Tissue regeneration of cartilage: a combined computational and experimental study

This is an automatically generated default intro template – please do not edit.

	Read full article
Article Title:	Tissue regeneration of cartilage: a combined computational and experimental study
Authors:	Iris Mateescu, Andrei Bancila, Laura Paun, Stefan Popescu, George Roata, Andreea Ciotec, Larisa Calu, Daniela Bratosin, Manuela Sidoroff
Affiliation:	National Institute of Research and Development for Biological Sciences, Bucharest, Romania
Abstract:	Computational modeling of whole biological systems from cells to organs is gaining momentum in cell biology, disease studies and tissue-engineered constructs. This computational modeling is a framework for obtaining an integrated understanding of key processes, which include: nutrient transport and utilization, matrix formation, cell population dynamics, cell attachment and migration, and local cell–cell interactions. Theoretical modeling has an enormous potential in applications ranging from the interpretation of experimental results and the identification of the main governing processes, to the optimization of practical tissue engineering protocol. This article introduces a series of mathematical and computational models that we have used to understand the mechanisms involved in obtaining biomaterials and optimizing practical tissue engineering protocols.
Keywords:	computational methods, modelling, P systems, tissue engineering, chondrocytes, cell proliferation, extracellular matrix, cellular division
References:	Alhazov A, Martin-Vide C, Pan L, Solving a PSPACE-complete problem by P systems with restricted active membranes. Fundamenta Informaticae, 58 (2), 67–77, 2003 Andreson D F, Stochastic models in biology, CIBM Seminar, (web), December 7th, 2010 Arora S, Rabani Y, Vazirani U, Simulating quadratic dynamical systems is PSPACE-complete (preliminary version). In: STOC 26. pp. 459–467,1994 Beaver D., A universal molecular computer. In: R.J. Lipton, E. B. (Ed.), DNA Based Computers. Vol. 27 of DIMACS. American Mathematical Society, 29–36, 1995. Ciobanu, G, Pan LQ, Paun G, P systems with minimal parallelism, Theoretical computer Science, Vol. 378 (1), 117-130, 2007. Besozzi D, Rozenberg G, Extended P systems for the analysis of (trans)membrane proteins, WMC7, 2006, 8-9, 2006. Brijder R, Cavaliere M, Riscos-Nunez A, Rozenberg G, Sburlan D, Membrane systems with marked membranes. Electronic Notes in Theoretical Computer Science, ENTCS, 171, 2 (2007), 25–36, 2007 Brijder R, Cavaliere M, Riscos-Nunez A, Rozenberg G, Sburlan D, Membrane systems with proteins embedded in membranes, Theoretical Computer Science, 404 (1-2), 26–39, 2008 Cardelli L, Brane calculi – interactions of biological membranes. In: Computa52 A. Paun et al. tional Methods in Systems Biology. Vol. 3082, Lecture Notes in Computer Science, Springer-Verlag, Berlin, 257–280, 2005 Cavaliere M, Sedwards S, Membrane systems with peripheral proteins: transport and evolution, CoSBi Technical Report 04/2006, www.cosbi.eu and Electronic Notes in Theoretical Computer Science, ENTCS, 171, 2 (2007), 37–53, 2006 Cavaliere M, Sedwards S, Modelling cellular processes using membrane systems with peripheral and integral proteins, Computational Methods in Systems Biology, Intern. Conference, Trento, (C. Priami, ed.), LNBI 4210, Springer, 108–126, 2006 Chawla K, Yu T, Stutts L, Yen M., Guan, Modulation of chondrocyte behavior through tailoring functional synthetic Z., saccharideepeptide hydrogels, Biomaterials, 33, 6052-6060, 2012 Chung C, Burdick J A, Engineering cartilage tissue, Advanced Drug Delivery, Reviews 60, 243–262, 2008 El-Ghannam A, Bone reconstruction: from bioceramics to tissue engineering, Expert Rev Med Devices, 2(1), 87-101, 2005 Dantsin E, Wolpert A, A robust DNA computation model that captures PSPACE. Int. J. Foundations Comp. Sci. 14 (5), 933–951, 2003 Fraj J R, Roc O, Bone tissue engineering: hope vs. hype, Biochem Biophys Res Commun 292, (1), 1–7, 2002 Freund R, Kari L, Paun G, DNA computing based on splicing: The existence of universal computers, Theory of Computing Systems, Vol. 32 (1), 69–112, 1999 Freund R, Martin-Vide C, Paun G, From regulated rewriting to computing with membranes: collapsing hierarchies, Theoretical Computer Science, Vol. 312 (2-3), 143–188, 2004 Frisco P, Computing with Cells. Advances in Membrane Computing. Oxford University Press, Oxford, 2009 Ibarra OH, Paun A, Counting Time in Computing with Cells, Proceedings of DNA11 conference, June 6-9, London Ontario, Canada, 112–128. Vol. 3892, Lecture Notes in Computer Science. Springer-Verlag, Berlin, pp. 112–128, 2005 Galban CJ, Locke BR, 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, 633-43, 1999 Gu WY, Lai WM, Janssen JD, Mow VC, A mixture theory for charged-hydrated soft tissues containing multi-electrolytes: passive transport and swelling behaviors, J Biomech Eng 120,169-80, 1998 Hunziker EB, Articular cartilage repair: basic science and clinical progress. A review of the current status and prospects, Osteoarthritis Cartilage 10(6), 432–63, 2001 Huyghe JM, Janssen JD, Quadriphasic mechanics of swelling incompressible porous media, Int J Eng Sci 35(8), 793-802, 1997 Krishna SN, Combining Brane Calculus and Membrane Computing, Proc. Bio-Inspired Computing – Theory and Applications Conf., BIC-TA 2006, Wuhan, China, September 2006, Membrane Computing Section and Journal of Automata Languages and Combinatory submitted, 2006 Krishna SN, On the computational power of flip-flop proteins on membranes, Proceedings of CiE’07 Computability and Logic in the Real World. Vol. 4497 of Lecture Notes in Computer Science, Springer-Verlag, Berlin, pp. 695–704, 2007 MacArthur BD, Tare RS, Please CP, Prescott P, Roc O, A non-invasive method for in situ quantification of subpopulation behavior in mixed cell culture, J R Soc Interface, 3(6), 63–9, 2005 Martin-Vide C, Paun G, Rozenberg G,Membrane systems with carriers, Theoretical Computer Science, Vol. 270 (1-2) 779–796, 2002 Mateescu A, Paun G, Rozenberg G, Simple splicing systems, Discrete Applied Mathematics, Vol. 84 (1-3), 145–163, 1998 Mauney JR, Volloch V, Kaplan DL, Role of adult mesenchymal stem cells in bone tissue engineering applications: current status and future prospects, Tissue Eng, 11(5–6),787–802, 2005 Mistry AS, Mikos AG, Tissue engineering strategies for bone regeneration, Adv Biochem Eng Biotechnol 94, 1–22, 2005 Nagda H, Paun A, Rodriguez-Paton A, P Systems with Symport/Antiport and Time, Pre-proceedings of Membrane Computing, International Workshop, WMC7, Leiden, The Netherlands, 429–442, 2006 Patrachari AR, Podichetty JT, Madihally SV, Application of computational fluid dynamics in tissue engineering, J. of Bioscience and Bioengineering, 114 (2), 123-132, 2012 Paun A, Paun M, Rodriguez-Paton A, Sidoroff M, “P Systems with Proteins on Membranes: A Survey”, Journal of Foundations of Computer Science, Volume No. 22, Issue No. 01, 39–53, 2011 Paun A, Paun G, The power of communication: P systems with symport/ antiport, New Generation Comput. 20 (3), 295–306, 2002 Paun A, Popa B, P systems with proteins on membranes, Fundamenta Informatica, 72, (4), 467-483, 2006. Paun A, Popa B, P systems with proteins on membranes and membrane division. In: Ibarra, O., Dang, Z. (Eds.), DLT Vol. 4036 of Lecture Notes in Computer Science. Springer-Verlag, Berlin, pp. 292–303, P Systems with Proteins on Membranes: A Survey 53, 2006 Paun G, Rozenberg G, Salomaa A (Eds.),The Oxford Handbook of Membrane Computing. Oxford University Press, Oxford, 2009 Paun G, Membrane Computing – An Introduction. Springer-Verlag, Berlin Paun G, Rozenberg G, Sticker systems, Theoretical Computer Science, Vol.204 (1-2), 183–203, 1998 Perez-Jimenez M, A computational complexity theory in membrane computing. In: Paun G, Perez-Jimenez M, Riscos-Nunez A (Eds.), Tenth Workshop on Membrane Computing (WMC10). Vol. 5957 of Lecture Notes in Computer Science.Springer-Verlag, Berlin, pp. 125–148, 2009 Pudlak P, Complexity theory and genetics: The computational power of crossing-over. Information and Computation 171, 201–223, 2001 Roc O, Cooper C, Mason C, Clements M Mesenchymal stem cells—lineage, plasticity, and skeletal therapeutic potential, Stem Cell Rev, 1(2),169–78, 2005 Romero-Campero FJ, Perez-Jimenez M, Modelling gene expression control using P systems: The Lac Operon, a case study. Biosystems 91(3), 438–457, 2008 Sengers BG, Taylor M, Please C P, Roc O, Computational modeling of cell spreading and tissue regeneration in porous scaffolds, Biomaterials 28, 1926-1940, 2007 Sosık P, The computational power of cell division in P systems: Beating down parallel computers? Natural Computing 2 (3), 287–298, 2003 Sosık P, Rodrıguez-Paton A, Membrane computing and complexity theory: A characterization of PSPACE. J. Comput. System Sci. 73 (1), 137–152, 2007 Sosık P, Rodrıguez-Paton A, On the Power of Computing with Proteins on Membranes, Preproceedings of Workshop on Membrane Computing 2009 and Vol. 5957 of Lecture Notes in Computer Science, Springer-Verlag, Berlin, pp. 448–460, 2010 Theise ND, d’Inverno M Understanding cell lineages as complex adaptive systems. Blood Cells Mol Dis 32, 17-20, 2004 van Emde Boas P, Machine models and simulations. In: van Leeuwen, J. (Ed.), Handbook of Theoretical Computer Science. Vol. A. Elsevier, Amsterdam, 1990 The P System Website: http://psystems.disco.unimib.it
*Correspondence:	Dr. Manuela Sidoroff, National Institute of Research & Development for Biological Sciences Spl. Independentei nº 296, 060031 Bucharest, Romania Tel/Fax: 40.21.2200881 E-mail: manuelasidoroff@yahoo.com