Cellular Element Research Articles

Modelling fracture in heterogeneous materials on HPC systems using a hybrid MPI/Fortran coarray multi-scale CAFE framework

A 3D multi-scale cellular automata finite element (CAFE) framework for modelling fracture in heterogeneous materials is described. The framework is implemented in a hybrid MPI/Fortran coarray code for efficient parallel execution on HPC platforms. Two open source BSD licensed libraries developed by the authors in modern Fortran were used: CGPACK, implementing cellular automata (CA) using Fortran coarrays, and ParaFEM, implementing finite elements (FE) using MPI. The framework implements a two-way concurrent hierarchical information exchange between the structural level (FE) and the microstructure (CA). MPI to coarrays interface and data structures are described. The CAFE framework is used to predict transgranular cleavage propagation in a polycrystalline iron round bar under tension. Novel results enabled by this CAFE framework include simulation of progressive cleavage propagation through individual grains and across grain boundaries, and emergence of a macro-crack from merging of cracks on preferentially oriented cleavage planes in individual crystals. Nearly ideal strong scaling up to at least tens of thousands of cores was demonstrated by CGPACK and by ParaFEM in isolation in prior work on Cray XE6. Cray XC30 and XC40 platforms and CrayPAT profiling were used in this work. Initially the strong scaling limit of hybrid CGPACK/ParaFEM CAFE model was 2000 cores. After replacing all-to-all communication patterns with the nearest neighbour algorithms the strong scaling limit on Cray XC30 was increased to 7000 cores. TAU profiling on non-Cray systems identified deficiencies in Intel Fortran 16 optimisation of remote coarray operations. Finally, coarray synchronisation challenges and opportunities for thread parallelisation in CA are discussed.

Pitting corrosion as a mixed system: coupled deterministic-probabilistic simulation of pit growth

Stochastic behavior of pitting corrosion poses a unique challenge in its computational analysis. However, it also stems from electrochemical activity causing general corrosion. In this paper, a framework for corrosion pit growth simulation based on the coupling of the Cellular Automaton (CA) and Boundary Element Methods (BEM) is presented. The framework assumes that pitting corrosion is controlled by electrochemical activity inside the pit cavity. The BEM provides the prediction of electrochemical activity given the geometrical data and polarization curves, while the CA is used to simulate the evolution of pit shapes based on electrochemical activity provided by BEM. To demonstrate the methodology, a sample case of local corrosion cells formed in pitting corrosion with varied dimensions and polarization functions is considered. Results show certain shapes tend to grow in certain types of environments. Some pit shapes appear to pose a higher risk by being potentially significant stress raisers or potentially increasing the rate of corrosion under the surface. Furthermore, these pits are comparable to commonly observed pit shapes in general corrosion environments.

Plasma cell differentiation is controlled by multiple cell division-coupled epigenetic programs

The genomic loci associated with B cell differentiation that are subject to transcriptional and epigenetic regulation in vivo are not well defined, leaving a gap in our understanding of the development of humoral immune responses. Here, using an in vivo T cell independent B cell differentiation model, we define a cellular division-dependent cis-regulatory element road map using ATAC-seq. Chromatin accessibility changes correlate with gene expression and reveal the reprogramming of transcriptional networks and the genes they regulate at specific cell divisions. A subset of genes in naive B cells display accessible promoters in the absence of transcription and are marked by H3K27me3, an EZH2 catalyzed repressive modification. Such genes encode regulators of cell division and metabolism and include the essential plasma cell transcription factor Blimp-1. Chemical inhibition of EZH2 results in enhanced plasma cell formation, increased expression of the above gene set, and premature expression of Blimp-1 ex vivo. These data provide insights into cell-division coupled epigenetic and transcriptional processes that program plasma cells.

Biochemical and hematological composition of blood of cattle fed with Chlorella

We researched the influence of the additive Chlorella cultivated in a closed bioreactor under the influence of an electrostatistic field, on the biochemical and hematological parameters of blood in different age groups of cattle. The experiment was conducted on two groups of three month old heifers and two groups of lactating cows in the 7th month of lactation, with 15 individuals in each group; all animals in the groups were given the basic diet. During the 120-day experiment, the experimental group of heifers was fed on a suspension of Chlorella cultivated with the technology using an electrostatic field, in the following amounts: 1–30th day – 1.51 g, 31–60th day – 1.82 g, 61–90th day – 2.01 g, 91–120th day – 2.28 g of dry substance per individual daily; the group of lactating cows during 60 days was given the Chlorella additive to the amount of 6 g of dry substance per individual per day. Over the following 30 days the heifers and lactating cows were kept under observation to determine the “aftereffects” of the Chlorella suspension fodder additive. On the first day of the experiment and after every 30 days, blood was drawn from the animals’ jugular veins for determination of the biochemical and hematological parameters of the blood During the experiment, the experimental groups of heifers and lactating cows were observed to have a strengthened antioxidant system due to increase in the activity of superoxide dismutase and catalase, and also to have a strengthened hematopoietic function and intensified metabolic and redox processes. Due to the stimulating effect of the suspension of Chlorella cultivated using the intense technology involving using an electrostatic field on the erythro- and leukopoiesis of different age groups of the cattle, we determined a strengthening of the cellular element of the animals’ immune system. During the following 30 days, the heifers and lactating cows of the experimental groups were observed to exhibit “aftereffects” of the Chlorella suspension additive, namely increases in the values of biochemical, hematological and morphological indicators of the blood in comparison with these indicators for the animals in the control groups. As a result, we concluded that feeding different age groups of cattle with suspension of Chlorella cultivated in the conditions of a closed bioreactor under the influence of an electrostatic field, in the dosage of 155 ml per kg of dry substance of the animals’ diet, contributes to the strengthening of non-specific defence of their organism, forming a potential for increasing the productive indicators and maintenance of the livestock.

Development and evaluation of data transfer protocols in the fully coupled random cellular automata finite element model of dynamic recrystallization

Development and application of the hybrid fully coupled, random cellular automata finite element (RCAFE) approach to modelling dynamic recrystallization phenomenon, during a high temperature deformation is the overall goal of the paper. The finite element (FE) solver provides information on equivalent stress, equivalent strain, temperature fields as well as on geometry of deformed computational domain after each time step. These data are transferred to the developed random cellular automata (RCA) model, which is responsible for evaluation of corresponding microstructure morphology evolution and dislocation density changes under dynamic recrystallization (DRX) conditions. Finally, a set of data from the RCA part is send back to the FE solver and used as an input for the next time step. As a result, the fully coupled RCAFE model for simulation of a DRX progress is established. Crucial developments of the RCA model related to the space deformation and efficient neighbors selection are presented within the paper. However, particular attention is put on the development of efficient communication algorithms and methods for input/output data transfer between the FE and RCA modules. The communication protocols based on text files and sockets have different levels of complexity but both are based on the Abaqus VUMAT subroutine. Their capabilities and limitations are evaluated within the paper. Finally, an application of the proposed RCAFE method to simulation of a dynamic recrystallization progress at the level of single grains is presented and discussed to highlight capabilities of the model.

Histomorphological study of the spleen in indigenous Gazelle (Gazella subgutturosa)

The study aimed to investigate the anatomical and histomorphometrical features of spleen in gazelle. To achieve this goal, spleens of 7 animals were used. The gross aspect of the study revealed that the spleen of gazelle appeared dark brown in color with elliptical shape and was situated at the left lateral surface of the rumen. It occupied the area extended from the 8th rib to 11th rib. Length and width of the spleens were calculated and the mean were 7.94±0.1, 5.88±0.2 respectively. There were three ligaments connected the spleen with adjacent structures, namely splenogastric, splenorenal and splenophrenic. The blood supply of the spleen was studied using X-rays and resin injection methods. The splenic artery was divided into three primary branches, each one subdivided into two secondary branches. The latter branched into tertiary branches which were distributed all over the splenic parenchyma. Microscopic findings showed that the capsule of spleen in gazelle was composed from of two layers, the outer one made of mainly of dense connective tissue; whereas the inner layer of capsule consisted of connective tissue fibers in addition to abundance of smooth muscle fibers interweaving among them. The total mean thickness of the capsule was 210.51+8.3 µm. The splenic parenchyma in gazelle consisted of white pulp represented by lymphoid follicles with their marginal zones and periarterial lymphatic sheath while the red pulp represented by splenic cords and sinusoids. The area of white pulp in the gazelle comprised about 9.6% of the spleen parenchyma. Red pulp composed mainly from cords of connective tissue and small sinuses or sinusoids filled with blood cellular element which extended among these cords and was lined by flattened endothelial cells with relatively large spaces or slits between them. The sinusoids were found to be lymphocytes, reticular, plasma, macrophages and occasional megakaryocytes whereas the megakaryocyte appeared large with acidophilic cytoplasm and dark elongated multilobated nucleus. This research work was performed in order to establish the basic histomorphological information helpful for the veterinary medical practice and veterinary surgions to developing their work on gazelle like designing the approach of some surgical operations like spleenectomy or any surgical entrance may be needed in these animal species.

Bovine Spongiform Encephalopathy and Public Health

Bovine Spongiform Encephalopathy (BSE) is a transmissible degenerative disease of the central nervous system. It belongs to a group of diseases which affect man and various kinds of animals and they have a similar histopathological appearance. The harmful agent of BSE and all the others spongiform encephalopathies have not been totally clarified. Today according to the predominant opinion this agent is consisted mainly or/and only of an abnormal protein, which is called prion. In various observations the harmful agent appears like proteinaceous cylinders which are consisted of aggregations or polymerized forms of the agent and it is called prion-protein (PrP). It has been proved that there are two isoforms of PrP. The first of them, called PrPc, is produced from many cells of man and animals and consists a cellular structural element. The second, called PrPs t, due to its specific properties, it is considered to be pathological and responsible for the spongiform encephalopathies. The replication of PrPsc seems to take place in the lysosomes of central nervous system cells, dendritic, and other reticular cells of the lymphatic organs through transformation of PrPc into PrPsc. It appears BSE caused by feeding meat and bone meals to cattle which were originated from scrapie infected sheep. Refering to the pathogenesis originating from experimental data it seems that initially the PrF* enters the body by food and afterwards is settled in various lymphoid organs where the first replication takes place. It is believed that BSE is transmitted through the nerves to the CNS, where it creates the characteristic lesions of vacuolar degeneration of the neurons and finally the spongiosis. Then the clinical signs are expressed. The nervous signs characterised by behavioural alterations of the animals and kinetic abnormalities. The diagnosis of the disease is made by the observation of the histopathological lesions, the detection of Scrapie Associated Fibrils-SAF by EM, the immunohistochemical detection of prpsc i n histological samples or by electrophoresis (Western blotting test). BSE was proved to be transmissible to other animals and there is a possibility that it could be done to man through the food chain. According to the above in these years, from the appearance of the disease until now, have been taken bans from Great Britain as well as from E.U. for the eradication of the disease and the protection of the public health. These instructions should be followed by the authorities and additionally the consumers ought to be informed for the possible danger of various animal products.

Predicting the Effect of Tool Configuration during Friction Stir Welding by Cellular Automata Finite Element (CAFE) Analyses

The present work aims at selecting the pin geometry for single-sided friction stir welding of steel, and modelling the double-sided FSW process, both through cellular automata finite element analyses. Cellular automata cells are used to hold initial grain size of the base sheets. The stirring action during the process is not modelled physically. Instead the heat flux and strain-rate attained are incorporated by models. In the first objective, by developing heat flux models, strain-rate and strain models for different pin profiles, and the final grain size distribution across the weld zone is predicted. The final pin profile predicted from the present work is not the same used by authors in the existing literature, as observed from grain size prediction. In the second objective, during double-sided friction stir welding, the grain size predictions are agreeing well with the existing data. The efficiency of the approach for tool selection has been demonstrated successfully. [Submitted 8 December 2016; Accepted 5 December 2017]

Predicting the effect of tool configuration during friction stir welding by cellular automata finite element analyses

Predicting the effect of tool configuration during friction stir welding by cellular automata finite element analyses

Simulation of austenite decomposition in continuous cooling conditions: a cellular automata-finite element modelling

ABSTRACTTransformation of austenite to ferrite under continuous cooling condition was investigated. The heat conduction problem was managed by finite element method while two-dimensional cellular automata modeling was simultaneously performed to predict the progress of austenite decomposition using a two-step algorithm to reduce surface-to-volume ratio. Continuous cooling experiments on low carbon steel were made and the ferrite structure was determined and compared with the simulation data. The predicted and the experimental results demonstrated an acceptable consistency and the activation energy for ferrite growth was determined as 171 kJ/mole. The rate of ferrite transformation increased under examined continuous cooling conditions owing to higher nucleation rate. Moreover, the initial austenite grain size has shown a significant impact on the rate of transformation e.g. in air-cooled samples as the austenite grain size decreased from 24 to 34 µm, the mean ferrite grain size decreased about 8 µm.

Numerical Study on Solidification Behavior and Structure of Continuously Cast U71Mn Steel

The solidification behavior and structure of continuous casting high rail U71Mn bloom, under different secondary cooling conditions and superheat, were numerically investigated using the Cellular Automaton-Finite Element (CAFE) model implemented with ProCAST software. Nail shooting and macro etch experiments of the bloom samples under different cooling conditions were conducted to verify the model of macroscopic solidification and structure. The results showed that the simulated results of the solidified shell and solidification structure are basically consistent with experimental results. The secondary cooling condition has little effect on the grain size and distribution of the bloom, while both the bloom surface and corner temperatures are higher and the temperature rise at the beginning of the air-cooling zone is smaller under the super-slow cooling condition. The percentage of center-equiaxed grains decreases from 44.6% to 20.1% and the grain average radius increases from 1.025 to 1.128 mm when the superheat increases from 15 to 40 K, with little change in the grain size occurring between 15 and 20 K. Moreover, for a step increase in the superheat of 5 K, the solidification end is lengthened by about 0.19 m and the surface temperature is enhanced by 3 K. The super-slow secondary cooling condition with the superheat controlled within 20 K is suitable for big-bloom casting.

An Enhanced Spring-Particle Model for Red Blood Cell Structural Mechanics: Application to the Stomatocyte-Discocyte-Echinocyte Transformation.

Red blood cells (RBCs) are the most abundant cellular element suspended in blood. Together with the usual biconcave-shaped RBCs, i.e., discocytes, unusual-shaped RBCs are also observed under physiological and experimental conditions, e.g., stomatocytes and echinocytes. Stomatocytes and echinocytes are formed from discocytes and in addition can revert back to being discocytes; this shape change is known as the stomatocyte-discocyte-echinocyte (SDE) transformation. To-date, limited research has been conducted on the numerical prediction of the full SDE transformation. Spring-particle RBC (SP-RBC) models are commonly used to numerically predict RBC mechanics and rheology. However, these models are incapable of predicting the full SDE transformation because the typically employed bending model always leads to numerical instability with severely deformed shapes. In this work, an enhanced SP-RBC model is proposed in order to extend the capability of this model type and so that the full SDE transformation can be reproduced. This is achieved through the leveraging of an advanced bending model. Transformed vesicle and RBC shapes are predicted for a range of reduced volume and reduced membrane area difference (MAD), and very good agreement is obtained in the comparison of predicted shapes with experimental observations. Through these predictions, vesicle and SDE transformation phase diagrams are developed and, importantly, in the SDE case, shape boundaries are proposed for the first time relating RBC shape categories to RBC reduced volume and reduced MAD.

A hybrid cellular automata-finite element model for the simulation of the grind-hardening process

Grind-hardening process is a hybrid process for the simultaneous finishing and heat treatment of the workpiece material. Several studies have been presented for the simulation of the process, using either analytical or finite element-based models. In the present paper, the cellular automata method is used for simulating the metallurgical changes in the workpiece material. The method is coupled with a finite element model for the macro-modelling of the process, allowing the prediction of the microstructure of the material as a function of the macro-process parameters.

Effect of Solidification Pressure on Compactness Degree of 19Cr14Mn0.9N High Nitrogen Steel Using CAFE Method

The cellular automaton-finite element (CAFE) model is used to simulate solidification structures of 19Cr14Mn0.9N high nitrogen steel under different solidification pressures. The effect of solidification pressure on model parameters is firstly investigated. After validation, this model is used to clarify the effect of solidification pressure on compactness degree with number of grains and primary dendrite arm spacing (λ1). The results show that increasing solidification pressure from 0.5 to 1.2 MPa exhibits a significant increment (200 W m2 K−1)) on heat transfer coefficient and slight change for other model parameters. The model validation indicates CAFE model can accurately simulate solidification structure under higher solidification pressure. Under higher solidification pressure, the primary dendrite arm spacing (λ1) of central equiaxed grain becomes smaller and the number of grains of the whole ingot increases obviously, revealing a further improvement on the compactness degree of ingot. At a given pressure, the decrement in the number of grains is obvious away from the edge of ingot. With increasing solidification pressure, a more significant increment in the number of grains exists at columnar grain zone than that at central equiaxed grain zone, suggesting a greater increasing tendency of compactness degree at columnar grain zone.

Linear-No-Threshold Default Assumptions are Unwarranted for Cytotoxic Endpoints Independently Triggered by Ultrasensitive Molecular Switches.

Crump's response in this issue to my critique of linear-no-threshold (LNT) default assumptions for noncancer and nongenotoxic cancer risks (Risk Analysis 2016; 36(3):589-604) is rebutted herein. Crump maintains that distinguishing between a low-dose linear dose response and a threshold dose response on the basis of dose-response data is impossible even for endpoints involving increased cytotoxicity. My rebuttal relies on descriptions and specific illustrations of two well-characterized ultrasensitive molecular switches that govern two key cytoprotective responses to cellular stress-heat shock response and antioxidant response element activation, respectively-each of which serve to suppress stress-induced apoptotic cell death unless overwhelmed. Because detailed dose-response data for each endpoint is shown to be J- or inverted-J-shaped with high confidence, and because independent pathways can explain background rates of apoptosis, LNT assumptions for this cytotoxic endpoint are unwarranted, at least in some cases and perhaps generally.

Mitochondrial Dysfunction in Airway Disease

There is increasing appreciation that mitochondria serve cellular functions beyond oxygen sensing and energy production. Accordingly, it has become important to explore noncanonical roles of mitochondria in normal and pathophysiological processes that influence airway structure and function in the context of diseases such as asthma and COPD. Mitochondria can sense upstream processes such as inflammation, infection, tobacco smoke, and environmental insults important in these diseases and in turn can respond to such stimuli through altered mitochondrial protein expression, structure, and resultant dysfunction. Conversely, mitochondrial dysfunction has downstream influences on cytosolic and mitochondrial calcium regulation, airway contractility, gene and protein housekeeping, responses to oxidative stress, proliferation, apoptosis, fibrosis, and certainly metabolism, which are all key aspects of airway disease pathophysiology. Indeed, mitochondrial dysfunction is thought to play a role even in normal processes such as aging and senescence and in conditions such as obesity, which impact airway diseases. Thus, understanding how mitochondrial structure and function play central roles in airway disease may be critical for the development of novel therapeutic avenues targeting dysfunctional mitochondria. In this case, it is likely that mitochondria of airway epithelium, smooth muscle, and fibroblasts play differential roles, consistent with their contributions to disease biology, underlining the challenge of targeting a ubiquitous cellular element of existential importance. This translational review summarizes the current state of understanding of mitochondrial processes that play a role in airway disease pathophysiology and identifying areas of unmet research need and opportunities for novel therapeutic strategies.

Numerical simulation of the macrostructure evolution of a heavy steel ingot

The macroscopic grain structure of a 234 t steel ingot was simulated by using cellular automaton and finite element method provided by ProCAST. The growing speed coefficient of Kurz–Giovanola–Trivedi model was modified to reflect the growing process of grains. Chilled fine grains, columnar grains and coarse equiaxed grains were obtained from surface to core of the ingot, which were roughly in agreement with the measured ones. The influences of the nucleation and growth parameters were investigated. It was found that the relationship between nucleation and growth determines the macrostructure profile. An index, the ratio of growing speed over the nucleated sites at certain undercooling was proposed to estimate the macrostructure tendency.

Simulation of stray grain formation in Ni-base single crystal turbine blades fabricated by HRS and LMC techniques

The simulation models of the thermal and macrostructural evolutions during directional solidification of Ni-base single crystal (SX) turbine blades under high rate solidification (HRS) and liquid metal cooling (LMC) have been constructed using ProCAST software, coupled with a 3D Cellular Automaton Finite Element (CAFE) model. The models were used to investigate the tendencies of stray grain (SG) formation in the platform region of turbine blades fabricated by HRS and LMC techniques. The results reveal that the LMC technique can prohibit SG formation by smoothing the concaved isotherm and in turn alleviating the undercooling in the platform ends to let the dendrites fill up the undercooled zone before SG nucleation. The simulation results agreed well with the experimental results, indicating that these models could be used to analyze the macrostructural evolution or to optimize process parameters to suppress SG formation. Using these models, the critical withdrawal rate for casting SX turbine blades without SG formation were determined to be around 75 μm·s-1 and 100 μm·s-1 for HRS and LMC respectively, suggesting that LMC can be used as an efficient technique in fabricating SX turbine blades without any SG defect formation.

Dynamic load balancing for CAFE multiscale modelling methods for heterogeneous hardware infrastructure

The paper presents new approach to Static and Dynamic Load Balancing (DBL) for loosely coupled multiscale modelling methods executed in heterogeneous hardware infrastructure. The most popular configurations of computing nodes composed of modern multicore CPUs, GPUs and co-processors, are used. The proposed load balancing approach takes into account previously determined computational character of methods applied in particular scales, which depends on a size of input data, operational intensity and limitations of hardware architecture. Such limitations are defined by the Roofline model and then used in the algorithm as boundary conditions, allowing to determine maximum performance of an algorithm for particular device. Multiscale calculations based on upscaling approach are analysed by using Cellular Automata Finite Element (CAFE) method. The qualitative results, obtained after application of proposed load balancing procedure, are discussed in the paper in details.

EXPRESSION OF GENES ENCODING Z-DISC PROTEINS IN CARDIAC HYPERTROPHY CAUSED BY RENOVASCULAR HYPERTENSION IN «2 KIDNEY, 1 CLIP» MODEL

Background. Cardiac hypertrophy is a violation of myocardium structure, that increases risk for development of various cardiovascular diseases. Pathological hypertrophy can be triggered by hemodynamic and neurohumoral factors. At cellular level structural element of cardiomyocytes Z-disk, containing a great number of proteins, plays a crucial role in hypertrophy progression. Involvement of Z-disk components in cardiac hypertrophy development is not throughly investigated. Objective. The goal of the work was to investigate expression of genes encoding Z-disk proteins in cardiac hypertrophy caused by renovascular hypertension. Design and methods. «2 kidney, 1 clip» model was performed on male Wistar rats. Animals were divided into groups regarding to model duration. Gene expression in right and left ventricles was analyzed by real-time PCR. Results. We demonstrated altered expression of cmya5, actn2, nebl: increase at the early stage (1, 2 weeks), followed by decrease to basal level in left ventricle and gradual increase to the later stage (8, 10 weeks) in right ventricle. Des was upregulated at the early stage in both ventricles. Conclusion. Stage of hypertrophy progression could affect expression of genes, encoding Z-disk proteins. Thus, confi rming involvement of Z-disc proteins in cardiac hypertrophy development caused by neurohumoral factors in left and right ventricles.