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particle-based modeling and GPU-accelerated simulation of cellular blood flow

COMPUTER PHYSICS COMMUNICATIONS 2025年 306卷

作者： Xia, Zehong Zhu, Ziwei Ye, Ting Sun, Ni Jilin Univ Sch Math Qianjin Ave 2699 Changchun 130012 Jilin Peoples R China

Computational modeling and simulation of cellular blood flow is highly desired for understanding blood microcirculation and blood-related diseases such as thrombosis and tumor, but it remains a challenging task primarily because blood in microvessels should be described as a dense suspension of different types of deformable cells. The focus of the present work is on the development of a particle-based and GPU-accelerated numerical method that is able to quickly simulate the various behaviors of deformable cells in three-dimensional arbitrarily complex geometries. We employ a two-fluid model to describe blood flow, incorporating the deformation and aggregation of cells. A smoothed dissipative particle dynamics is used to solve the two-fluid model, and a discrete microstructure model is applied for the cell deformation, as well as a Morse potential model for the cell aggregation. The heterogeneous CPU-GPU environment is established, where each GPU thread is dedicated to a particle, and the CPU is mainly responsible for loading and exporting data. Five test cases are conducted against analytical theory, experimental data, and previous numerical results, for pure fluid, cell deformation, cell aggregation, cell suspension and the cellular flow in a complex network, respectively. It is shown that the methodology can accurately predict various behaviors of cells, and the GPU is well suited for particle-based modeling. Especially for cellular blood flow, where calculating cellular forces is a compute-intensive and timeconsuming task, the GPU offers exceptional parallel capabilities, significantly enhancing the simulation efficiency. The speedup is about 3.5 times faster than the CPU parallelization with 96 cores for the pure fluid, and this acceleration nearly reaches 20 times when cells are included in the simulations. Particularly, the calculations for deformation and aggregation forces demonstrate a substantial speedup, achieving the improvements of up to 120 and 640 tim

关键词： Cell simulation Blood simulation Red blood cell particle-based modeling GPU parallelization

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particle-based modeling of the compaction of fiber yarns and woven textiles

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TEXTILE RESEARCH JOURNAL 2014年第11期84卷 1159-1173页

作者： Samadi, Reza Robitaille, Francois Univ Ottawa Dept Mech Engn Ottawa ON K1N 6N5 Canada

This paper proposes a particle-based modeling method for predicting the constitutive behavior of textiles when subjected to various compressive loading conditions. The method, which is demonstrated for stacked layers of plain woven textiles, utilizes discrete mechanics as an alternative to traditional continuum mechanics. Fibers are modeled as a series of conjoined points, and their configurations are determined mechanistically using a modified Metropolis algorithm and inter-particle strain energy terms. The implementation presented in this paper enables intricate geometric modeling of textiles at microscopic, mesoscopic and macroscopic scales. It also enables extensive mechanical modeling of the textiles, from first principles, as they are loaded upon manufacturing of typical technical textile structures. While this paper focuses on the compaction behavior of weaves, the modeling method is readily adaptable to the analysis of shear, bending, buckling, punching, relaxation and other loading scenarios applied on a wide array of different textile types. These scenarios will be demonstrated in forthcoming publications. Comparative data from in silico and in situ testing shows excellent agreement. Results demonstrate an improvement in simulation accuracy over prior comparable modeling techniques. The method presented here successfully predicts the actual behavior of yarns, single-layer and double-layer textile stacks in compaction.

关键词： yarns weaves textile mechanics numerical simulation particle-based modeling Metropolis algorithm compaction

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A PCISPH implementation using distributed multi-GPU acceleration for simulating industrial engineering applications

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INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2020年第4期34卷 450-464页

作者： Verma, Kevin McCabe, Christopher Peng, Chong Wille, Robert ESS Engn Software Steyr GmbH A-4400 Steyr Austria Johannes Kepler Univ Linz Inst Integrated Circuits Linz Austria Univ Bodenkultur Inst Geotech Vienna Austria

Predictive-corrective incompressible smoothed particle hydrodynamics (PCISPH) is a promising variant of the particle-based fluid modeling technique smoothed particle hydrodynamics (SPH). In PCISPH, a dedication prediction-correction scheme is employed which allows for using a larger time step and thereby outperforms other SPH variants by up to one order of magnitude. However, certain characteristics of the PCISPH lead to severe synchronization problems that, thus far, prevented PCISPH from being applied to industrial scenarios where high performance computing techniques need to leveraged in order to simulate in appropriate resolution. In this work, we are for the first time, presenting a highly accelerated PCISPH implementation which employs a distributed multi-GPU architecture. To that end, dedicated optimization techniques are presented that allow to overcome the drawbacks caused by the algorithmic characteristics of PCISPH. Experimental evaluations on a standard dam break test case and an industrial water splash scenario confirm that PCISPH can be efficiently employed to model real-world scenarios involving a large number of particles.

关键词： Computational fluid dynamics particle-based modeling smoothed particle hydrodynamics multi-GPU domain decomposition

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particle-based simulation of the interaction between fluid and knitwear

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SIGNAL IMAGE AND VIDEO PROCESSING 2014年第3期8卷 415-422页

作者： Gudukbay, Ugur Bayraktar, Serkan Koca, Cetin Ozguc, Bulent Bilkent Univ Dept Comp Engn TR-06800 Bilkent Turkey

We present a particle-based method to simulate and visualize the interaction of knitwear with fluids. The knitwear is modeled using spring-mass systems and the fluid is modeled using the smoothed particle hydrodynamics method. Two-way coupling is achieved by considering surface tension, capillary, and interparticle forces between the fluid and knitwear. The simulation of fluid and knitwear particles is performed on the graphics processing unit. Photorealistic rendering of knitwear and fluid is achieved by using a hardware-accelerated rasterization-based rendering technique. Our method is able to simulate and visualize the macro- and microstructure of free-form knitwear and reflective and refractive characteristics of the fluid surface.

关键词： Physically-based modeling Fluid simulation particle-based modeling Smoothed particle hydrodynamics Knitwear Graphics processing unit Lumislice

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Kinetic and structural requirements for a CO₂ adsorbent in sorption enhanced catalytic reforming of methane - Part I: Reaction kinetics and sorbent capacity

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FUEL 2012年 99卷 154-164页

作者： Halabi, M. H. de Croon, M. H. J. M. van der Schaaf, J. Cobden, P. D. Schouten, J. C. Eindhoven Univ Technol Dept Chem Engn & Chem Lab Chem Reactor Engn NL-5600 MB Eindhoven Netherlands Energy Res Ctr Netherlands NL-1755 ZG Petten Netherlands

This paper presents a fundamental model-based analysis for the applicability of integration of a highly active Rh/Ce alpha Zr1-alpha O2 catalyst with two candidate CO2 sorbents for pure H-2 production in low temperature sorption-enhanced steam reforming of methane. K-promoted hydrotalcite and lithium zirconate solids are considered in the investigation as CO2 sorbents. The process is analyzed using multi-scale modeling levels of a heterogeneous particle-based model, a heterogeneous bulk-scale model, and a homogenous bulk-scale model. The presence of this active catalyst dictates strict requirements on the sorbent in terms of fast adsorption kinetics for an efficient process performance. The maximum CH4 conversion enhancement is determined to be a strong function of sorption kinetics. This enhancement is not affected by a higher sorbent capacity at slow adsorption kinetics. The process is studied using two fixed bed configurations of an integrated dual function particle and an admixture bed of catalyst/sorbent particles. Optimal operating conditions for the hydrotalcite-based system are identified to provide CH4 conversion of 98% with high H-2 purity of 99.8% and low CO2 contamination (<250 ppm). The lithium zirconate-based system can provide CH4 conversion and H-2 purity of 99.9% at identical conditions. based on the end application of H-2 produced, the process can be tuned to feed gas turbine cycles, fuel cells, or petrochemical plants. (C) 2012 Elsevier Ltd. All rights reserved.

关键词： Sorption enhanced steam reforming Hydrogen production particle-based modeling Rh-based catalyst Hydrotalcite and lithium zirconate sorbents

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Multivariate quadrature for representing cloud condensation nuclei activity of aerosol populations

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JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES 2017年第18期122卷 9867-9878页

作者： Fierce, Laura McGraw, Robert L. Brookhaven Natl Lab Climate & Environm Sci Dept Upton NY 11973 USA Univ Corp Atmospher Res Visiting Scientist Programs Boulder CO 80305 USA

Atmospheric aerosol is composed of distinct multicomponent particles that are continuously modified as they are transported in the atmosphere. Resolving variability in particle physical and chemical properties requires tracking high-dimensional probability density functions, which is not practical in large-scale atmospheric simulations. Reduced representations of atmospheric aerosol are needed for efficient regional-and global-scale chemical transport models. Although the aerosol size-composition distribution is described by a high-dimensional probability density function, here we show that cloud condensation nuclei activity of aerosol populations can be represented with high accuracy using an optimized set of representative particles. The sparse representation of the aerosol mixing state, designed for use in quadrature-based moment models, is constructed from a linear program that is combined with an entropy-inspired cost function. Unlike reduced representations common to large-scale atmospheric models, such as modal and sectional schemes, the maximum-entropy approach described here is not confined to predetermined size bins or assumed distribution shapes. This study is a first step toward a quadrature-based aerosol scheme that will track multivariate aerosol distributions with sufficient computational efficiency for large-scale simulations.

关键词： aerosol modeling cloud condensation nuclei particle-based modeling quadrature method of moments

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ADVANCED OBJECT-ORIENTED METHODS AND CONCEPTS FOR SIMULATIONS OF MULTIBODY SYSTEMS

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JOURNAL OF VISUALIZATION AND COMPUTER ANIMATION 1993年第2期4卷 95-111页

作者： KUHN, V MULLER, W TH DARMSTADT INTERACT GRAPH SYST GRP W-6100 DARMSTADT GERMANY

A common way to simulate the motion and behaviour of a complex system is to approximate it with a multi-body system based on particles, and to evaluate the particle interactions over time. Normally, the calculations require such a large amount of computer power that methods have been developed to decrease computation time by taking advantage of new computer architectures. These methods have been in use since the early 1980s, but there is still a lack of concepts supporting the application of these methods, to build highly efficient simulation systems with reusable entities. In this paper we describe a new approach for the development of flexible, efficient methods and techniques to control multi-body systems. The major goal of our concept is the integration of advanced modern simulation techniques such as particle-based modelling and simulated annealing, and efficient data structures such as octrees and the Greengard algorithm. We introduce high-level concepts represented by agents, environments, and controllers based on and supported by the object-oriented paradigm. We demonstrate the flexibility of our new simuation system for applications related to environmental research and air quality control.

关键词： COMPUTER GRAPHICS VISUALIZATION REAL-TIME COMPUTER ANIMATION AND SIMULATION MOTION CONTROL PHYSICALLY-based modeling particle-based modeling FAST MULTIPOLE METHOD

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particle-based simulation and visualization of fluid flows through porous media

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JOURNAL OF VISUALIZATION 2010年第4期13卷 327-336页

作者： Bayraktar, Serkan Gudukbay, Ugur Ozguc, Bulent Bilkent Univ Dept Comp Engn TR-06800 Ankara Turkey

We propose a method of fluid simulation where boundary conditions are designed in such a way that fluid flow through porous media, pipes, and chokes can be realistically simulated. Such flows are known to be low Reynolds number incompressible flows and occur in many real life situations. To obtain a high quality fluid surface, we include a scalar value in isofunction. The scalar value indicates the relative position of each particle with respect to the fluid surface.

关键词： Physically based modeling Fluid simulation particle-based modeling Smoothed particle hydrodynamics

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A physically-based particle model of woven cloth

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The Visual Computer 1992年第5-6期8卷 264-277页

作者： Breen, David E. House, Donald H. Getto, Phillip H. Rensselaer Design Research Center Rensselaer Polytechnic Institute Troy 12180-3590 NY United States Department of Computer Science Williams College Williamstown 01267 MA United States Rasna Corporation San Jose 95131 CA 2590 N. First St. Suite 200 United States

Every time a tablecloth is draped over a table it will fold and pleat in unique ways. We report on a physically-based model and a simulation methodology, which when used together are able to reproduce many of the attributes of this characteristic behavior of cloth. Our model utilizes a microscopic particle representation that directly treats the mechanical constraints between the threads in woven material rather than using a macroscopic continuum approximation. The simulation technique is hybrid, employing force methods for gross movement and energy methods to enforce constraints within the material. The model is developed and demonstrated within a visualization environment that allows full interaction between the simulated material and conventional constructive-solid-geometry models. © 1992 Springer-Verlag.

关键词： Cloth modeling Metropolis algorithm particle-based modeling Physically based modeling Visualization

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Incomplete Cell Sorting Creates Engineerable Structures with Long-Term Stability

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CELL REPORTS PHYSICAL SCIENCE 2021年第1期2卷

作者： Tordoff, Jesse Krajnc, Matej Walczak, Nicholas Lima, Matthew Beal, Jacob Shvartsman, Stanislav Weiss, Ron MIT Computat & Syst Biol Program 77 Massachusetts Ave Cambridge MA 02139 USA Princeton Univ Lewis Sigler Inst Integrat Genom Princeton NJ 08544 USA Raytheon BBN Technol Waltham MA 02451 USA MIT Dept Biol Engn Synthet Biol Ctr 77 Massachusetts Ave Cambridge MA 02139 USA Princeton Univ Dept Chem & Biol Engn Princeton NJ 08544 USA Princeton Univ Dept Mol Biol Princeton NJ 08544 USA

Adhesion-mediated cell sorting has long been considered an organizing principle in developmental biology. While most computational models have emphasized the dynamics of segregation to fully sorted structures, cell sorting can also generate a plethora of transient, incompletely sorted states. The timescale of such states in experimental systems is unclear: if they are long-lived, they can be harnessed by development or engineered in synthetic tissues. Here, we use experiments and computational modeling to demonstrate how such structures can be systematically designed by quantitative control of cell composition. By varying the number of highly adhesive and less adhesive cells in multicellular aggregates, we find the cell-type ratio and total cell count control pattern formation, with resulting structures maintained for several days, Our work takes a step toward mapping the design space of self-assembling structures in development and provides guidance to the emerging field of shape engineering with synthetic biology.

关键词： self-organization particle-based modeling cell sorting synthetic morphogenesis synthetic biology

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