C haste : incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library

2009 ◽  
Vol 367 (1895) ◽  
pp. 1907-1930 ◽  
Author(s):  
Miguel O. Bernabeu ◽  
Rafel Bordas ◽  
Pras Pathmanathan ◽  
Joe Pitt-Francis ◽  
Jonathan Cooper ◽  
...  
Keyword(s):  
Open Source ◽  
Computational Efficiency ◽  
Large Scale ◽  
Three Dimensional ◽  
Testing Procedure ◽  
Two Dimensions ◽  
Multi Scale ◽  
Bidomain Equations ◽  
Cancer Modelling ◽  
Set Up

Recent work has described the software engineering and computational infrastructure that has been set up as part of the Cancer, Heart and Soft Tissue Environment (C haste ) project. C haste is an open source software package that currently has heart and cancer modelling functionality. This software has been written using a programming paradigm imported from the commercial sector and has resulted in a code that has been subject to a far more rigorous testing procedure than that is usual in this field. In this paper, we explain how new functionality may be incorporated into C haste . Whiteley has developed a numerical algorithm for solving the bidomain equations that uses the multi-scale (MS) nature of the physiology modelled to enhance computational efficiency. Using a simple geometry in two dimensions and a purpose-built code, this algorithm was reported to give an increase in computational efficiency of more than two orders of magnitude. In this paper, we begin by reviewing numerical methods currently in use for solving the bidomain equations, explaining how these methods may be developed to use the MS algorithm discussed above. We then demonstrate the use of this algorithm within the C haste framework for solving the monodomain and bidomain equations in a three-dimensional realistic heart geometry. Finally, we discuss how C haste may be developed to include new physiological functionality—such as modelling a beating heart and fluid flow in the heart—and how new algorithms aimed at increasing the efficiency of the code may be incorporated.

scholarly journals Vibration characteristics of triple-gear-rotor system in compressed air energy storage under variable torque load

2021 ◽  
Vol 104 (1) ◽  
pp. 003685042098705
Author(s):  
Xinran Wang ◽  
Yangli Zhu ◽  
Wen Li ◽  
Dongxu Hu ◽  
Xuehui Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Three Dimensional ◽  
Element Model ◽  
Rotor System ◽  
Dynamic Responses ◽  
System Response ◽  
Rotating Speed ◽  
Torque Load ◽  
Set Up ◽  
Two Stages

This paper focuses on the effects of the off-design operation of CAES on the dynamic characteristics of the triple-gear-rotor system. A finite element model of the system is set up with unbalanced excitations, torque load excitations, and backlash which lead to variations of tooth contact status. An experiment is carried out to verify the accuracy of the mathematical model. The results show that when the system is subjected to large-scale torque load lifting at a high rotating speed, it has two stages of relatively strong periodicity when the torque load is light, and of chaotic when the torque load is heavy, with the transition between the two states being relatively quick and violent. The analysis of the three-dimensional acceleration spectrum and the meshing force shows that the variation in the meshing state and the fluctuation of the meshing force is the basic reasons for the variation in the system response with the torque load. In addition, the three rotors in the triple-gear-rotor system studied show a strong similarity in the meshing states and meshing force fluctuations, which result in the similarity in the dynamic responses of the three rotors.

The structure of weakly compressible grid-generated turbulence

2001 ◽  
Vol 432 ◽  
pp. 219-283 ◽  
Author(s):  
G. BRIASSULIS ◽  
J. H. AGUI ◽  
Y. ANDREOPOULOS
Keyword(s):  
Mach Number ◽  
Large Scale ◽  
Isotropic Turbulence ◽  
Three Dimensional ◽  
High Amplitude ◽  
Time Dependent ◽  
Wide Range ◽  
Dynamical Flow ◽  
Set Up ◽  
Decay Exponent

A decaying compressible nearly homogeneous and nearly isotropic grid-generated turbulent flow has been set up in a large scale shock tube research facility. Experiments have been performed using instrumentation with spatial resolution of the order of 7 to 26 Kolmogorov viscous length scales. A variety of turbulence-generating grids provided a wide range of turbulence scales with bulk flow Mach numbers ranging from 0.3 to 0.6 and turbulent Reynolds numbers up to 700. The decay of Mach number fluctuations was found to follow a power law similar to that describing the decay of incompressible isotropic turbulence. It was also found that the decay coefficient and the decay exponent decrease with increasing Mach number while the virtual origin increases with increasing Mach number. A possible mechanism responsible for these effects appears to be the inherently low growth rate of compressible shear layers emanating from the cylindrical rods of the grid. Measurements of the time-dependent, three dimensional vorticity vectors were attempted for the first time with a 12-wire miniature probe. This also allowed estimates of dilatation, compressible dissipation and dilatational stretching to be obtained. It was found that the fluctuations of these quantities increase with increasing mean Mach number of the flow. The time-dependent signals of enstrophy, vortex stretching/tilting vector and dilatational stretching vector were found to exhibit a rather strong intermittent behaviour which is characterized by high-amplitude bursts with values up to 8 times their r.m.s. within periods of less violent and longer lived events. Several of these bursts are evident in all the signals, suggesting the existence of a dynamical flow phenomenon as a common cause.

scholarly journals Computational generation of an annotated gigalibrary of synthesizable, composite peptidic macrocycles

2020 ◽  
Vol 117 (40) ◽  
pp. 24679-24690
Author(s):  
Ishika Saha ◽  
Eric K. Dang ◽  
Dennis Svatunek ◽  
Kendall N. Houk ◽  
Patrick G. Harran
Keyword(s):  
Virtual Screening ◽  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Three Dimensional ◽  
Pharmacological Properties ◽  
Robust Methods ◽  
Small Peptide ◽  
Multistep Reaction ◽  
Condensed Heterocycles

Peptidomimetic macrocycles have the potential to regulate challenging therapeutic targets. Structures of this type having precise shapes and drug-like character are particularly coveted, but are relatively difficult to synthesize. Our laboratory has developed robust methods that integrate small-peptide units into designed scaffolds. These methods create macrocycles and embed condensed heterocycles to diversify outcomes and improve pharmacological properties. The hypothetical scope of the methodology is vast and far outpaces the capacity of our experimental format. We now describe a computational rendering of our methodology that creates an in silico three-dimensional library of composite peptidic macrocycles. Our open-source platform, CPMG (Composite Peptide Macrocycle Generator), has algorithmically generated a library of 2,020,794,198 macrocycles that can result from the multistep reaction sequences we have developed. Structures are generated based on predicted site reactivity and filtered on the basis of physical and three-dimensional properties to identify maximally diverse compounds for prioritization. For conformational analyses, we also introduce ConfBuster++, an RDKit port of the open-source software ConfBuster, which allows facile integration with CPMG and ready parallelization for better scalability. Our approach deeply probes ligand space accessible via our synthetic methodology and provides a resource for large-scale virtual screening.

Simulation of Ideal Grain Growth Using the Multi-Phase-Field Model

2007 ◽  
Vol 558-559 ◽  
pp. 1177-1181 ◽  
Author(s):  
Philippe Schaffnit ◽  
Markus Apel ◽  
Ingo Steinbach
Keyword(s):  
Grain Size ◽  
Grain Growth ◽  
Phase Field ◽  
Large Scale ◽  
Field Model ◽  
Three Dimensional ◽  
Phase Field Model ◽  
Two Dimensions ◽  
Von Neumann ◽  
Average Grain Size

The kinetics and topology of ideal grain growth were simulated using the phase-field model. Large scale phase-field simulations were carried out where ten thousands grains evolved into a few hundreds without allowing coalescence of grains. The implementation was first validated in two-dimensions by checking the conformance with square-root evolution of the average grain size and the von Neumann-Mullins law. Afterwards three-dimensional simulations were performed which also showed fair agreement with the law describing the evolution of the mean grain size against time and with the results of S. Hilgenfeld et al. in 'An Accurate von Neumann's Law for Three-Dimensional Foams', Phys. Rev. Letters, 86(12)/2685, March 2001. Finally the steady state grain size distribution was investigated and compared to the Hillert theory.

scholarly journals Multi-Scale 3D Cryo-Correlative Microscopy for Vitrified Cells

2020 ◽  
Author(s):  
Gong-Her Wu ◽  
Patrick G. Mitchell ◽  
Jesus G. Galaz-Montoya ◽  
Corey W. Hecksel ◽  
Emily M. Sontag ◽  
...  
Keyword(s):  
Large Scale ◽  
Focused Ion Beam ◽  
Electron Tomography ◽  
3D Visualization ◽  
Ion Beam ◽  
Three Dimensional ◽  
Yeast Cells ◽  
Multi Scale ◽  
Fluorescence Confocal Microscopy ◽  
Cryo Electron Tomography

SUMMARYThree-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labelled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could be used for large-scale phenotypic studies of frozen-hydrated specimens in a variety of healthy and diseased conditions with and without treatments.

scholarly journals Wave-activity conservation laws for the three-dimensional anelastic and Boussinesq equations with a horizontally homogeneous background flow

2007 ◽  
Vol 594 ◽  
pp. 493-506 ◽  
Author(s):  
TIFFANY A. SHAW ◽  
THEODORE G. SHEPHERD
Keyword(s):  
Conservation Laws ◽  
Large Scale ◽  
Three Dimensional ◽  
Phase Speed ◽  
Wave Activity ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Dimensional Problem ◽  
Background Flow ◽  
Homogeneous Background

Wave-activity conservation laws are key to understanding wave propagation in inhomogeneous environments. Their most general formulation follows from the Hamiltonian structure of geophysical fluid dynamics. For large-scale atmospheric dynamics, the Eliassen–Palm wave activity is a well-known example and is central to theoretical analysis. On the mesoscale, while such conservation laws have been worked out in two dimensions, their application to a horizontally homogeneous background flow in three dimensions fails because of a degeneracy created by the absence of a background potential vorticity gradient. Earlier three-dimensional results based on linear WKB theory considered only Doppler-shifted gravity waves, not waves in a stratified shear flow. Consideration of a background flow depending only on altitude is motivated by the parameterization of subgrid-scales in climate models where there is an imposed separation of horizontal length and time scales, but vertical coupling within each column. Here we show how this degeneracy can be overcome and wave-activity conservation laws derived for three-dimensional disturbances to a horizontally homogeneous background flow. Explicit expressions for pseudoenergy and pseudomomentum in the anelastic and Boussinesq models are derived, and it is shown how the previously derived relations for the two-dimensional problem can be treated as a limiting case of the three-dimensional problem. The results also generalize earlier three-dimensional results in that there is no slowly varying WKB-type requirement on the background flow, and the results are extendable to finite amplitude. The relationship $A^{\cal E}\,{=}\,cA^{\cal P}$ between pseudoenergy $A^{\cal E}$ and pseudomomentum $A^{\cal P}$, where c is the horizontal phase speed in the direction of symmetry associated with $A^{\cal P}$, has important applications to gravity-wave parameterization and provides a generalized statement of the first Eliassen–Palm theorem.

Small-Scale Models for Testing Masonry Structures

2010 ◽  
Vol 133-134 ◽  
pp. 497-502 ◽  
Author(s):  
Alvaro Quinonez ◽  
Jennifer Zessin ◽  
Aissata Nutzel ◽  
John Ochsendorf
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Three Dimensional ◽  
Model Testing ◽  
Scale Model ◽  
Small Scale ◽  
Material Strength ◽  
Masonry Structures ◽  
Scale Models ◽  
Set Up

Experiments may be used to verify numerical and analytical results, but large-scale model testing is associated with high costs and lengthy set-up times. In contrast, small-scale model testing is inexpensive, non-invasive, and easy to replicate over several trials. This paper proposes a new method of masonry model generation using three-dimensional printing technology. Small-scale models are created as an assemblage of individual blocks representing the original structure’s geometry and stereotomy. Two model domes are tested to collapse due to outward support displacements, and experimental data from these tests is compared with analytical predictions. Results of these experiments provide a strong understanding of the mechanics of actual masonry structures and can be used to demonstrate the structural capacity of masonry structures with extensive cracking. Challenges for this work, such as imperfections in the model geometry and construction problems, are also addressed. This experimental method can provide a low-cost alternative for the collapse analysis of complex masonry structures, the safety of which depends primarily on stability rather than material strength.

scholarly journals OptiJ: Open-source optical projection tomography of large organ samples

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Pedro P. Vallejo Ramirez ◽  
Joseph Zammit ◽  
Oliver Vanderpoorten ◽  
Fergus Riche ◽  
Francois-Xavier Blé ◽  
...  
Keyword(s):  
Open Source ◽  
Low Cost ◽  
Three Dimensional ◽  
Optical Projection Tomography ◽  
Optical Components ◽  
Adult Mice ◽  
Optical Projection ◽  
Set Up ◽  
Imagej Plugin ◽  
Lung Lobes

Abstract The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.

scholarly journals The influence of uncertain loading on topology-optimized designs

2021 ◽  
Author(s):  
Philipp Hofer ◽  
Erich Wehrle
Keyword(s):  
Topology Optimization ◽  
Open Source ◽  
Large Scale ◽  
Three Dimensional ◽  
Applied Force ◽  
Structural Performance ◽  
Optimized Design ◽  
Applied Forces ◽  
Reducing Costs ◽  
The Relationship

The design of structures using topology optimization can improve the structural performance and save material, in turn reducing costs. Using a framework of large-scale, three-dimensional topology optimization implemented by the authors in an open-source multiphysical software, we investigate the influence of uncertain loading on the optimized design. Direct differentiation is used to reveal the relationship between displacements and applied force, giving an efficient and effective tool to postprocess optimized topologies. The developed methodology for the assessment of the sensitivity with respect to applied forces is explored using two three-dimensional examples: the classic MBB cantilever and a cableway pylon. The advantages and limitations of this method are discussed.

Virtual Demonstration Tests of Large-Scale and Complex Artifacts Using an Open Source Parallel CAE System, ADVENTURE

2006 ◽  
Vol 110 ◽  
pp. 133-142 ◽  
Author(s):  
Shinobu Yoshimura
Keyword(s):  
Open Source ◽  
Large Scale ◽  
Three Dimensional ◽  
Element Model ◽  
General Purpose ◽  
Full Scale ◽  
Grid Environments ◽  
Dimensional Finite Element ◽  
Three Dimensional Finite Element ◽  
Cae System

The ADVENTURE project started as one of the research projects in the "Computational Science & Engineering" field selected for the "Research for the Future" Program sponsored by the Japan Society for the Promotion of Science during 1997-2002. Since March 2002, the project has continued as an independent project. In the project we have been developing an advanced general-purpose computational mechanics system, named ADVENTURE, running in various kinds of parallel and ditributed environments. The system is designed to be able to analyze a three-dimensional finite element model of arbitrary shape with 10-100 million DOFs mesh, and additionally to enable parametric and non-parametric shape optimization. The first version of the system has been released from the project website as open source software since March, 2002. 2,049 registered users in academia and industries have downloaded 12,827 modules and been using them, while one company has developed and released its commercial version named ADVENTUREcluster. The ADVENTURE system has been successfully implemented in various types of parallel and distributed environments including PC clusters, massively parallel processers such as Hitachi SR8000/MPP and the Earth Simulator, and Grid environments such as ITBL (IT-based Laboratory). The system has been successfully applied to solve various real world problems such as response of a full scale nuclear pressure vessel model and thermoelastic deformation of full scale electric mounting board of a mobile PC.

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