Abstract
The Human Immune System is a complex system responsible for protecting the organism against diseases. Although understanding how it works is essential to develop better treatments against diseases, its complexity makes this task extremely hard. In this work a three-dimensional mathematical and computational model of part of this system, the innate immune system, is presented. The high computational costs associated to simulations lead the development of a parallel version of the code, which has achieved a speedup of about 72 times over its sequential counterpart.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Pigozzo, A.B., Macedo, G.C., dos Santos, R.W., Lobosco, M.: Implementation of a Computational Model of the Innate Immune System. In: Liò, P., Nicosia, G., Stibor, T. (eds.) ICARIS 2011. LNCS, vol. 6825, pp. 95–107. Springer, Heidelberg (2011)
Pigozzo, A., Macedo, G., Weber, R., Lobosco, M.: On the computational modelling of the innate immune system. BMC Bioinformatics (2012) (Submitted, review in progress)
Pigozzo, A.B., Lobosco, M., dos Santos, R.W.: Parallel implementation of a computational model of the his using openmp and mpi. In: International Symposium on Computer Architecture and High Performance Computing Workshops, pp. 67–72. IEEE Computer Society (2010)
Opal, S.M., DePalo, V.A.: Anti-inflammatory cytokines. Chest 117(4), 1162–1172 (2000)
Fiorentino, D., Zlotnik, A., Mosmann, T., Howard, M., O’Garra, A.: Il-10 inhibits cytokine production by activated macrophages. The Journal of Immunology 147(11), 3815–3822 (1991)
de Waal Malefyt, R., Abrams, J., Bennett, B., Figdor, C., de Vries, J.: Interleukin 10(il-10) inhibits cytokine synthesis by human monocytes: an autoregulatory role of il-10 produced by monocytes. J. Exp. Med. 174(5), 1209–1220 (1991)
Cassatella, M.A., Meda, L., Bonora, S., Ceska, M., Constantin, G.: Interleukin 10 (il-10) inhibits the release of proinflammatory cytokines from human polymorphonuclear leukocytes. evidence for an autocrine role of tumor necrosis factor and il-1 beta in mediating the production of il-8 triggered by lipopolysaccharide. The Journal of Experimental Medicine 178(6), 2207–2211 (1993)
Marie, C., Pitton, C., Fitting, C., Cavaillon, J.M.: Regulation by anti-inflammatory cytokines (il-4, il-io, il-13, tgf)of interleukin-8 production by lps and/or tnf-activated human polymorphonuclear cells. Mediators of Inflammation 5, 334–340 (1996)
Kennedy, A., DeLeo, F.: Neutrophil apoptosis and the resolution of infection. Immunologic Research 43, 25–61 (2009), 10.1007/s12026-008-8049-6
Lucas, M., Stuart, L., Zhang, A., Hodivala-Dilke, K., Febbraio, M., Silverstein, R., Savill, J., Lacy-Hulbert, A.: Requirements for apoptotic cell contact in regulation of macrophage responses. J. Immunol. 177(6), 4047–4054 (2006)
Voll, R.E., Herrmann, M., Roth, E.A., Stach, C., Kalden, J.R., Girkontaite, I.: Immunosuppressive effects of apoptotic cells. Nature 390(6658), 350–351 (1997)
Fachada, N.: Agent-based simulation of the immune system. Master’s thesis, Instituto Superior Tcnico de Lisboa (2008)
Cohen, I.R.: Modeling immune behavior for experimentalists. Immunological Reviews 216(1), 232–236 (2007)
Moore, K.W., de Waal Malefyt, R., Coffman, R.L., O’Garra, A.: Interleukin-10 and the interleukin-10 receptor. Annual Review of Immunology 19(1), 683–765 (2001)
Borregaard, N., Cowland, J.B.: Granules of the human neutrophilic polymorphonuclear leukocyte. Blood 10, 3503–3521 (1997)
Goutelle, S., Maurin, M., Rougier, F., Barbaut, X., Bourguignon, L., Ducher, M., Maire, P.: The hill equation: a review of its capabilities in pharmacological modelling. Fundamental & Clinical Pharmacology 22(6), 633–648 (2008)
LeVeque, R.J.: Finite Difference Methods for Ordinary and Partial Differential Equations. Society for Industrial and Applied Mathematics (2007)
Price, T., Ochs, H., Gershoni-Baruch, R., Harlan, J., Etzioni, A.: In vivo neutrophil and lymphocyte function studies in a patient with leukocyte adhesion deficiency type ii. Blood 84(5), 1635–1639 (1994)
Su, B., Zhou, W., Dorman, K.S., Jones, D.E.: Mathematical modelling of immune response in tissues. Computational and Mathematical Methods in Medicine: An Interdisciplinary Journal of Mathematical, Theoretical and Clinical Aspects of Medicine 10, 1748–6718 (2009)
Felder, S., Kam, Z.: Human neutrophil motility: Time-dependent three-dimensional shape and granule diffusion. Cell Motility and the Cytoskeleton 28(4), 285–302 (1994)
Chettibi, S., Lawrence, A., Young, J., Lawrence, P., Stevenson, R.: Dispersive locomotion of human neutrophils in response to a steroid-induced factor from monocytes. J. Cell Sci. 107(11), 3173–3181 (1994)
Pennington, S.V., Berzins, M.: New nag library software for first-order partial differential equations. ACM Trans. Math. Softw. 20(1), 63–99 (1994)
Kirk, D., Hwu, W.: Massively Parallel Processors: A Hands-on Approach. Morgan Kaufmann (2010)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Rocha, P.A.F. et al. (2012). A Three-Dimensional Computational Model of the Innate Immune System. In: Murgante, B., et al. Computational Science and Its Applications – ICCSA 2012. ICCSA 2012. Lecture Notes in Computer Science, vol 7333. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31125-3_52
Download citation
DOI: https://doi.org/10.1007/978-3-642-31125-3_52
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-31124-6
Online ISBN: 978-3-642-31125-3
eBook Packages: Computer ScienceComputer Science (R0)