SEM2: Introducing mechanics in cell and tissue modeling using coarse-grained homogeneous particle dynamics

被引:0
|
作者
Chattaraj, Sandipan [1 ]
Torre, Michele [2 ]
Kalcher, Constanze [3 ]
Stukowski, Alexander [3 ]
Morganti, Simone [2 ]
Reali, Alessandro [2 ]
Pasqualini, Francesco Silvio [1 ]
机构
[1] Univ Pavia, Dept Civil Engn & Architecture, Synth Physiol Lab, Pavia, Italy
[2] Univ Pavia, Dept Civil Engn & Architecture, Comp Mech & Adv Mat Grp, Pavia, Italy
[3] OVITO GmbH, Darmstadt, Germany
基金
欧洲研究理事会;
关键词
PLURIPOTENT STEM-CELL; DATA SCIENCE; IN-VITRO; GENERATION; MIGRATION; NUCLEUS; DRIVEN;
D O I
10.1063/5.0166829
中图分类号
R318 [生物医学工程];
学科分类号
0831 ;
摘要
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.
引用
收藏
页数:14
相关论文
共 36 条
  • [1] Mechanics of cellulose nanopaper using a scalable coarse-grained modeling scheme
    Upamanyu Ray
    Zhenqian Pang
    Teng Li
    Cellulose, 2021, 28 : 3359 - 3372
  • [2] Mechanics of cellulose nanopaper using a scalable coarse-grained modeling scheme
    Ray, Upamanyu
    Pang, Zhenqian
    Li, Teng
    CELLULOSE, 2021, 28 (06) : 3359 - 3372
  • [3] Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics
    Parker, David
    Bryant, Zev
    Delp, Scott L.
    CELLULAR AND MOLECULAR BIOENGINEERING, 2009, 2 (03) : 366 - 374
  • [4] Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics
    David Parker
    Zev Bryant
    Scott L. Delp
    Cellular and Molecular Bioengineering, 2009, 2 : 366 - 374
  • [5] Modeling for Heterogeneous Oxidative Aging of Polymers Using Coarse-Grained Molecular Dynamics
    Ishida, Takato
    Doi, Yuya
    Uneyama, Takashi
    Masubuchi, Yuichi
    MACROMOLECULES, 2023, 56 (21) : 8474 - 8483
  • [6] Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin
    Nde, Jules
    Zhang, Pengzhi
    Ezerski, Jacob C.
    Lu, Wei
    Knapp, Kaitlin
    Wolynes, Peter G.
    Cheung, Margaret S.
    FRONTIERS IN MOLECULAR BIOSCIENCES, 2021, 8
  • [7] Modeling the mechanical behavior of coarse-grained soil using additive manufactured particle analogs
    Ahmed, Sheikh Sharif
    Martinez, Alejandro
    ACTA GEOTECHNICA, 2020, 15 (10) : 2829 - 2847
  • [8] Modeling the mechanical behavior of coarse-grained soil using additive manufactured particle analogs
    Sheikh Sharif Ahmed
    Alejandro Martinez
    Acta Geotechnica, 2020, 15 : 2829 - 2847
  • [9] Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield
    Bhadra, Pratiti
    Pal, Debnath
    COMPUTERS IN BIOLOGY AND MEDICINE, 2017, 83 : 134 - 142
  • [10] Coarse-Grained Modeling of Pore Dynamics on the Red Blood Cell Membrane under Large Deformations
    Razizadeh, Meghdad
    Nikfar, Mehdi
    Paul, Ratul
    Liu, Yaling
    BIOPHYSICAL JOURNAL, 2020, 119 (03) : 471 - 482