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Dinter C, Gumprecht A, Menze MA, Azizan A, Niehoff PJ, Hansen S, Büchs J. Validation of computational fluid dynamics of shake flask experiments at moderate viscosity by liquid distributions and volumetric power inputs. Sci Rep 2024; 14:3658. [PMID: 38351095 PMCID: PMC10864319 DOI: 10.1038/s41598-024-53980-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Computational fluid dynamics (CFD) has recently become a pivotal tool in the design and scale-up of bioprocesses. While CFD has been extensively utilized for stirred tank reactors (STRs), there exists a relatively limited body of literature focusing on CFD applications for shake flasks, almost exclusively concentrated on fluids at waterlike viscosity. The importance of CFD model validation cannot be overstated. While techniques to elucidate the internal flow field are necessary for model validation in STRs, the liquid distribution, caused by the orbital shaking motion of shake flasks, can be exploited for model validation. An OpenFOAM CFD model for shake flasks has been established. Calculated liquid distributions were compared to suitable, previously published experimental data. Across a broad range of shaking conditions, at waterlike and moderate viscosity (16.7 mPa∙s), the CFD model's liquid distributions align excellently with the experimental data, in terms of overall shape and position of the liquid relative to the direction of the centrifugal force. Additionally, the CFD model was used to calculate the volumetric power input, based on the energy dissipation. Depending on the shaking conditions, the computed volumetric power inputs range from 0.1 to 7 kW/m3 and differed on average by 0.01 kW/m3 from measured literature data.
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Affiliation(s)
- Carl Dinter
- RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Andreas Gumprecht
- Evonik Operations GmbH, Rodenbacher Chaussee 4, 63457, Hanau-Wolfgang, Germany
| | | | - Amizon Azizan
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia
| | | | - Sven Hansen
- Evonik Operations GmbH, Paul-Baumann-Straße 1, 45772, Marl, Germany
| | - Jochen Büchs
- RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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2
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Simões LC, Oliveira I, Borges A, Gomes IB, Simões M. A procedure to harmonize the hydrodynamic force during microbial cultivation in shaking flasks. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2023; 24:e00099-23. [PMID: 38107998 PMCID: PMC10720470 DOI: 10.1128/jmbe.00099-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/14/2023] [Indexed: 12/19/2023]
Abstract
Shake flask cultivation is a routine technique in microbiology and biotechnology laboratories where cell growth can be affected by the hydrodynamic conditions, which depend on the agitation velocity, shaking diameter, and shake flask size. Liquid agitation is implemented inherently to increase aeration, substrate transfer to the cells, and prevent sedimentation, disregarding the role of hydrodynamics in microbial growth and metabolism. Here, we present a simple approach to help standardize the hydrodynamic forces in orbital shakers to increase the experimental accuracy and reproducibility and give students a better knowledge of the significance of the agitation process in microbial growth.
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Affiliation(s)
- Lúcia Chaves Simões
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- LABBELS-Associate Laboratory, University of Minho, Braga/Guimarães, Portugal
| | - Isabel Oliveira
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto, Portugal
- Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Anabela Borges
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto, Portugal
- Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Inês Bezerra Gomes
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto, Portugal
- Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Manuel Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto, Portugal
- Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
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3
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Lin A, Álvarez-Salvado E, Milicic N, Pujara N, Ehrlich DE. Multisensory navigational strategies of hatchling fish for dispersal. Curr Biol 2023; 33:4917-4925.e4. [PMID: 37865093 PMCID: PMC10842570 DOI: 10.1016/j.cub.2023.09.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
Animals influence how they disperse in the environment by sensing local cues and adapting how they move. However, controlling dispersal can present a particular challenge early in life when animals tend to be more limited in their capacities to sense and move. To what extent and by what mechanisms can newly hatched fish control how they disperse? Here, we reveal hatchling sensorimotor mechanisms for controlling dispersal by combining swim tracking and precise sensory manipulations of a model species, zebrafish. In controlled laboratory experiments, if we physically constrained hatchlings or blocked sensations of motion through vision and the lateral line, hatchlings responded by elevating their buoyancy and passively moving with faster surface currents. Complementarily, in stagnant water, hatchlings covered more ground using hyperstable swimming, strongly orienting based on graviception. Using experimentally calibrated hydrodynamic simulations, we show that these hatchling behaviors nearly tripled diffusivity and made dispersal robust to local conditions, suggesting this multisensory strategy may provide important advantages for early life in a variable environment.
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Affiliation(s)
- Allia Lin
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Efrén Álvarez-Salvado
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nikola Milicic
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrative Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nimish Pujara
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David E Ehrlich
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrative Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Rohacs D, Yasar O, Kale U, Ekici S, Yalcin E, Midilli A, Karakoc TH. Past and current components-based detailing of particle image velocimetry: A comprehensive review. Heliyon 2023; 9:e14404. [PMID: 36950576 PMCID: PMC10025931 DOI: 10.1016/j.heliyon.2023.e14404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/25/2022] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Particle image velocimetry has been widely used in various sectors from the automotive to aviation, research, and development, energy, medical, turbines, reactors, electronics, education, refrigeration for flow characterization and investigation. In this study, articles examined in open literature containing the particle image velocimetry techniques are reviewed in terms of components, lasers, cameras, lenses, tracers, computers, synchronizers, and seeders. The results of the evaluation are categorized and explained within the tables and figures. It is anticipated that this paper will be a starting point for researchers willing to study in this area and industrial companies willing to include PIV experimenting in their portfolios. In addition, the study shows in detail the advantages and disadvantages of past and current technologies, which technologies in existing PIV laboratories can be renewed, and which components are used in the PIV laboratories to be installed.
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Affiliation(s)
- Daniel Rohacs
- Department of Aeronautics and Naval Architecture, Faculty of Transportation Engineering and Vehicle Engineering, Budapest University of Technology and Economics, HU-1111, Budapest, Hungary
| | - Onur Yasar
- Aviation Academy, Amsterdam University of Applied Sciences, Amsterdam, Netherlands
| | - Utku Kale
- Department of Aeronautics and Naval Architecture, Faculty of Transportation Engineering and Vehicle Engineering, Budapest University of Technology and Economics, HU-1111, Budapest, Hungary
- Aviation Academy, Amsterdam University of Applied Sciences, Amsterdam, Netherlands
- Corresponding author.
| | - Selcuk Ekici
- Department of Aviation, Iğdır University, TR-76000, Iğdır, Turkey
| | - Enver Yalcin
- Aviation Academy, Amsterdam University of Applied Sciences, Amsterdam, Netherlands
| | - Adnan Midilli
- Faculty of Mechanical Engineering, Department of Mechanical Engineering, Yıldız Technical University, TR-34349, İstanbul, Turkey
| | - T. Hikmet Karakoc
- Faculty of Aeronautics and Astronautics, Eskişehir Technical University, TR-26000, Eskişehir, Turkey
- Information Technology Research and Application Center, Istanbul Ticaret University, Istanbul, Turkey
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Meng F, Cheng H, Qian J, Dai X, Huang Y, Fan Y. In vitro fluidic systems: Applying shear stress on endothelial cells. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2022. [DOI: 10.1016/j.medntd.2022.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Salinas EY, Donahue RP, Herrera JM, Hu JC, Athanasiou KA. The functionality and translatability of neocartilage constructs are improved with the combination of fluid-induced shear stress and bioactive factors. FASEB J 2022; 36:e22225. [PMID: 35224777 PMCID: PMC9045489 DOI: 10.1096/fj.202101699r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/28/2022] [Accepted: 02/10/2022] [Indexed: 11/11/2022]
Abstract
Neocartilage tissue engineering aims to address the shortcomings of current clinical treatments for articular cartilage indications. However, advancement is required toward neocartilage functionality (mechanical and biochemical properties) and translatability (construct size, gross morphology, passage number, cell source, and cell type). Using fluid-induced shear (FIS) stress, a potent mechanical stimulus, over four phases, this work investigates FIS stress' efficacy toward creating large neocartilage derived from highly passaged minipig costal chondrocytes, a species relevant to the preclinical regulatory process. In Phase I, FIS stress application timing was investigated in bovine articular chondrocytes and found to improve the aggregate modulus of neocartilage by 151% over unstimulated controls when stimulated during the maturation stage. In Phase II, FIS stress stimulation was translated from bovine articular chondrocytes to expanded minipig costal chondrocytes, yielding a 46% improvement in aggregate modulus over nonstimulated controls. In Phase III, bioactive factors were combined with FIS stress to improve the shear modulus by 115% over bioactive factor-only controls. The translatability of neocartilage was improved in Phase IV by utilizing highly passaged cells to form constructs more than 9-times larger in the area (11 × 17 mm), yielding an improved aggregate modulus by 134% and a flat morphology compared to free-floating, bioactive factor-only controls. Overall, this study represents a significant step toward generating mechanically robust, large constructs necessary for animal studies, and eventually, human clinical studies.
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Affiliation(s)
- Evelia Y Salinas
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Ryan P Donahue
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Jessica M Herrera
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Jerry C Hu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Kyriacos A Athanasiou
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
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Arshad M, Rowland EM, Riemer K, Sherwin SJ, Weinberg PD. Improvement and validation of a computational model of flow in the swirling well cell culture model. Biotechnol Bioeng 2021; 119:72-88. [PMID: 34612513 DOI: 10.1002/bit.27951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/11/2021] [Accepted: 09/24/2021] [Indexed: 01/19/2023]
Abstract
Effects of fluid dynamics on cells are often studied by growing the cells on the base of cylindrical wells or dishes that are swirled on the horizontal platform of an orbital shaker. The swirling culture medium applies a shear stress to the cells that varies in magnitude and directionality from the center to the edge of the vessel. Computational fluid dynamics methods are used to simulate the flow and hence calculate shear stresses at the base of the well. The shear characteristics at each radial location are then compared with cell behavior at the same position. Previous simulations have generally ignored effects of surface tension and wetting, and results have only occasionally been experimentally validated. We investigated whether such idealized simulations are sufficiently accurate, examining a commonly-used swirling well configuration. The breaking wave predicted by earlier simulations was not seen, and the edge-to-center difference in shear magnitude (but not directionality) almost disappeared, when surface tension and wetting were included. Optical measurements of fluid height and velocity agreed well only with the computational model that incorporated surface tension and wetting. These results demonstrate the importance of including accurate fluid properties in computational models of the swirling well method.
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Affiliation(s)
- Mehwish Arshad
- Department of Bioengineering, Imperial College London, London, UK.,Department of Aeronautics, Imperial College London, London, UK
| | - Ethan M Rowland
- Department of Bioengineering, Imperial College London, London, UK
| | - Kai Riemer
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Peter D Weinberg
- Department of Bioengineering, Imperial College London, London, UK
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Seidel S, Maschke RW, Werner S, Jossen V, Eibl D. Oxygen Mass Transfer in Biopharmaceutical Processes: Numerical and Experimental Approaches. CHEM-ING-TECH 2020. [DOI: 10.1002/cite.202000179] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Stefan Seidel
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
| | - Rüdiger W. Maschke
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
| | - Sören Werner
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
| | - Valentin Jossen
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
| | - Dieter Eibl
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
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9
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Salinas EY, Aryaei A, Paschos N, Berson E, Kwon H, Hu JC, Athanasiou KA. Shear stress induced by fluid flow produces improvements in tissue-engineered cartilage. Biofabrication 2020; 12:045010. [PMID: 32640430 DOI: 10.1088/1758-5090/aba412] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tissue engineering aims to create implantable biomaterials for the repair and regeneration of damaged tissues. In vitro tissue engineering is generally based on static culture, which limits access to nutrients and lacks mechanical signaling. Using shear stress is controversial because in some cases it can lead to cell death while in others it promotes tissue regeneration. To understand how shear stress works and how it may be used to improve neotissue function, a series of studies were performed. First, a tunable device was designed to determine optimal levels of shear stress for neotissue formation. Then, computational fluid dynamics modeling showed the device applies fluid-induced shear (FIS) stress spanning three orders of magnitude on tissue-engineered cartilage (neocartilage). A beneficial window of FIS stress was subsequently identified, resulting in up to 3.6-fold improvements in mechanical properties of neocartilage in vitro. In vivo, neocartilage matured as evidenced by the doubling of collagen content toward native values. Translation of FIS stress to human derived neocartilage was then demonstrated, yielding analogous improvements in mechanical properties, such as 168% increase in tensile modulus. To gain an understanding of the beneficial roles of FIS stress, a mechanistic study was performed revealing a mechanically gated complex on the primary cilia of chondrocytes that is activated by FIS stress. This series of studies places FIS stress into the arena as a meaningful mechanical stimulation strategy for creating robust and translatable neotissues, and demonstrates the ease of incorporating FIS stress in tissue culture.
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Affiliation(s)
- E Y Salinas
- Department of Biomedical Engineering, University of California Irvine, 3131 Engineering Hall, Irvine, CA, 92697, United States of America. Authors contributed equally to this work
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Pereiro I, Fomitcheva-Khartchenko A, Kaigala GV. Shake It or Shrink It: Mass Transport and Kinetics in Surface Bioassays Using Agitation and Microfluidics. Anal Chem 2020; 92:10187-10195. [PMID: 32515583 DOI: 10.1021/acs.analchem.0c01625] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Surface assays, such as ELISA and immunofluorescence, are nothing short of ubiquitous in biotechnology and medical diagnostics today. The development and optimization of these assays generally focuses on three aspects: immobilization chemistry, ligand-receptor interaction, and concentrations of ligands, buffers, and sample. A fourth aspect, the transport of the analyte to the surface, is more rarely delved into during assay design and analysis. Improving transport is generally limited to the agitation of reagents, a mode of flow generation inherently difficult to control, often resulting in inconsistent reaction kinetics. However, with assay optimization reaching theoretical limits, the role of transport becomes decisive. This perspective develops an intuitive and practical understanding of transport in conventional agitation systems and in microfluidics, the latter underpinning many new life science technologies. We give rules of thumb to guide the user on system behavior, such as advection regimes and shear stress, and derive estimates for relevant quantities that delimit assay parameters. Illustrative cases with examples of experimental results are used to clarify the role of fundamental concepts such as boundary and depletion layers, mass diffusivity, or surface tension.
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Affiliation(s)
- Iago Pereiro
- IBM Research-Europe, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | | | - Govind V Kaigala
- IBM Research-Europe, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
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11
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Warboys CM, Ghim M, Weinberg PD. Understanding mechanobiology in cultured endothelium: A review of the orbital shaker method. Atherosclerosis 2019; 285:170-177. [PMID: 31096159 PMCID: PMC6570700 DOI: 10.1016/j.atherosclerosis.2019.04.210] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/30/2019] [Accepted: 04/04/2019] [Indexed: 12/04/2022]
Abstract
A striking feature of atherosclerosis is its highly non-uniform distribution within the arterial tree. This has been attributed to variation in the haemodynamic wall shear stress (WSS) experienced by endothelial cells, but the WSS characteristics that are important and the mechanisms by which they lead to disease remain subjects of intensive investigation despite decades of research. In vivo evidence suggests that multidirectional WSS is highly atherogenic. This possibility is increasingly being studied by culturing endothelial cells in wells that are swirled on an orbital shaker. The method is simple and cost effective, has high throughput and permits chronic exposure, but interpretation of the results can be difficult because the fluid mechanics are complex; hitherto, their description has largely been restricted to the engineering literature. Here we review the findings of such studies, which indicate that putatively atherogenic flow characteristics occur at the centre of the well whilst atheroprotective ones occur towards the edge, and we describe simple mathematical methods for choosing experimental variables that avoid resonance, wave breaking and uncovering of the cells. We additionally summarise a large number of studies showing that endothelium cultured at the centre of the well expresses more pro-inflammatory and fewer homeostatic genes, has higher permeability, proliferation, apoptosis and senescence, and shows more endothelial-to-mesenchymal transition than endothelium at the edge. This simple method, when correctly interpreted, has the potential to greatly increase our understanding of the homeostatic and pathogenic mechanobiology of endothelial cells and may help identify new therapeutic targets in vascular disease.
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Affiliation(s)
| | - Mean Ghim
- Department of Bioengineering, Imperial College London, UK
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