A framework for multiscale bioengineering simulation

Dernowsek, Janaina; Noritomi, Pedro Yoshito; Kemmoku, Daniel Takanori; Kersanach, Maria Bolina; Brandão, Sirley Rocha; Idogava, Henrique Takashi; Decarli, Monize Caiado; Vilalba, Fabio Albuquerque; Nogueira, Júlia A.; Bonacin, Rodrigo; Rezende, Rodrigo Alvarenga; Silva, Jorge Vicente Lopes da

doi:10.24243/jmeb/2.5.177

Cited by 1 publication

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“…Mathematical and computational modeling have increasingly proven to be key methods for the simulation, analysis and prediction of complex and multiscale biological phenomena [152][153][154]. Analogously to simulation of industrial processes, these tools can be used to reduce time and costs for the understanding, design and mass production of spheroid and tissues in the near future [126].…”

Section: Mathematical and Computational Modeling Of Spheroidsmentioning

confidence: 99%

“…Then the equations that specifically describe the study scenario are identified and interrelated, and this is summarized in a mathematical model. Finally, parameters extracted from the scenario are used for the validation of the mathematical model developed [153,154].…”

Section: Mathematical and Computational Modeling Of Spheroidsmentioning

confidence: 99%

“…CompuCell 3D allows users to swiftly build biological simulations without extensive programming or software development experience, featuring a variety of simulations for complex multiscale phenomena such as spheroid and cancer growth, developmental biology, evolution and the immune system [168]. Several studies focusing on spheroids were developed in this platform [46,153,157]. Systems-Biology, in turn, is a software owned by the Bayer pharmaceutical company that aims to offer comprehensive understanding of biological systems, their interaction with pharmaceutical products and the dynamic processes involved, as in the comparative study of cell growth kinetics in monolayers and spheroids by Radszuweit et al [169].…”

Section: Mathematical and Computational Modeling Of Spheroidsmentioning

confidence: 99%

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Cell spheroids as a versatile research platform: formation mechanisms, high throughput production, characterization and applications

et al. 2021

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Three-dimensional (3D) cell culture has tremendous advantages to closely mimic the in vivo architecture and microenvironment of healthy tissue and organs, as well as of solid tumors. Spheroids are currently the most attractive 3D model to produce uniform reproducible cell structures as well as a potential basis for engineering large tissues and complex organs. In this review we discuss, from an engineering perspective, processes to obtain uniform 3D cell spheroids, comparing dynamic and static cultures and considering aspects such as mass transfer and shear stress. In addition, computational and mathematical modeling of complex cell spheroid systems are discussed. The non-cell-adhesive hydrogel-based method and dynamic cell culture in bioreactors are focused in detail and the myriad of developed spheroid characterization techniques is presented. The main bottlenecks and weaknesses are discussed, especially regarding the analysis of morphological parameters, cell quantification and viability, gene expression profiles, metabolic behavior and high-content analysis. Finally, a vast set of applications of spheroids as tools for in vitro study model systems is examined, including drug screening, tissue formation, pathologies development, tissue engineering and biofabrication, 3D bioprinting and microfluidics, together with their use in high-throughput platforms.

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