interface. Numerical examples for simulating 3D dendritic solidification phenomenons are also presented

Cylindrical nano-indentation on metal film/elastic substrate system with discrete dislocation plasticity analysis: A simple model for nano-indentation size effect

AbstractThe cylindrical nano-indentation on metal film/elastic substrate is computationally studied using two-dimensional discrete dislocation plasticity combined with the commercial software ANSYS®, with a focus on the storage volume for geometrically necessary dislocations (GNDs) inside the films and the nano-indentation size effect (NISE). Our calculations show that almost all GNDs are stored in a rectangular area determined by the film thickness and the actual contact width. The variations of indentation contact width with indentation depth for various film thicknesses and indenter radii are fitted by an exponential relation, and then the GND density underneath the indenter is estimated. Based on the Taylor dislocation model and Tabor formula, a simple model for the dependence of the nano-indentation hardness of the film/substrate system on the indentation depth, the indenter radius and the film thickness is established, showing a good agreement with the present numerical results

Discrete dislocation dynamics modelling of mechanical deformation of nickel-based single crystal superalloys

Discrete dislocation dynamics (DDD) has been used to model the deformation of nickelbased single crystal superalloys with a high volume fraction of precipitates at high temperature. A representative volume cell (RVC), comprising of both the precipitate and the matrix phase, was employed in the simulation where a periodic boundary condition was applied. The dislocation Frank–Read sources were randomly assigned with an initial density on the 12 octahedral slip systems in the matrix channel. Precipitate shearing by superdislocations was modelled using a back force model, and the coherency stress was considered by applying an initial internal stress field. Strain-controlled loading was applied to the RVC in the [0 0 1] direction. In addition to dislocation structure and density evolution, global stress–strain responses were also modelled considering the influence of precipitate shearing, precipitate morphology, internal microstructure scale (channel width and precipitate size) and coherency stress. A three-stage stress–strain response observed in the experiments was modelled when precipitate shearing by superdislocations was considered. The polarised dislocation structure deposited on the precipitate/matrix interface was found to be the dominant strain hardening mechanism. Internal microstructure size, precipitate shape and arrangement can significantly affect the deformation of the single crystal superalloy by changing the constraint effect and dislocation mobility. The coherency stress field has a negligible influence on the stress–strain response, at least for cuboidal precipitates considered in the simulation. Preliminary work was also carried out to simulate the cyclic deformation in a single crystal Ni-based superalloy using the DDD model, although no cyclic hardening or softening was captured due to the lack of precipitate shearing and dislocation cross slip for the applied strain considered

Modelling plastic deformation in a single-crystal nickel-based superalloy using discrete dislocation dynamics

Background: Nickel-based superalloys are usually exposed to high static or cyclic loads in non-ambient environment, so a reliable prediction of their mechanical properties, especially plastic deformation, at elevated temperature is essential for improved damage-tolerance assessment of components. Methods: In this paper, plastic deformation in a single-crystal nickel-based superalloy CMSX4 at elevated temperature was modelled using discrete dislocation dynamics (DDD). The DDD approach was implemented using a representative volume element with explicitly-introduced precipitate and periodic boundary condition. The DDD model was calibrated using stress-strain response predicted by a crystal plasticity model, validated against tensile and cyclic tests at 850°C for and crystallographic orientations, at a strain rate of 1/s. Results: The DDD model was capable to capture the global stress-strain response of the material under both monotonic and cyclic loading conditions. Considerably higher dislocation density was obtained for the orientation, indicating more plastic deformation and much lower flow stress in the material, when compared to that for orientation. Dislocation lines looped around the precipitate, and most dislocations were deposited on the surface of precipitate, forming a network of dislocation lines. Simple unloading resulted in a reduction of dislocation density. Conclusions: Plastic deformation in metallic materials is closely related to dynamics of dislocations, and the DDD approach can provide a more fundamental understanding of crystal plasticity and the evolution of heterogeneous dislocation networks, which is useful when considering such issues as the onset of damage in the material during plastic deformation

3D DDD modelling of dislocation-precipitate interaction in a nickel-based single crystal superalloy under cyclic deformation

Strain-controlled cyclic deformation of a nickel-based single crystal superalloy has been modelled by using three-dimensional (3D) discrete dislocation dynamics (DDD) for both [001] and [111] orientations. The work focused on the interaction between dislocations and precipitates during cyclic plastic deformation at elevated temperature, which has not been well studied yet. A representative volume element (RVE) with cubic γ’-precipitates was chosen to represent the material, with enforced periodical boundary conditions. In particular, cutting of superdislocations into precipitates was simulated by a back-force method. The global cyclic stress-strain responses were captured well by the DDD model when compared to experimental data, particularly the effects of crystallographic orientation. Dislocation evolution showed that considerably high density of dislocations was produced for [111] orientation when compared to [001] orientation. Cutting of dislocations into the precipitates had a significant effect on the plastic deformation, leading to material softening. Contour plots of in-plane shear strain proved the development of heterogeneous strain field, resulting in the formation of shear-band embryos

Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) Studies on α1A-Adrenergic Receptor Antagonists Based on Pharmacophore Molecular Alignment

The α1A-adrenergic receptor (α1A-AR) antagonist is useful in treating benign prostatic hyperplasia, lower urinary tract symptoms, and cardiac arrhythmia. Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed on a set of α1A-AR antagonists of N-aryl and N-nitrogen class. Statistically significant models constructed from comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were established based on a training set of 32 ligands using pharmacophore-based molecular alignment. The leave-oneout cross-validation correlation coefficients were q2 CoMFA = 0.840 and q2 CoMSIA = 0.840. The high correlation between the cross-validated/predicted and experimental activities of a test set of 12 ligands revealed that the CoMFA and CoMSIA models were robust (r2 pred/CoMFA = 0.694; r2 pred/CoMSIA = 0.671). The generated models suggested that electrostatic, hydrophobic, and hydrogen bonding interactions play important roles between ligands and receptors in the active site. Our study serves as a guide for further experimental investigations on the synthesis of new compounds. Structural modifications based on the present 3D-QSAR results may lead to the discovery of other α1A-AR antagonists

A heterozygous moth genome provides insights into herbivory and detoxification

How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants1, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood2. We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.Minsheng You … Simon W Baxter … et al

Accessibility and Update Status of Published Software: Benefits and Missed Opportunities

Online accessibility and continuous updating of software packages is important for their application and resource-sharing. We evaluated the accessibility and update status of 214 software packages published in Molecular Ecology Resources in the past 15 years (2001–2015) and reported the associated benefits and missed opportunities. Original publications describing these software packages have been cited 31,886 times in total, with 19.6% of them being cited more than 100 times. However, 41.6% (89/214) of the source websites provided in the original papers were inaccessible, of which only 29.2% (26/89) had alternative websites. Up to 63.1% (135/214) of the software packages had not been updated since their publication or were inaccessible. A huge disparity in accessibility, 100% (41/41) vs. 63.6% (110/173), was observed between websites deposited in long-term servers vs. academic institution websites, personal homepages, or e-mails, respectively. In addition, software packages that were accessible and updated were significantly more likely to be cited, compared to those that were inaccessible and un-updated. By guaranteeing the accessibility of their published software packages, for instance, by depositing them in long-term servers and keeping the software packages updated, software developers will further resource-sharing and promote reproduction and citation of their software