SEM2:利用粗粒度均质颗粒动力学在细胞和组织建模中引入力学原理

IF 6.6 3区 医学 Q1 ENGINEERING, BIOMEDICAL APL Bioengineering Pub Date : 2023-12-01 DOI:10.1063/5.0166829
Sandipan Chattaraj, Michele Torre, Constanze Kalcher, Alexander Stukowski, Simone Morganti, A. Reali, F. Pasqualini
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引用次数: 0

摘要

在可变形的工程组织(如类器官和芯片上的器官)中建立多尺度力学模型既重要又具有挑战性。事实上,很难模拟由离散细胞水平行为(如迁移和增殖)介导的相关组织水平的大型非线性变形。解决这一问题的一种方法是亚细胞元素建模(SEM),其中粗粒度颗粒的集合通过经验定义的电位相互作用,用于模拟单个细胞,同时保留细胞流变学。然而,在SEM中没有明确的多尺度力学处理。在这里,我们在开源软件SEM++中结合了颗粒水平应力和应变的分析和可视化,创建了一个新的框架,我们称之为亚细胞元素建模和力学或SEM2。为了证明SEM2,我们对经典的SEM模拟进行了详细的力学处理,包括单细胞蠕变、迁移和增殖。我们还引入了一个额外的力来控制核在迁移和扩散过程中的定位。最后,我们展示了SEM2如何用于模拟工程细胞培养平台(如类器官和芯片上器官)中的增殖。对于每种情况,我们都提供了SEM++提供的细胞紧急行为分析以及SEM2可能的应力或应变分布示例。在整个研究过程中,我们只使用第一原理文献值或参数研究,因此我们将我们的见解与最近发表的结果进行定性比较。SEM2的代码可在GitHub上获得https://github.com/Synthetic-Physiology-Lab/sem2。
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SEM2: Introducing mechanics in cell and tissue modeling using coarse-grained homogeneous particle dynamics
Modeling multiscale mechanics in shape-shifting engineered tissues, such as organoids and organs-on-chip, is both important and challenging. In fact, it is difficult to model relevant tissue-level large non-linear deformations mediated by discrete cell-level behaviors, such as migration and proliferation. One approach to solve this problem is subcellular element modeling (SEM), where ensembles of coarse-grained particles interacting via empirically defined potentials are used to model individual cells while preserving cell rheology. However, an explicit treatment of multiscale mechanics in SEM was missing. Here, we incorporated analyses and visualizations of particle level stress and strain in the open-source software SEM++ to create a new framework that we call subcellular element modeling and mechanics or SEM2. To demonstrate SEM2, we provide a detailed mechanics treatment of classical SEM simulations including single-cell creep, migration, and proliferation. We also introduce an additional force to control nuclear positioning during migration and proliferation. Finally, we show how SEM2 can be used to model proliferation in engineered cell culture platforms such as organoids and organs-on-chip. For every scenario, we present the analysis of cell emergent behaviors as offered by SEM++ and examples of stress or strain distributions that are possible with SEM2. Throughout the study, we only used first-principles literature values or parametric studies, so we left to the Discussion a qualitative comparison of our insights with recently published results. The code for SEM2 is available on GitHub at https://github.com/Synthetic-Physiology-Lab/sem2.
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来源期刊
APL Bioengineering
APL Bioengineering ENGINEERING, BIOMEDICAL-
CiteScore
9.30
自引率
6.70%
发文量
39
审稿时长
19 weeks
期刊介绍: APL Bioengineering is devoted to research at the intersection of biology, physics, and engineering. The journal publishes high-impact manuscripts specific to the understanding and advancement of physics and engineering of biological systems. APL Bioengineering is the new home for the bioengineering and biomedical research communities. APL Bioengineering publishes original research articles, reviews, and perspectives. Topical coverage includes: -Biofabrication and Bioprinting -Biomedical Materials, Sensors, and Imaging -Engineered Living Systems -Cell and Tissue Engineering -Regenerative Medicine -Molecular, Cell, and Tissue Biomechanics -Systems Biology and Computational Biology
期刊最新文献
Substrate stiffness modulates collective colony expansion of the social bacterium Myxococcus xanthus. Stem cell mechanoadaptation. I. Effect of microtubule stabilization and volume changing stresses on cytoskeletal remodeling. Stem cell mechanoadaptation. II. Microtubule stabilization and substrate compliance effects on cytoskeletal remodeling. Unpleasant odors compared to pleasant ones cause higher cortical activations detectable by fNIRS and observable mostly in females. Organs-on-chips: Advanced engineered living systems.
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