Modeling and simulation of Trypanosoma cruzi using coarse-grained methods a new approach to Chagas disease research

dc.contributor.advisorVillalobos Camargo, Gabriel
dc.coverage.spatialColombia
dc.creatorCastillo, Alberto Mario
dc.creator.degreeMagíster en Modelado y Simulación
dc.date.accessioned2022-04-20T21:53:54Z
dc.date.available2022-04-20T21:53:54Z
dc.date.created2022
dc.description.abstractEste trabajo presenta un modelo acoplado de la forma infectiva del T. cruzi -parásito que causa la enfermedad de Chagas- con un modelo de flujo sanguíneo. Se desarrolló una red de resortes armónicos para representar el cuerpo celular y se implementó el método de dinámica de partículas disipativas (DPD) para producir flujos laminares. Se buscaron extensamente parámetros de la estructura del cuerpo celular para garantizar su estabilidad; la motilidad celular es el resultado de la transición entre diferentes formas celulares obtenidas después de que se discretizó el movimiento del parásito. Se comprobó la concordancia del flujo sanguíneo con la distribución que caracteriza las velocidades en un fluído, así como el cumplimiento del teorema de Fluctuación-Disipación. Una vez integrados los modelos, se obtuvo información sobre la dinámica de la célula en respuesta a diferentes flujos laminares. Se encontró que los resultados sobre la elongación celular corresponden a los de los experimentos. Se encontró ajuste parcial con los ensayos in vivo para el desplazamiento del centro de masa; la correlación del consumo de energía con la velocidad del flujo derivó en la propuesta de una posible estrategia de compensación de energía.spa
dc.description.abstractenglishThis work presents the coupling of a model of the infective form of the T. cruzi, the causative agent of Chagas disease, with a model of blood flow. A network of harmonic springs was developed to represent the cell body, and the Dissipative Particles Dynamics (DPD) method was implemented to produce laminar flows. Parameters of the cell body structure were extensively searched to grant its stability and cell motility is the result of the transition between different cell shapes obtained after the motion of the parasite was discretized. Agreement of the blood flow to the characteristic velocity distribution was confirmed, as well as the fulfillment of the Fluctuation-Dissipation theorem. Once the models were integrated, information on cell dynamics in response to different laminar flows was retrieved. It was found that results on cell elongation correspond to those from experiments. Partial agreement with in vivo assays was obtained for the center of mass displacement, and the energy consumption correlation with flow velocity derived in the proposal of a possible trade-off strategy for energy compensation.spa
dc.description.hashtag#ModelingAndSimulationOfTrypanosomaCruziUsingCoarse-grainedMethodsANewApproachToChagasDiseaseResearchspa
dc.description.rda1 recurso en línea (archivo de texto)
dc.format.extent49 páginasspa
dc.format.mimetypeapplication/pdfspa
dc.identifier.urihttps://hdl.handle.net/20.500.12010/26084
dc.language.isospaspa
dc.publisherUniversidad de Bogotá Jorge Tadeo Lozanospa
dc.publisher.facultyFacultad de Ciencias Naturales e Ingeniería
dc.publisher.programMaestría en Modelado y Simulación MM&S
dc.relation.referencesB. Alberts, D. Bray, J. Lewis, M. Ra , K. Roberts, J. D. Watson, and A. Grimstone. Molecular biology of the cell (3rd edn). Trends in Biochemical Sciences, 20(5):210 210, 1995.spa
dc.relation.referencesD. Alizadehrad, T. Krüger, M. Engstler, and H. Stark. Simulating the complex cell design of trypanosoma brucei and its motility. PLoS Comput Biol, 11(1):e1003967, 2015.spa
dc.relation.referencesL. O. Andrade, L. Galvão, M. d. N. S. Meirelles, E. Chiari, S. D. Pena, and A. M. Macedo. Di erential tissue tropism of trypanosoma cruzi strains: an in vitro study. Memorias do Instituto Oswaldo Cruz, 105(6):834 837, 2010spa
dc.relation.referencesN. Ashton. Physiology of red and white blood cells. Anaesthesia & Intensive Care Medicine, 6(14):261 266, 2013.spa
dc.relation.referencesJ. Backer, C. Lowe, H. Hoefsloot, and P. Iedema. Poiseuille ow to measure the viscosity of particle model uids. The Journal of chemical physics, 122(15):154503, 2005.spa
dc.relation.referencesD. L. Bader and M. M. Knight. Biomechanical analysis of structural deformation in living cells. Medical & biological engineering & computing, 46(10):951 963, 2008.spa
dc.relation.referencesJ. E. Bennett, R. Dolin, and M. J. Blaser. Principles and practice of infectious diseases. Elsevier Health Sciences, 2014.spa
dc.relation.referencesH. Berra, E. Piaggio, S. Revelli, and A. Luquita. Blood viscosity changes in experimentally trypanosoma cruzi-infected rats. Clinical hemorheology and microcirculation, 32(3):175 182, 2005.spa
dc.relation.referencesM. Bessis. Corpuscles. Springer Science & Business Media, 1974spa
dc.relation.referencesC. Bishop and D. M. Surgenor. The red blood cell. Academic Press, 1964.spa
dc.relation.referencesB. Blasi, A. D'Alessandro, N. Ramundo, and L. Zolla. Red blood cell storage and cell morphology. Transfusion medicine, 22(2):90 96, 2012.spa
dc.relation.referencesA. K. Bryan, V. C. Hecht, W. Shen, K. Payer, W. H. Grover, and S. R. Manalis. Measuring single cell mass, volume, and density with dual suspended microchannel resonators. Lab on a Chip, 14(3):569 576, 2014.spa
dc.relation.referencesL. Casares, R. Vincent, D. Zalvidea, N. Campillo, D. Navajas, M. Arroyo, and X. Trepat. Hydraulic fracture during epithelial stretching. Nature materials, 14(3):343 351, 2015.spa
dc.relation.referencesM. Castillo-Riquelme, F. Guhl, B. Turriago, N. Pinto, F. Rosas, M. F. Martínez, J. Fox-Rushby, C. Davies, and D. Campbell-Lendrum. The costs of preventing and treating chagas disease in colombia. PLoS Negl Trop Dis, 2(11):e336, 2008.spa
dc.relation.referencesD. T. Chen, M. Heymann, S. Fraden, D. Nicastro, and Z. Dogic. Atp consumption of eukaryotic agella measured at a single-cell level. Biophysical journal, 109(12):2562 2573, 2015.spa
dc.relation.referencesW. E. Committee et al. Control of chagas disease. World Health Organization technical report series, 905:i, 2002spa
dc.relation.referencesN. Cunha-e Silva, C. Sant'Anna, M. G. Pereira, I. Porto-Carreiro, A. L. Jeovanio, and W. de Souza. Reservosomes: multipurpose organelles? Parasitology research, 99(4):325 327, 2006.spa
dc.relation.referencesW. Curtin and H. Scher. Mechanics modeling using a spring network. Journal of Materials Research, 5(03):554 562, 1990spa
dc.relation.referencesW. de Souza, T. M. U. de Carvalho, and E. S. Barrias. Review on trypanosoma cruzi: host cell interaction. International journal of cell biology, 2010, 2010.spa
dc.relation.referencesW. de Souza, C. Sant'Anna, and N. L. Cunha-e Silva. Electron microscopy and cytochemistry analysis of the endocytic pathway of pathogenic protozoa. Progress in Histochemistry and Cytochemistry, 44(2):67 124, 2009.spa
dc.relation.referencesD. Despommier, J. Karapelou, et al. Parasite life cycles. Parasite life cycles., 1987.spa
dc.relation.referencesR. Docampo and S. N. Moreno. The acidocalcisome. Molecular and biochemical parasitology, 114(2):151 159, 2001.spa
dc.relation.referencesG. P. Downey, D. E. Doherty, B. Schwab, E. Elson, P. Henson, and G. Worthen. Retention of leukocytes in capillaries: role of cell size and deformability. Journal of Applied Physiology, 69(5):1767 1778, 1990.spa
dc.relation.referencesM. Esin, E. Pasternak, and A. Dyskin. Stability of 2d discrete mass-spring systems with negative sti ness springs. physica status solidi (b), 2016.spa
dc.relation.referencesD. Fedosov, B. Caswell, S. Suresh, and G. Karniadakis. Quantifying the biophysical characteristics of plasmodium-falciparum-parasitized red blood cells in microcirculation. Proceedings of the National Academy of Sciences, 108(1):35 39, 2011.spa
dc.relation.referencesD. A. Fedosov. Multiscale modeling of blood ow and soft matter. Brown University, 2010.spa
dc.relation.referencesD. A. Fedosov, B. Caswell, and G. E. Karniadakis. Wall shear stress-based model for adhesive dynamics of red blood cells in malaria. Biophysical journal, 100(9):2084 2093, 2011.spa
dc.relation.referencesD. A. Fedosov, H. Lei, B. Caswell, S. Suresh, and G. E. Karniadakis. Multiscale modeling of red blood cell mechanics and blood ow in malaria. PLoS Comput. Biol, 7(12):e1002270, 2011.spa
dc.relation.referencesE. J. Finkelsztein, J. C. Diaz-Soto, J. C. Vargas-Zambrano, E. Suesca, F. Guzmán, M. C. López, M. C. Thomas, M. Forero-Shelton, A. Cuellar, C. J. Puerta, et al. Altering the motility of trypanosoma cruzi with rabbit polyclonal anti-peptide antibodies reduces infection to susceptible mammalian cells. Experimental parasitology, 150:36 43, 2015.spa
dc.relation.referencesW. H. Grover, A. K. Bryan, M. Diez-Silva, S. Suresh, J. M. Higgins, and S. R. Manalis. Measuring single-cell density. Proceedings of the National Academy of Sciences, 108(27):10992 10996, 2011.spa
dc.relation.referencesK. Gull. The cytoskeleton of trypanosomatid parasites. Annual Reviews in Microbiology, 53(1):629 655, 1999.spa
dc.relation.referencesA. A. Gusev. Finite element mapping for spring network representations of the mechanics of solids. Physical review letters, 93(3):034302, 2004.spa
dc.relation.referencesR. J. Hayes and C. J. Scho eld. Estimación de las tasas de incidencia de infecciones y parasitosis crónicas a partir de la prevalencia: La enfermedad de chagas en américa latina. Boletín de la O cina Sanitaria Panamericana, 108(4):308 316, 1990.spa
dc.relation.referencesC. Hoare, F. Wallace, et al. Developmental stages of trypanosomatid agellates: a new terminology. Nature, 212:1385 6, 1966.spa
dc.relation.referencesA. Hochstetter and T. Pfohl. Motility, force generation, and energy consumption of unicellular parasites. Trends in parasitology, 32(7):531 541, 2016.spa
dc.relation.referencesP. Hoogerbrugge and J. Koelman. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. EPL (Europhysics Letters), 19(3):155, 1992.spa
dc.relation.referencesH. W. Hou, Q. Li, G. Lee, A. Kumar, C. Ong, and C. T. Lim. Deformability study of breast cancer cells using micro uidics. Biomedical microdevices, 11(3):557 564, 2009.spa
dc.relation.referencesA. Jagota and S. Bennison. Spring-network and nite-element models for elasticity and fracture. In Nonlinearity and Breakdown in Soft Condensed Matter, pages 186 201. Springer, 1994.spa
dc.relation.referencesA. M. Jansen, S. C. Xavier, and A. L. R. Roque. The multiple and complex and changeable scenarios of the trypanosoma cruzi transmission cycle in the sylvatic environment. Acta tropica, 2015.spa
dc.relation.referencesN. A. Khan. Emerging protozoan pathogens. Taylor & Francis, 2008.spa
dc.relation.referencesA. E. Knight and J. E. Molloy. Coupling atp hydrolysis to mechanical work. Nature Cell Biology, 1(4):E87 E89, 1999.spa
dc.relation.referencesM. Kong, Y. Wu, G. Li, and R. G. Larson. A bead-spring model for running and tumbling of agellated swimmers: detailed predictions compared to experimental data for e. coli. Soft matter, 11(8):1572 1581, 2015.spa
dc.relation.referencesT. Krüger and M. Engstler. Flagellar motility in eukaryotic human parasites. In Seminars in cell & developmental biology, volume 46, pages 113 127. Elsevier, 2015.spa
dc.relation.referencesD. N. Ku. Blood ow in arteries. Annual Review of Fluid Mechanics, 29(1):399 434, 1997spa
dc.relation.referencesP. Kundu, I. Cohen, and D. Dowling. Fluid Mechanics. Elsevier Science, 2015.spa
dc.relation.referencesE. Lauga and T. R. Powers. The hydrodynamics of swimming microorganisms. Rep. Prog. Phys, 72(096601):096601, 2009spa
dc.relation.referencesB. Y. Lee, K. M. Bacon, M. E. Bottazzi, and P. J. Hotez. Global economic burden of chagas disease: a computational simulation model. The Lancet infectious diseases, 13(4):342 348, 2013.spa
dc.relation.referencesD. Lee and J. Chen. Numerical simulation of steady ow elds in a model of abdominal aorta with its peripheral branches. Journal of Biomechanics, 35(8):1115 1122, 2002.spa
dc.relation.referencesM. Levesque and R. Nerem. The elongation and orientation of cultured endothelial cells in response to shear stress. 1985.spa
dc.relation.referencesC. R. Marinho, D. Z. Bucci, M. L. Z. Dagli, K. R. Bastos, M. G. Grisotto, L. R. Sardinha, C. R. Baptista, C. P. Gonçalves, M. R. D. Lima, and J. M. Álvarez. Pathology a ects di erent organs in two mouse strains chronically infected by a trypanosoma cruzi clone: a model for genetic studies of chagas' disease. Infection and immunity, 72(4):2350 2357, 2004.spa
dc.relation.referencesR. M. Martins, C. Covarrubias, R. G. Rojas, A. M. Silber, and N. Yoshida. Use of l-proline and atp production by trypanosoma cruzi metacyclic forms as requirements for host cell invasion. Infection and Immunity, 77(7):3023 3032, 2009spa
dc.relation.referencesM. J. McConville, K. A. Mullin, S. C. Ilgoutz, and R. D. Teasdale. Secretory pathway of trypanosomatid parasites. Microbiology and Molecular Biology Reviews, 66(1):122 154, 2002.spa
dc.relation.referencesJ. L. McWhirter, H. Noguchi, and G. Gompper. Flow-induced clustering and alignment of vesicles and red blood cells in microcapillaries. Proceedings of the National Academy of Sciences, 106(15):6039 6043, 2009.spa
dc.relation.referencesR. Melo and Z. Brener. Tissue tropism of di erent trypanosoma cruzi strains. The Journal of parasitology, pages 475 482, 1978.spa
dc.relation.referencesJ. R. Meyer-Fernandes, J. Saad-Nehme, C. E. Peres-Sampaio, R. Belmont-Firpo, D. F. Bisaggio, L. C. Do Couto, A. L. Fonseca de Souza, A. H. Lopes, and T. Souto-Padron. A mg-dependent ecto-atpase is increased in the infective stages of trypanosoma cruzi. Parasitology Research, 93(1):41 50, 2004.spa
dc.relation.referencesK. Miranda, M. Benchimol, R. Docampo, and W. de Souza. The ne structure of acidocalcisomes in trypanosoma cruzi. Parasitology research, 86(5):373 384, 2000.spa
dc.relation.referencesK. Molnar and M. Labouesse. The plastic cell: mechanical deformation of cells and tissues. Open Biology, 11(2):210006, 2021.spa
dc.relation.referencesA. Moncayo and M. Ortiz Yanine. An update on chagas disease (human american trypanosomiasis). Annals of Tropical Medicine & Parasitology, 100(8):663 677, 2006.spa
dc.relation.referencesM. Nakamura, S. Bessho, and S. Wada. Spring-network-based model of a red blood cell for simulating mesoscopic blood ow. International journal for numerical methods in biomedical engineering, 29(1):114 128, 2013.spa
dc.relation.referencesP. Nikunen, M. Karttunen, and I. Vattulainen. How would you integrate the equations of motion in dissipative particle dynamics simulations? Computer Physics Communications, 153(3):407 423, 2003.spa
dc.relation.referencesN. Nogueira and Z. Cohn. Trypanosoma cruzi: mechanism of entry and intracellular fate in mammalian cells. The Journal of experimental medicine, 143(6):1402 1420, 1976.spa
dc.relation.referencesM. C. P. Nunes, W. Dones, C. A. Morillo, J. J. Encina, et al. Chagas disease: an overview of clinical and epidemiological aspects. Journal of the American College of Cardiology, 62(9):767 776, 2013.spa
dc.relation.referencesT. Omori, T. Ishikawa, D. Barthès-Biesel, A.-V. Salsac, J. Walter, Y. Imai, and T. Yamaguchi. Comparison between spring network models and continuum constitutive laws: Application to the large deformation of a capsule in shear ow. Physical Review E, 83(4):041918, 2011.spa
dc.relation.referencesW. H. Organization et al. Research priorities for chagas disease, human african trypanosomiasis and leishmaniasis. World Health Organization technical report series, (975):v, 2012.spa
dc.relation.referencesN. R. Patel, M. Bole, C. Chen, C. C. Hardin, A. T. Kho, J. Mih, L. Deng, J. Butler, D. Tschumperlin, J. J. Fredberg, et al. Cell elasticity determines macrophage function. 2012.spa
dc.relation.referencesC. D. Perdomo Gómez et al. Nanotúbulos en trypanosoma cruzi como mecanismo de resistencia al ujo. 2021.spa
dc.relation.referencesC. J. Perez, A. J. Lymbery, and R. A. Thompson. Reactivation of chagas disease: Implications for global health. Trends in parasitology, 2015.spa
dc.relation.referencesA. Prata. Clinical and epidemiological aspects of chagas disease. The Lancet infectious diseases, 1(2):92 100, 2001.spa
dc.relation.referencesA. Rassi and J. M. de Rezende. American trypanosomiasis (chagas disease). Infectious disease clinics of North America, 26(2):275 291, 2012.spa
dc.relation.referencesA. Rassi and J. A. Marin-Neto. Chagas disease. The Lancet, 375(9723):1388 1402, 2010.spa
dc.relation.referencesJ. Rastetter. Atlas of Clinical Hematology. Number Ed. 6. Springer Science & Business Media, 2004.spa
dc.relation.referencesU. S. Schwarz. Physical constraints for pathogen movement. In Seminars in cell & developmental biology, volume 46, pages 82 90. Elsevier, 2015.spa
dc.relation.referencesS. Sell, E. E. Max, and I. Berkower. Immunology, immunopathology and immunity. ASM press Washington, DC, 2001.spa
dc.relation.referencesT. A. Shapiro and P. T. Englund. The structure and replication of kinetoplast dna. Annual Reviews in Microbiology, 49(1):117 143, 1995.spa
dc.relation.referencesJ. R. Shewchuk. Triangle: Engineering a 2d quality mesh generator and delaunay triangulator. In Applied computational geometry towards geometric engineering, pages 203 222. Springer, 1996.spa
dc.relation.referencesM. A. Shikanai-Yasuda and N. B. Carvalho. Oral transmission of chagas disease. Clinical Infectious Diseases, page cir956, 2012.spa
dc.relation.referencesS. Shin, Y. Ku, M.-S. Park, and J.-S. Suh. Deformability of red blood cells: a determinant of blood viscosity. Journal of mechanical science and technology, 19(1):216 223, 2005.spa
dc.relation.referencesW. Souza. Basic cell biology of trypanosoma cruzi. Current pharmaceutical design, 8(4):269 285, 2002.spa
dc.relation.referencesW. d. Souza. Electron microscopy of trypanosomes: a historical view. Memórias do Instituto Oswaldo Cruz, 103(4):313 325, 2008.spa
dc.relation.referencesW. d. Souza. Structural organization of trypanosoma cruzi. Memorias do Instituto Oswaldo Cruz, 104:89 100, 2009spa
dc.relation.referencesJ. D. Stanaway and G. Roth. The burden of chagas disease: estimates and challenges. Global Heart, 10(3):139 144, 2015.spa
dc.relation.referencesJ. Telleria and M. Tibayrenc. American trypanosomiasis: Chagas disease one hundred years of research. Elsevier, 2010.spa
dc.relation.referencesA. Trautmann. Extracellular atp in the immune system: more than just a danger signal . Sci signal, 2(56):e6, 2009.spa
dc.relation.referencesK.-i. Tsubota. Elongation deformation of a red blood cell under shear ow as stretch testing. Journal of the Mechanics and Physics of Solids, 152:104345, 2021.spa
dc.relation.referencesK. Tyler and D. Engman. The life cycle of trypanosoma cruzi revisited. International journal for parasitology, 31(5):472 481, 2001.spa
dc.relation.referencesS. Uppaluri. Unicellular parasite motility: a quantitative perspective. 2011.spa
dc.relation.referencesG. Villalobos, F. Kun, and J. D. Muñoz. E ect of disorder on temporal uctuations in drying-induced cracking. Physical Review E, 84(4):041114, 2011.spa
dc.relation.referencesF. Villalta, J. Scharfstein, A. W. Ashton, K. M. Tyler, F. Guan, S. Mukherjee, M. F. Lima, S. Alvarez, L. M. Weiss, H. Huang, et al. Perspectives on the trypanosoma cruzi host cell receptor interactions. Parasitology research, 104(6):1251 1260, 2009.spa
dc.relation.referencest. f. e. Wikipedia. The six main morphologies of trypanosomatids. https://commons.wikimedia.org/wiki/ File%3ATrypanosomatidMorphologies_PlainSVG.svg, 2011. [Online; accessed October 26, 2015].spa
dc.relation.referencesB. J. Williams, S. V. Anand, J. Rajagopalan, and M. T. A. Saif. A self-propelled biohybrid swimmer at low reynolds number. Nature communications, 5, 2014.spa
dc.relation.referencesL. S. Wilson, A. M. Strosberg, and K. Barrio. Cost-e ectiveness of chagas disease interventions in latin america and the caribbean: Markov models. The American journal of tropical medicine and hygiene, 73(5):901 910, 2005.spa
dc.relation.referencesD. M. Wootton and D. N. Ku. Fluid mechanics of vascular systems, diseases, and thrombosis. Annual review of biomedical engineering, 1(1):299 329, 1999.spa
dc.relation.referencesJ. Zhang, P. C. Johnson, and A. S. Popel. Red blood cell aggregation and dissociation in shear ows simulated by lattice boltzmann method. Journal of biomechanics, 41(1):47 55, 2008.spa
dc.rights.accessrightsinfo:eu-repo/semantics/openAccessspa
dc.rights.localAbierto (Texto Completo)spa
dc.sourcereponame:Expeditio Repositorio Institucional UJTL
dc.sourceinstname:Universidad de Bogotá Jorge Tadeo Lozano
dc.subjectModelado y simulaciónspa
dc.subjectTrypanosomaspa
dc.subjectEnfermedad de Chagasspa
dc.subject.lembTrypanosomaspa
dc.subject.lembEnfermedad de chagasspa
dc.subject.lembParásitosspa
dc.subject.lembFlujo sanguíneospa
dc.subject.lembVelocidad del flujo sanguineospa
dc.titleModeling and simulation of Trypanosoma cruzi using coarse-grained methods a new approach to Chagas disease researchspa
dc.type.coarhttp://purl.org/coar/resource_type/c_bdccspa
dc.type.driverinfo:eu-repo/semantics/masterThesis
dc.type.hasversioninfo:eu-repo/semantics/acceptedVersion
dc.type.localTrabajo de grado de maestría

Archivos

Bloque original

Mostrando 1 - 1 de 1
Cargando...
Miniatura
Nombre:
Thesis_Alberto-Mario_Castillo.pdf
Tamaño:
11.62 MB
Formato:
Adobe Portable Document Format
Descripción:
Ver documento

Bloque de licencias

Mostrando 1 - 3 de 3
Cargando...
Miniatura
Nombre:
license.txt
Tamaño:
2.87 KB
Formato:
Item-specific license agreed upon to submission
Descripción:
Cargando...
Miniatura
Nombre:
FOR-EFE-GDB-007_AUTORIZACION_DE_PUBLICACION_DE_TESIS_O_TRABAJO_DE_GRADO-1_Alberto-Mario_Castillo.pdf
Tamaño:
88.81 KB
Formato:
Adobe Portable Document Format
Descripción:
Autorización
Cargando...
Miniatura
Nombre:
Tratamiento de datos - Titulo Electrónico_AlbertoMarioCastillo.pdf
Tamaño:
101.26 KB
Formato:
Adobe Portable Document Format
Descripción:
Anexos