Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations

Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from laptops to petascale supercomputers, including combinations of these. Our work features two multiscale applications, in-stent restenosis and cerebrovascular bloodflow, which combine multiple existing single-scale applications to create a multiscale simulation. These applications can be efficiently coupled, deployed and executed on computers up to the largest (peta) scale, incurring a coupling overhead of 1–10% of the total execution time.

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Hierarchical Multiscale Modeling of Tire–Soil Interaction for Off-Road Mobility Simulation

Journal of Computational and Nonlinear Dynamics ◽

10.1115/1.4042510 ◽

2019 ◽

Vol 14 (6) ◽

Cited By ~ 2

Author(s):

Hiroki Yamashita ◽

Guanchu Chen ◽

Yeefeng Ruan ◽

Paramsothy Jayakumar ◽

Hiroyuki Sugiyama

Keyword(s):

High Performance ◽

Computational Models ◽

Computational Cost ◽

Interaction Model ◽

High Fidelity ◽

Wheel Load ◽

Mobility Performance ◽

Wide Range ◽

Computationally Intensive ◽

Soil Bin

A high-fidelity computational terrain dynamics model plays a crucial role in accurate vehicle mobility performance prediction under various maneuvering scenarios on deformable terrain. Although many computational models have been proposed using either finite element (FE) or discrete element (DE) approaches, phenomenological constitutive assumptions in FE soil models make the modeling of complex granular terrain behavior very difficult and DE soil models are computationally intensive, especially when considering a wide range of terrain. To address the limitations of existing deformable terrain models, this paper presents a hierarchical FE–DE multiscale tire–soil interaction simulation capability that can be integrated in the monolithic multibody dynamics solver for high-fidelity off-road mobility simulation using high-performance computing (HPC) techniques. It is demonstrated that computational cost is substantially lowered by the multiscale soil model as compared to the corresponding pure DE model while maintaining the solution accuracy. The multiscale tire–soil interaction model is validated against the soil bin mobility test data under various wheel load and tire inflation pressure conditions, thereby demonstrating the potential of the proposed method for resolving challenging vehicle-terrain interaction problems.

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The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2008.0081 ◽

2008 ◽

Vol 366 (1879) ◽

pp. 3343-3360 ◽

Cited By ~ 70

Author(s):

D.J.W Evans ◽

P.V Lawford ◽

J Gunn ◽

D Walker ◽

D.R Hose ◽

...

Keyword(s):

Coronary Artery ◽

Spatial Scales ◽

Multiscale Model ◽

Multiscale Modelling ◽

Agent Based ◽

Stent Restenosis ◽

Biomedical Systems ◽

Single Scale ◽

Wide Range ◽

Generic Description

The inherent complexity of biomedical systems is well recognized; they are multiscale, multiscience systems, bridging a wide range of temporal and spatial scales. While the importance of multiscale modelling in this context is increasingly recognized, there is little underpinning literature on the methodology and generic description of the process. The COAST (complex autonoma simulation technique) project aims to address this by developing a multiscale, multiscience framework, coined complex autonoma (CxA), based on a hierarchical aggregation of coupled cellular automata (CA) and agent-based models (ABMs). The key tenet of COAST is that a multiscale system can be decomposed into N single-scale CA or ABMs that mutually interact across the scales. Decomposition is facilitated by building a scale separation map on which each single-scale system is represented according to its spatial and temporal characteristics. Processes having well-separated scales are thus easily identified as the components of the multiscale model. This paper focuses on methodology, introduces the concept of the CxA and demonstrates its use in the generation of a multiscale model of the physical and biological processes implicated in a challenging and clinically relevant problem, namely coronary artery in-stent restenosis.

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Combined Microstructure and Heat Conduction Modeling of Heterogeneous Interfaces and Materials

Journal of Heat Transfer ◽

10.1115/1.4023583 ◽

2013 ◽

Vol 135 (6) ◽

Cited By ~ 8

Author(s):

Ishan Srivastava ◽

Sridhar Sadasivam ◽

Kyle C. Smith ◽

Timothy S. Fisher

Keyword(s):

Transport Properties ◽

High Performance ◽

Energy Transport ◽

Heterogeneous Materials ◽

Operating Conditions ◽

High Fidelity ◽

Energy Materials ◽

Wide Range ◽

Material State ◽

Random Structures

Heterogeneous materials are becoming more common in a wide range of functional devices, particularly those involving energy transport, conversion, and storage. Often, heterogeneous materials are crucial to the performance and economic scalability of such devices. Heterogeneous materials with inherently random structures exhibit a strong sensitivity of energy transport properties to processing and operating conditions. Therefore, improved predictive modeling capabilities are needed that quantify the detailed microstructure of such materials based on various manufacturing processes and correlate them with transport properties. In this work, we integrate high fidelity microstructural and transport models, which can aid in the development of high performance energy materials. Heterogeneous materials are generally comprised of nanometric or larger length scale domains of different materials or different phases of the same material. State-of-the-art structural optimization models demonstrate the predictability of the microstructure for heterogeneous materials manufactured via powder compaction of variously shaped and sized particles. The ability of existing diffusion models to incorporate the essential multiscale features in random microstructures is assessed. Lastly, a comprehensive approach is presented for the combined modeling of a high fidelity microstructure and heat transport therein. Exemplary results are given that reinforce the importance of developing predictive models with rich stochastic output that connect microstructural information with physical transport properties.

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SERPENT/SUBCHANFLOW COUPLED CALCULATIONS FOR A VVER CORE AT HOT FULL POWER

EPJ Web of Conferences ◽

10.1051/epjconf/202124704006 ◽

2021 ◽

Vol 247 ◽

pp. 04006

Author(s):

Diego Ferraro ◽

Manuel García ◽

Uwe Imke ◽

Ville Valtavirta ◽

Riku Tuominen ◽

...

Keyword(s):

High Performance ◽

Neutron Transport ◽

Coupling Scheme ◽

High Fidelity ◽

Reactor Physics ◽

Coupled Calculation ◽

Final Goal ◽

Wide Range ◽

Computational Resources ◽

Full Core

An increasing interest on the development of highly accurate methodologies in reactor physics is nowadays observed, mainly stimulated by the availability of vast computational resources. As a result, an on-going development of a wide range of coupled calculation tools is observed within diverse projects worldwide. Under this framework, the McSAFE European Union project is a coordinated effort aimed to develop multiphysics tools based on Monte Carlo neutron transport and subchannel thermal-hydraulics codes. These tools are aimed to be suitable for high-fidelity calculations both for PWR and VVER reactors, with the final goal of performing pin-by-pin coupled calculations at full core scope including burnup. Several intermediate steps are to be analyzed in-depth before jumping into this final goal in order to provide insights and to identify resources requirements. As part of this process, this work presents the results for a pin-by-pin coupling calculation using the Serpent 2 code (developed by VTT, Finland) and the subchannel code SUBCHANFLOW (SCF, developed by KIT, Germany) for a full-core VVER model. For such purpose, a recently refurbished master-slave coupling scheme is used within a High Performance Computing architecture. A full-core benchmark for a VVER-1000 that provides experimental data is considered, where the first burnup step (i.e. fresh core at hot-full rated power state) is calculated. For such purpose a detailed (i.e. pin-by-pin) coupled Serpent-SCF model is developed, including a simplified equilibrium xenon distribution (i.e. by fuel assembly). Comparisons with main global reported results are presented and briefly discussed, together with a raw estimation of resources requirements and a brief demonstration of the inherent capabilities of the proposed approach. The results presented here provide valuable insights and pave the way to tackle the final goals of the on-going high-fidelity project.

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In-stent restenosis in the mid-term period after successful coronary arteries chronic total occlusion recanalization by antegrade approach

Proceedings of the National Academy of Sciences of Belarus Medical series ◽

10.29235/1814-6023-2019-16-1-65-76 ◽

2019 ◽

Vol 16 (1) ◽

pp. 65-76

Author(s):

V. I. Stelmashok

Keyword(s):

Coronary Artery ◽

Coronary Arteries ◽

Chronic Total Occlusion ◽

Total Occlusion ◽

Stent Restenosis ◽

Antegrade Approach ◽

Wide Range ◽

The Right ◽

Range Of Values ◽

In Stent Restenosis

The results on the in-stent restenosis in the mid-term period after successful coronary arteries chronic total occlusion (CTO) recanalization by the antegrade approach are assessed. The study included 117 patients who underwent coronary artery CTO recanalization for the period from 2009 to 2012. After 6.1 ± 0.9 months (stage К1) and 12.7 ± 1.6 months (stage К2), all patients were examined by coronary angiography, intravascular ultrasound and optical coherence tomography. During the frst half of the year after the CTO recanalization, there was a more frequent in-stent restenosis rate in the right coronary artery (in 25.6 %) as well as a predominance of focal types of restenosis (59.1 % of the total). The incidence of restenosis depending on the DES type varied over a wide range of values (from 0 to 52.4 % in the frst half of the year and from 0 to 41.2 % in the second half of the year). A signifcant increase in the incidence of restenosis was observed after the trapidil eluting stents implantation (52.4 % in the frst half of the year, 26.3 % in the second half of the year) and sirolimus eluting stents (38.9 % in the frst half, 41.2 % in the second half of the year). Our data show that different types of DES differently determine the changes in the vascular lumen during the medium term period after the successful CTO recanalization.

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