A Multi-Paradigm Modeling Framework to Simulate Dynamic Reciprocity in a Bioreactor

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Kaul, Himanshu ^a   Cui, Zhanfeng ^a   Ventikos, Yiannis ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

APOPTOSIS; ARTICLE; BIOMECHANICS; BIOREACTOR; BIOREACTOR DESIGN; CELL GROWTH; CELL MIGRATION; CELL PROLIFERATION; CHEMOTAXIS; COMPUTER SIMULATION; DYNAMIC RECIPROCITY; HYDRODYNAMICS; TRANSPORT KINETICS; VIRTUAL REALITY;

BIOLOGICAL TRANSPORT; BIOREACTORS; CELL COMMUNICATION; CELL MOVEMENT; HYDRODYNAMICS; MODELS, BIOLOGICAL; OXYGEN;

EID: 84875629075     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059671     Document Type: Article

References (67)

1. Murry CE, Keller G, (2008) Differentiation of embryonic stem cells to clinically relevant populations: Lessons from embryonic development. Cell 132: 661-680.
2. Freshney I, Obradovic B, Grayson W, Cannizzaro C, Vunjak-Novakovic G (2007) Principles of tissue culture and bioreactor design. In: Lanza R, Langer R, Vacanti J, editors. Principles of Tissue Engineering (3rd ed). Burlington: Elsevier Academic Press. 155-184.
3. Wendt D, Riboldi SA, Cioffi M, Martin I (2009) Bioreactors in Tissue Engineering: Scientific Challenges and Clinical Perspectives. In: Kasper C, van Griensven M, Portner R, editors. Bioreactor Systems in Tissue Engineering. Berlin: Springer-Verlag. 1-27.
4. Place ES, Evans ND, Stevens MM, (2009) Complexity in biomaterials for tissue engineering. Nat Matter 8: 457-470.
5. Chung CA, Yang CW, Chen CW, (2006) Analysis of cell growth and diffusion in a scaffold for cartilage tissue engineering. Biotechnol Bioeng 94: 1138-1146.
6. Langer R, Vacanti JP, (1993) Tissue Engineering. Science 260: 920-926.
7. Mertsching H, Hansmann J (2009) Bioreactor Technology in Cardiovascular Tissue Engineering In: Kasper C, van Griensven M, Portner R, editors. Bioreactor Systems in Tissue Engineering. Verlag, Berlin: Springer. 29-37.
8. Fuchs JR, Nasseri BA, Vacanti JP, (2001) Tissue engineering: A 21st century solution to surgical reconstruction. Ann Thorac Surg 72: 577-591.
9. Khademhosseini A, Langer R, (2007) Microengineered hydrogels for tissue engineering. Biomaterials 28: 5087-5092.
10. Burdick JA, Vunjak-Novakovic G, (2009) Engineered microenvironments for controlled stem cell differentiation. Tissue Eng Part A 15: 205-219.
11. Viswanathan S, Zandstra PW (2003) Towards predictive models of stem cell fate. Cytotechnology 41(2-3), 75-92.
12. Singh H, Hutmacher D (2009) Bioreactor studies and Computational Fluid Dynamics. In: Kasper C, van Griensven M, Portner R, editors. Bioreactor Systems in Tissue Engineering. Berlin: Springer-Verlag. 231-249.
13. Weyand B, Israelowitz M, von Schroeder H, Vogt P (2009) Fluid Dynamics in Bioreactor Design: Considerations for the Theoretical and Practical Approach. In: Kasper C, van Griensven M, Portner R, editors. Bioreactor Systems in Tissue Engineering. Berlin: Springer-Verlag. 251-268.
14. Chung CA, Lin TH, Chen SD, Huang HI, (2010) Hybrid cellular automaton modeling of nutrient modulated cell growth in tissue engineering constructs. J Theor Biol 262: 267-278.
15. Cheng G, Youssef BB, Markenscoff P, Zygourakis K, (2006) Cell population dynamics modulate the rates of tissue growth processes. Biophys J 90: 713-724.
16. Cheng G, Markenscoff P, Zygourakis K, (2009) A 3D hybrid model for tissue growth: The interplay between cell population and mass transport dynamics. Biophys J 97: 401-414.
17. Richmond P, Walker D, Coakley S, Romano D, (2010) High performance cellular level agent-based simulation with FLAME for the GPU. Brief Bioinform 11: 334-347.
18. Thorne BC, Bailey AM, Pierce SM, (2007) Combining experiments with multi-cell agent-based modeling to study biological tissue patterning. Brief Bioinform 8: 245-257.
19. Chavali AK, Gianchandani EP, Tung KS, Lawrence MB, Peirce SM, et al. (2008) Characterising emergent properties of immunological systems with multi-cellular rule-based computational modeling. Trends Immunol 29: 589-599.
20. Lee Y, Kouvroukoglou S, McIntire LV, Zygourakis K, (1995) A cellular-automaton model for the proliferation of migrating contact-inhibited cells. Biophys J 69: 1284-1298.
21. Galbusera F, Cioffi A, Raimondi MT, Pietrabissa R, (2007) Computational modeling of combined cell population dynamics and oxygen transport in engineered tissue subject to interstitial perfusion. Comput Methods Biomech Biomed Engin 10: 279-287.
22. Galbusera F, Cioffi M, Raimondi MT, (2008) An in silico bioreactor for simulating laboratory experiments in tissue engineering. Biomed Microdevices 10: 547-554.
23. Farnoosh N, K Adamiak, Castle GSP, (2011) 3-D Numerical Simulation of Particle Concentration Effect on a Single-wire ESP Performance for Collecting Poly-dispersed Particles. IEEE Trans Dielectr Electr Insul 18: 211-220.
24. Amaziane B, El Ossmani M, Serres C, (2008) Numerical modeling of the flow and transport of radionuclides in heterogeneous porous media. Comput Geosci 12: 437-449.
25. Tsompanopoulou PE, (2008) Performance study of GasTurbnLab, an agent-based multi-physics problem solving environment for the gas turbine engine simulation. J Comput Inf Sci Eng 8: 031008.1-031008.8.
26. De Santis V, Feliziani M, Maradei F, (2008) Hybrid finite element/finite difference (FE/FD) model to analyze thermal transients in biological vascularized tissues. COMPEL 27: 1307-1318.
27. Portillo PM, Muzzio FJ, Ierapetritou MG, (2007) Hybrid DEM-compartment modeling approach for granular mixing. AICHE J 53: 119-128.
28. Lapin A, Paaschen T, Junghans K, Lubbert A, (2002) Bubble column fluid dynamics, flow structures in slender columns with large-diameter ring-spargers. Chem Eng Sci 57: 1419-1424.
29. Bourloutski E, Sommerfeld M (2004) Euler/Lagrange calculations of gas-liquid-solid-flows in bubble columns with phase interaction. In: Sommerfeld M, editor. Bubbly Flows: Analysis, Modelling and Calculation, Heat and Mass Transfer (series). Freyburg: Colloquium on Analysis, Modelling and Numerical Calculations of Multiphase Flow. 243-259.
30. Annaland MS, Deen NG, Kuipers JAM, (2005) Numerical simulation of gas-liquid-solid flows using a combined front tracking and discrete particle method. Chem Eng Sci 60: 6188-6198.
31. Galban CJ, Locke BR, (1999a) Analysis of cell growth kinetics and substrate diffusion in a polymer scaffold. Biotechnol Bioeng 65: 121-132.
32. Galban CJ, Locke BR, (1999b) Effects of spatial variation of cells and nutrient and product concentrations coupled with product inhibition on cell growth in a polymer scaffold. Biotechnol Bioeng 64: 633-643.
33. Lemon G, King JR, (2006) Multiphase modeling of cell behavior on artificial scaffolds: effects of nutrient depletion and spatially non-uniform porosity. Math Med Biol 24: 57-83.
34. Flaibani M, Magrofuoco E, Elvassore N, (2010) Computational modeling of cell growth heterogeneity in a perfused 3D scaffold. Ind Eng Chem Res 49: 859-869.
35. Lapin A, Muller D, Reuss M, (2004) Dynamic behavior of microbial populations in stirred bioreactors simulated with Euler-Lagrange methods: Traveling along the lifelines of single cells. Ind Eng Chem Res 43: 4647-4656.
36. Lapin A, Schmid J, Reuss M, (2006) Modeling the dynamics of E-coli populations in the three-dimensional turbulent field of a stirred-tank bioreactor- A structured-segregated approach. Chem Eng Sci 61: 4783-4797.
37. Lapin A, Klann M, Reuss M (2010) Multi-Scale Spatio-Temporal Modeling: Lifelines of Microorganisms in Bioreactors and Tracking Molecules in Cells. In Wittmann C, Krull R, editors. Biosystems Engineering Ii: Linking Cellular Networks and Bioprocesses. 23-43.
38. Emonet T, Macal CM, North MJ, Wickersham CE, Cluzel P, (2005) AgentCell: a digital single-cell assay for bacterial chemotaxis. Bioinformatics 21: 2714-2721.
39. Bonabeau E, (2002) Agent-based modeling: Methods and techniques for simulating human systems. Proc Natl Acad Sci USA 99: 7280-7287.
40. Bissell MJ, Hall HG, Parry G, (1982) How does the extracellular-matrix direct gene-expression. J Theor Biol 99: 31-68.
41. Nelson CM, Bissell MJ, (2006) Of extracellular matrix, scaffolds, and signaling: Tissue architecture regulates development, homeostasis, and cancer. Annu Rev Cell Dev Biol 22: 287-309.
42. Adra S, Sun T, MacNeil S, Holcombe M, Smallwood R, (2010) Development of a three dimensional multiscale computational model of the human epidermis. PLoS One 5: e8511.
43. Smallwood R, Holcombe M, (2006) The Epitheliome Project: Multiscale agent-based modeling of epithelial cells. 3rd IEEE International Symposium on Biomedical Imaging: Macro to Nano Vols 1-3: 816-819.
44. Tao S, McMinn P, Coakley S, Holcombe M, Smallwood R, et al. (2007) An integrated systems biology approach to understanding the rules of keratinocyte colony formation. J R Soc Interface 4: 1077-1092.
45. Sun T, Adra S, Smallwood R, Holcombe M, MacNeil S, (2009) Exploring hypotheses of the actions of TGF-beta 1 in epidermal wound healing using a 3D computational multiscale model of the human epidermis. PLoS One 4: e8515.
46. Jennings NR, (2000) On agent-based software engineering. Artif Intell 117: 277-296.
47. Kiran M, Coakley S (2010) Flexible large-scale agent-based modeling environment user manual, University of Sheffield.
48. Ferziger J, Peric M (2002) Computational methods for fluid dynamics (3rd, illustrated ed.). New York: Springer-Verlag.
49. van Doormaal JP, Raithby GD, (1984) Enhancements of the SIMPLE method for predicting incompressible fluid-flows. Numer Heat Transfer 7: 147-163.
50. Lonsdale R, (1993) An algebraic multigrid solver for the Navier-Stokes equations on unstructured meshes. Int J Numer Meth Heat Fluid Flow 3: 3-14.
51. Patankar SV (1980) Numerical heat transfer and fluid flow. Washington; London: Hemisphere.
52. Liu T, Laurell C, Selivanova G, Lundeberg J, Nilsson P, et al. (2007) Hypoxia induces p53-dependent transactivation and Fas/CD95-dependent apoptosis. Cell Death Differ 14: 411-421.
53. Lee Y (1994) Computer-assisted analysis of endothelial cell migration and proliferation. PhD, Rice Univerisity, Houston, TX.
54. Burgess BT, Myles JL, Dickinson RB, (2000) Quantitative analysis of adhesion-mediated cell migration in three-dimensional gels of RGD-grafted collagen. Ann Biomed Eng 28: 110-118.
55. Weidt C, Niggemann B, Hatzmann W, Zanker KS, Dittmar T, (2004) Differential effects of culture conditions on the migration pattern of stromal cell-derived factor stimulated hematopoietic stem cells. Stem Cells 22: 890-896.
56. Condeelis J, Singer RH, Segall JE, (2005) The great escape: When cancer cells hijack the genes for chemotaxis and motility. Annu Rev Cell Dev Biol 21: 695-718.
57. Stathopoulos GT, Sherrill TP, Han W, Sadikot RT, Yull FE, et al. (2008) Host nuclear factor-kappa B activation potentiates lung cancer metastasis. Mol Cancer Res 6: 364-371.
58. Wang W, Wyckoff JB, Frohlich VC, Oleynikov Y, Hüttelmaier S, et al. (2002) Single cell behavior in metastatic primary mammary tumors correlated with gene expression patterns revealed by molecular profiling. Cancer Res 62: 6278-6288.
59. Kedrin D, van Rheenen J, Hernandez L, Condeelis J, Segall JE, (2007) Cell motility and cytoskeletal regulation in invasion and metastasis. J Mammary Gland Biol Neoplasia 12: 143-152.
60. Muinonen-Martin AJ, Veltman DM, Kalna G, Insall RH, (2010) An Improved Chamber for Direct Visualisation of Chemotaxis. PLoS One 5: e15309.
61. Wells A, (2000) Tumor invasion: Role of growth factor-induced cell motility. Adv Cancer Res 78: 31-101.
62. Muinonen-Martin A "RE: Insall Chamber- PLoS One", Message to Himanshu Kaul. Email. 20 November 2012.
63. Muinonen-Martin A "RE: Insall Chamber- PLoS One", Message to Himanshu Kaul. Email. 21 November 2012.
64. Selivanova OM, Shiryaev VM, Tiktopulo EI, Potekhin SA, Spirin AS, (2003) Compact globular structure of Thermus thermophilus ribosomal protein S1 in solution- Sedimentation and calorimetric study. J Biol Chem 278: 36311-36314.
65. Guilak F, Cohen DM, Estes BT, Gimble JM, Liedtke W, et al. (2009) Control of stem cell fate by physical interactions with the extracellular matrix. Cell Stem Cell 5: 17-26.
66. McBeath R, Pirone DM, Nelson CM, Bhadriraju K, Chen CS, (2004) Cell shape, cytoskeletal tension, and RhoA regulate stem cell lineage commitment. Dev Cell 6: 483-495.
67. Zhao M, Song B, Pu J, Wada T, Reid B, et al. (2006) Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-gamma and PTEN. Nature 442: 457-460.