Multi-Scale Simulation of MBE-Grown SiC/Si Nanostructures

2006 ◽  
Vol 527-529 ◽  
pp. 315-318 ◽  
Author(s):  
Alexander A. Schmidt ◽  
Yuri V. Trushin ◽  
K.L. Safonov ◽  
V.S. Kharlamov ◽  
Dmitri V. Kulikov ◽  
...  
Keyword(s):  
Kinetic Monte Carlo ◽  
Spatial Scales ◽  
Cluster Formation ◽  
Three Dimensional ◽  
Bulk Diffusion ◽  
Simulation Method ◽  
Atomic Scale ◽  
Rate Equations ◽  
Surface Evolution ◽  
Multi Scale

The main obstacle for the implementation of numerical simulation for the prediction of the epitaxial growth is the variety of physical processes with considerable differences in time and spatial scales taking place during epitaxy: deposition of atoms, surface and bulk diffusion, nucleation of two-dimensional and three-dimensional clusters, etc. Thus, it is not possible to describe all of them in the framework of a single physical model. In this work there was developed a multi-scale simulation method for molecular beam epitaxy (MBE) of silicon carbide nanostructures on silicon. Three numerical methods were used in a complex: Molecular Dynamics (MD), kinetic Monte Carlo (KMC), and the Rate Equations (RE). MD was used for the estimation of kinetic parameters of atoms at the surface, which are input parameters for other simulation methods. The KMC allowed the atomic-scale simulation of the cluster formation, which is the initial stage of the SiC growth, while the RE method gave the ability to study the growth process on a longer time scale. As a result, a full-scale description of the surface evolution during SiC formation on Si substrates was developed.

scholarly journals Quantification of Myocyte Disarray in Human Cardiac Tissue

2021 ◽  
Vol 12 ◽  
Author(s):  
Francesco Giardini ◽  
Erica Lazzeri ◽  
Giulia Vitale ◽  
Cecilia Ferrantini ◽  
Irene Costantini ◽  
...  
Keyword(s):  
Spatial Scale ◽  
Cardiac Tissue ◽  
Spatial Scales ◽  
Three Dimensional ◽  
Structural Data ◽  
Multi Scale ◽  
Tissue Organization ◽  
Human Cardiac Tissue ◽  
Microscopy Techniques ◽  
Scale Of Analysis

Proper three-dimensional (3D)-cardiomyocyte orientation is important for an effective tension production in cardiac muscle. Cardiac diseases can cause severe remodeling processes in the heart, such as cellular misalignment, that can affect both the electrical and mechanical functions of the organ. To date, a proven methodology to map and quantify myocytes disarray in massive samples is missing. In this study, we present an experimental pipeline to reconstruct and analyze the 3D cardiomyocyte architecture in massive samples. We employed tissue clearing, staining, and advanced microscopy techniques to detect sarcomeres in relatively large human myocardial strips with micrometric resolution. Z-bands periodicity was exploited in a frequency analysis approach to extract the 3D myofilament orientation, providing an orientation map used to characterize the tissue organization at different spatial scales. As a proof-of-principle, we applied the proposed method to healthy and pathologically remodeled human cardiac tissue strips. Preliminary results suggest the reliability of the method: strips from a healthy donor are characterized by a well-organized tissue, where the local disarray is log-normally distributed and slightly depends on the spatial scale of analysis; on the contrary, pathological strips show pronounced tissue disorganization, characterized by local disarray significantly dependent on the spatial scale of analysis. A virtual sample generator is developed to link this multi-scale disarray analysis with the underlying cellular architecture. This approach allowed us to quantitatively assess tissue organization in terms of 3D myocyte angular dispersion and may pave the way for developing novel predictive models based on structural data at cellular resolution.

scholarly journals Effect of atomic scale plasticity on hydrogen diffusion in iron: Quantum mechanically informed and on-the-fly kinetic Monte Carlo simulations

2008 ◽  
Vol 23 (10) ◽  
pp. 2757-2773 ◽  
Author(s):  
A. Ramasubramaniam ◽  
M. Itakura ◽  
M. Ortiz ◽  
E.A. Carter
Keyword(s):  
Monte Carlo ◽  
Density Functional ◽  
Hydrogen Diffusion ◽  
Kinetic Monte Carlo ◽  
Computational Cost ◽  
Bulk Diffusion ◽  
Density Functional Theory Calculations ◽  
Atomic Scale ◽  
Energy Barriers ◽  
Eam Potential

We present an off-lattice, on-the-fly kinetic Monte Carlo (KMC) model for simulating stress-assisted diffusion and trapping of hydrogen by crystalline defects in iron. Given an embedded atom (EAM) potential as input, energy barriers for diffusion are ascertained on the fly from the local environments of H atoms. To reduce computational cost, on-the-fly calculations are supplemented with precomputed strain-dependent energy barriers in defect-free parts of the crystal. These precomputed barriers, obtained with high-accuracy density functional theory calculations, are used to ascertain the veracity of the EAM barriers and correct them when necessary. Examples of bulk diffusion in crystals containing a screw dipole and vacancies are presented. Effective diffusivities obtained from KMC simulations are found to be in good agreement with theory. Our model provides an avenue for simulating the interaction of hydrogen with cracks, dislocations, grain boundaries, and other lattice defects, over extended time scales, albeit at atomistic length scales.

scholarly journals A tool for multi-scale modelling of the renal nephron

2011 ◽  
Vol 1 (3) ◽  
pp. 417-425 ◽  
Author(s):  
David P. Nickerson ◽  
Jonna R. Terkildsen ◽  
Kirk L. Hamilton ◽  
Peter J. Hunter
Keyword(s):  
Mathematical Model ◽  
Spatial Scales ◽  
Three Dimensional ◽  
Scale Model ◽  
Model Description ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
One Dimensional ◽  
Multi Scale ◽  
The Mathematical Model

We present the development of a tool, which provides users with the ability to visualize and interact with a comprehensive description of a multi-scale model of the renal nephron. A one-dimensional anatomical model of the nephron has been created and is used for visualization and modelling of tubule transport in various nephron anatomical segments. Mathematical models of nephron segments are embedded in the one-dimensional model. At the cellular level, these segment models use models encoded in CellML to describe cellular and subcellular transport kinetics. A web-based presentation environment has been developed that allows the user to visualize and navigate through the multi-scale nephron model, including simulation results, at the different spatial scales encompassed by the model description. The Zinc extension to Firefox is used to provide an interactive three-dimensional view of the tubule model and the native Firefox rendering of scalable vector graphics is used to present schematic diagrams for cellular and subcellular scale models. The model viewer is embedded in a web page that dynamically presents content based on user input. For example, when viewing the whole nephron model, the user might be presented with information on the various embedded segment models as they select them in the three-dimensional model view. Alternatively, the user chooses to focus the model viewer on a cellular model located in a particular nephron segment in order to view the various membrane transport proteins. Selecting a specific protein may then present the user with a description of the mathematical model governing the behaviour of that protein—including the mathematical model itself and various simulation experiments used to validate the model against the literature.

Three-dimensional Reconstruction of Microscopic Image Based on Multi-ST Algorithm

2020 ◽  
Vol 64 (2) ◽  
pp. 20506-1-20506-7
Author(s):  
Min Zhu ◽  
Rongfu Zhang ◽  
Pei Ma ◽  
Xuedian Zhang ◽  
Qi Guo
Keyword(s):  
3D Reconstruction ◽  
Three Dimensional ◽  
Scale Model ◽  
Microscopic Image ◽  
Multi Scale ◽  
Gaussian Pyramid ◽  
Cost Aggregation ◽  
Dimensional Reconstruction ◽  
Image Pairs ◽  
Accurate Matching

Abstract Three-dimensional (3D) reconstruction is extensively used in microscopic applications. Reducing excessive error points and achieving accurate matching of weak texture regions have been the classical challenges for 3D microscopic vision. A Multi-ST algorithm was proposed to improve matching accuracy. The process is performed in two main stages: scaled microscopic images and regularized cost aggregation. First, microscopic image pairs with different scales were extracted according to the Gaussian pyramid criterion. Second, a novel cost aggregation approach based on the regularized multi-scale model was implemented into all scales to obtain the final cost. To evaluate the performances of the proposed Multi-ST algorithm and compare different algorithms, seven groups of images from the Middlebury dataset and four groups of experimental images obtained by a binocular microscopic system were analyzed. Disparity maps and reconstruction maps generated by the proposed approach contained more information and fewer outliers or artifacts. Furthermore, 3D reconstruction of the plug gauges using the Multi-ST algorithm showed that the error was less than 0.025 mm.

scholarly journals Data-Informed Decomposition for Localized Uncertainty Quantification of Dynamical Systems

Vibration ◽  
2020 ◽  
Vol 4 (1) ◽  
pp. 49-63
Author(s):  
Waad Subber ◽  
Sayan Ghosh ◽  
Piyush Pandita ◽  
Yiming Zhang ◽  
Liping Wang
Keyword(s):  
Dynamical Systems ◽  
Computational Cost ◽  
Three Dimensional ◽  
Region Of Interest ◽  
System Response ◽  
Computational Domain ◽  
User Interest ◽  
Numerical Resolution ◽  
Multi Scale ◽  
Operation Conditions

Industrial dynamical systems often exhibit multi-scale responses due to material heterogeneity and complex operation conditions. The smallest length-scale of the systems dynamics controls the numerical resolution required to resolve the embedded physics. In practice however, high numerical resolution is only required in a confined region of the domain where fast dynamics or localized material variability is exhibited, whereas a coarser discretization can be sufficient in the rest majority of the domain. Partitioning the complex dynamical system into smaller easier-to-solve problems based on the localized dynamics and material variability can reduce the overall computational cost. The region of interest can be specified based on the localized features of the solution, user interest, and correlation length of the material properties. For problems where a region of interest is not evident, Bayesian inference can provide a feasible solution. In this work, we employ a Bayesian framework to update the prior knowledge of the localized region of interest using measurements of the system response. Once, the region of interest is identified, the localized uncertainty is propagate forward through the computational domain. We demonstrate our framework using numerical experiments on a three-dimensional elastodynamic problem.

scholarly journals Strata behavior and control strategy of backfilling collaborate with caving fully-mechanized mining

2020 ◽  
Vol 12 (1) ◽  
pp. 703-717
Author(s):  
Yin Wei ◽  
Wang Jiaqi ◽  
Bai Xiaomin ◽  
Sun Wenjie ◽  
Zhou Zheyuan
Keyword(s):  
Numerical Simulation ◽  
Control Strategy ◽  
Three Dimensional ◽  
Simulation Method ◽  
Mine Pressure ◽  
Hydraulic Support ◽  
Transition Area ◽  
Pressure Concentration ◽  
Strata Behavior ◽  
And Control

AbstractThis article analyzes the technical difficulties in full-section backfill mining and briefly introduces the technical principle and advantages of backfilling combined with caving fully mechanized mining (BCCFM). To reveal the strata behavior law of the BCCFM workface, this work establishes a three-dimensional numerical model and designs a simulation method by dynamically updating the modulus parameter of the filling body. By the analysis of numerical simulation, the following conclusions about strata behavior of the BCCFM workface were drawn. (1) The strata behavior of the BCCFM workface shows significant nonsymmetrical characteristics, and the pressure in the caving section is higher than that in the backfilling section. φ has the greatest influence on the backfilling section and the least influence on the caving section. C has a significant influence on the range of abutment pressure in the backfilling section. (2) There exits the transition area with strong mine pressure of the BCCFM workface. φ and C have significant effect on the degree of pressure concentration but little effect on the influence range of strong mine pressure in the transition area. (3) Under different conditions, the influence range of strong mine pressure is all less than 6 m. This article puts forward a control strategy of mine pressure in the transition area, which is appropriately improving the strength of the transition hydraulic support within the influence range (6 m) in the transition area according to the pressure concentration coefficient. The field measurement value of Ji15-31010 workface was consistent with numerical simulation, which verifies the reliability of control strategy of the BCCFM workface.

scholarly journals Complex community responses underpin biodiversity change following invasion

2021 ◽  
Author(s):  
Alessandra R. Kortz ◽  
Anne E. Magurran
Keyword(s):  
Invasive Species ◽  
Species Richness ◽  
Spatial Scales ◽  
Species Abundance ◽  
Ecological Systems ◽  
Multi Scale ◽  
Mechanistic Approach ◽  
Α Diversity ◽  
Biodiversity Change ◽  
Insight Into

AbstractHow do invasive species change native biodiversity? One reason why this long-standing question remains challenging to answer could be because the main focus of the invasion literature has been on shifts in species richness (a measure of α-diversity). As the underlying components of community structure—intraspecific aggregation, interspecific density and the species abundance distribution (SAD)—are potentially impacted in different ways during invasion, trends in species richness provide only limited insight into the mechanisms leading to biodiversity change. In addition, these impacts can be manifested in distinct ways at different spatial scales. Here we take advantage of the new Measurement of Biodiversity (MoB) framework to reanalyse data collected in an invasion front in the Brazilian Cerrado biodiversity hotspot. We show that, by using the MoB multi-scale approach, we are able to link reductions in species richness in invaded sites to restructuring in the SAD. This restructuring takes the form of lower evenness in sites invaded by pines relative to sites without pines. Shifts in aggregation also occur. There is a clear signature of spatial scale in biodiversity change linked to the presence of an invasive species. These results demonstrate how the MoB approach can play an important role in helping invasion ecologists, field biologists and conservation managers move towards a more mechanistic approach to detecting and interpreting changes in ecological systems following invasion.

scholarly journals Porous Characteristics of Three-Dimensional Disordered Graphene Networks

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 127
Author(s):  
YongChao Wang ◽  
YinBo Zhu ◽  
HengAn Wu
Keyword(s):  
Pore Size ◽  
Low Temperatures ◽  
Gas Adsorption ◽  
Three Dimensional ◽  
Md Simulations ◽  
Structural Features ◽  
Atomic Scale ◽  
Critical Factors ◽  
Chlorination Process ◽  
Porous Morphology

The porous characteristics of disordered carbons are critical factors to their performance on hydrogen storage and electrochemical capacitors. Even though the porous information can be estimated indirectly by gas adsorption experiments, it is still hard to directly characterize the porous morphology considering the complex 3D connectivity. To this end, we construct full-atom disordered graphene networks (DGNs) by mimicking the chlorination process of carbide-derived carbons using annealing-MD simulations, which could model the structure of disordered carbons at the atomic scale. The porous characteristics, including pore volume, pore size distribution (PSD), and specific surface area (SSA), were then computed from the coordinates of carbon atoms. From the evolution of structural features, pores grow dramatically during the formation of polyaromatic fragments and sequent disordered framework. Then structure is further graphitized while the PSD shows little change. For the obtained DGNs, the porosity, pore size, and SSA increase with decreasing density. Furthermore, SSA tends to saturate in the low-density range. The DGNs annealed at low temperatures exhibit larger SSA than high-temperature DGNs because of the abundant free edges.

scholarly journals Study of the Effect of Centrifugal Force on Rotor Blade Icing Process

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Zhengzhi Wang ◽  
Chunling Zhu
Keyword(s):  
Numerical Simulation ◽  
Centrifugal Force ◽  
Rotor Blade ◽  
Flow Direction ◽  
Three Dimensional ◽  
Simulation Method ◽  
Two Phase ◽  
Numerical Simulation Method ◽  
Calculation Results ◽  
Flow Field Characteristics

In view of the rotor icing problems, the influence of centrifugal force on rotor blade icing is investigated. A numerical simulation method of three-dimensional rotor blade icing is presented. Body-fitted grids around the rotor blade are generated using overlapping grid technology and rotor flow field characteristics are obtained by solving N-S equations. According to Eulerian two-phase flow, the droplet trajectories are calculated and droplet impingement characteristics are obtained. The mass and energy conservation equations of ice accretion model are established and a new calculation method of runback water mass based on shear stress and centrifugal force is proposed to simulate water flow and ice shape. The calculation results are compared with available experimental results in order to verify the correctness of the numerical simulation method. The influence of centrifugal force on rotor icing is calculated. The results show that the flow direction and distribution of liquid water on rotor surfaces change under the action of centrifugal force, which lead to the increasing of icing at the stagnation point and the decreasing of icing on both frozen limitations.

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