OpenPFC:An open-source framework for high performance 3D phase field crystal simulations

We present OpenPFC (https://github.com/VTT-ProperTune/OpenPFC), a state-of-the-art phase field crystal (PFC) simulation platform designed to be scalable for massive high-performance computation environments. OpenPFC can efficiently handle large-scale simulations, as demonstrated by our strong and weak scaling analyses up to an 81923 grid on 65 536 cores. Our results indicate that meaningful PFC simulations can be conducted on grids of size 20483 or even 40963, provided there is a sufficient number of cores and ample disk storage available. In addition, we introduce an efficient implementation of moving boundary conditions that eliminates the need for copying field values between MPI processes or adding an advection term to the evolution equations. This scheme enhances the computational efficiency in simulating large scale processes such as long directional solidification. To showcase the robustness of OpenPFC, we apply it to simulations of rapid solidification in the regime of metal additive manufacturing using a recently developed quantitative solid-liquid-vapor PFC model, parametrized for pure tungsten (body-centered cubic) and aluminum (face-centered cubic).</p

Orientation gradients in rapidly solidified pure aluminum thin films: comparison of experiments and phase-field crystal simulations

Rapid solidification experiments on thin film aluminum samples reveal the presence of lattice orientation gradients within crystallizing grains. To study this phenomenon, a single-component phase-field crystal (PFC) model that captures the properties of solid, liquid, and vapor phases is proposed to model pure aluminium quantitatively. A coarse-grained amplitude representation of this model is used to simulate solidification in samples approaching micrometer scales. The simulations reproduce the experimentally observed orientation gradients within crystallizing grains when grown at experimentally relevant rapid quenches. We propose a causal connection between formation of defects and orientation gradients

Sex-related differences in aging rate are associated with sex chromosome system in amphibians

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture-recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the "unguarded X/Z effect") or repeat-rich Y/W chromosome (the "toxic Y/W effect") could accelerate aging in the heterogametic sex in some vertebrate clades.Peer reviewe

Classical nucleation theory in the phase field crystal model

An understanding of polycrystalline materials, ranging from alloys to certain ceramics and polymers and beyond, is of great importance for modern society. These materials typically form through the process of nucleation, a thermally activated phase transition. The numerical modeling of this phase transition is problematic for traditional numerical techniques: the commonly used phase field methods' resolution does not extend to the atomic scales at which nucleation takes places, while atomistic methods such as Molecular Dynamics are incapable of scaling to the mesoscale regime where late-stage growth and structure formation takes place following earlier nucleation. As such, there is interest in examining whether the Phase Field Crystal (PFC) model, which attempts to bridge the atomic and mesoscale regimes, is capable of modeling nucleation. In this work, we numerically calculate nucleation rates and incubation times in the PFC model. We show qualitative agreement with classical nucleation theory (CNT), a single-variable stochastic model. Notably, we show that nucleation rates in the PFC model are time-dependent. We also examine the form and behavior of nuclei at early formation times, finding disagreement with some basic assumptions of CNT. We then argue that a quantitatively correct nucleation theory for the PF Cmodel would require extending CNT to a multi-variable theory.Une compréhension des matériaux polycristallins, allant des alliages à certaines céramiques et polymères et au-delà, revêt une grande importance pour la société moderne. Ces matériaux se forment généralement à travers le processus de nucléation, une transition de phase activée thermiquement. La modélisation numérique de cette transition de phase est problématique pour les techniques numériques traditionnelles: la résolution des méthodes de champ de phase ('phase field') couramment répandue ne s'étend pas aux échelles atomiques auxquelles la nucléation prend place, tandis que les méthodes atomiques telles que la dynamique moléculaire ('molecular dynamics')sont incapables de s'adapter au régime mésoéchelle où la croissance de la phase crystalline et la formation de la structure ont lieu suite à une nucléation antérieure. Entant que tel, il est intéressant d'examiner si le modèle de 'Phase Field Crystal' (PFC), qui tente de combler les régimes atomique et mésoéchelle, est capable de modéliser la nucléation. Dans ce travail, nous calculons numériquement les taux de nucléation et les temps d'incubation dans le modèle PFC. Nous montrons un accord qualitatif avec la théorie classique de la nucléation (CNT), un modèle stochastique à variable unique. Notamment, nous montrons que les taux de nucléation dans le modèle PFC dépendent du temps. Nous examinons également la forme et le comportement des noyaux aux premiers temps de formation, constatant un désaccord avec certaines hypothèses de base de CNT. Nous soutenons alors qu'une théorie de nucléation quantitativement correcte pour le modèle PFC nécessiterait d'étendre CNT à une théorie multi-variable

Multiscale analysis of crystalline defect formation in rapid solidification of pure aluminium and aluminium–copper alloys

International audienceRapid solidification leads to unique microstructural features, where a less studied topic is the formation of various crystalline defects, including high dislocation densities, as well as gradients and splitting of the crystalline orientation. As these defects critically affect the material’s mechanical properties and performance features, it is important to understand the defect formation mechanisms, and how they depend on the solidification conditions and alloying. To illuminate the formation mechanisms of the rapid solidification induced crystalline defects, we conduct a multiscale modelling analysis consisting of bond-order potential-based molecular dynamics (MD), phase field crystal-based amplitude expansion simulations, and sequentially coupled phase field–crystal plasticity simulations. The resulting dislocation densities are quantified and compared to past experiments. The atomistic approaches (MD, PFC) can be used to calibrate continuum level crystal plasticity models, and the framework adds mechanistic insights arising from the multiscale analysis

Multiscale analysis of crystal defect formation in rapid solidification of pure aluminium and aluminium-copper alloys

Rapid solidification leads to unique microstructural features, where a less studied topic is the formation of various crystalline defects, including high dislocation densities, as well as gradients and splitting of the crystalline orientation. As these defects critically affect the material's mechanical properties and performance features, it is important to understand the defect formation mechanisms, and how they depend on the solidification conditions and alloying. To illuminate the formation mechanisms of the rapid solidification induced crystalline defects, we conduct a multiscale modeling analysis consisting of bond-order potential based molecular dynamics (MD), phase field crystal based amplitude expansion (PFC-AE) simulations, and sequentially coupled phase field -- crystal plasticity (PF--CP) simulations. The resulting dislocation densities are quantified and compared to past experiments. The atomistic approaches (MD, PFC) can be used to calibrate continuum level crystal plasticity models, and the framework adds mechanistic insights arising from the multiscale analysis

Sex‐related differences in aging rate are associated with sex chromosome system in amphibians

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat-rich Y/W chromosome (the “toxic Y/W effect”) could accelerate aging in the heterogametic sex in some vertebrate clades

Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity

Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging. Copyright © 2022 The AuthorsNational Institutes of Health, NIH: R01AG049416; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, SNF: 31003A_182265This study was supported by National Institutes of Health grant R01AG049416 (to A.M.B., F.J.J., and D.A.W.M.). H.C. was supported as a postdoctoral researcher by the Swiss National Science Foundation (grant no. 31003A_182265)