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Computational Modelling of Biophysical Processes at Multiple Scales

Type of activity
Competitive project
Acronym
COMBIOMUS
Funding entity
AGENCIA ESTATAL DE INVESTIGACION
Funding entity code
PGC2018-095456-B-I00
Amount
48.400,00 €
Start date
2019-01-01
End date
2021-12-31
Keywords
agent-based models, canales iónicos, cardiac electrophysiology, cell locomotion, ciencia no-lineal, ecuaciones de reacción-difusión, electrofisiología cardíaca, epidemiology, epidemiología, hybrid models, ionic channels, modelos basados en agentes, modelos estocásticos, modelos híbridos, movimiento celular, nonlinear science, reaction-diffusion equations, stochastic modelling, tuberculosis
Abstract
In the last decades, there has been a huge advance in the understanding of biological processes due to sophisticated experimental
techniques, accompanied by an increasing acknowledgment of the importance of theoretical modeling. This modeling has been conducted
at a large variety of levels, from the atomic and molecular description to the consideration of the whole organ, individual or community of
individuals. Typically each level makes use of a set of specific techniques. However, the interaction of biophysical processes acting at very
diverse spatial and temporal scales makes often necessary to consider different levels of description for the distinct elements considered in
the model, leading naturally to hybrid approaches.
The first aim of this project is to handle specific biophysical processes at different scales with hybrid models. The project comprises a
series of specific objectives related to both the cell polarization phenomena and pulmonary infectious diseases. On the one hand,
polarization is studied from intracellular to cell level (individual ion channels, polarization and cell locomotion), and from cell to tissue scale
(calcium waves in cardiac tissue). On the other hand, pulmonary diseases are studied at scales from cell to tissue (granuloma growth and
control), and from tissue to individual and population (tuberculosis infection in a virtual lung, and the role of space in its epidemiology). The
specific objectives in each of the bioprocesses have been selected both by their scientific interest and by their potential social impact. The
main methodologies used in the hybrid approaches will be agent-based models, reaction-diffusion equations, stochastic ordinary and
partial differential equations and/or spatial discrete methods. We will make use of High Performance Computing techniques in the most
complex codes, which will be parallelized and run in computer parallel environments.
The second purpose of this project is methodological. All the biological processes included as specific objectives share some common
characteristics: (1) they are constituted by discrete elements, from molecular structures in the cellular membrane to a population of
individuals; (2) their behaviors have stochastic elements; and (3) it is essential to consider space to understand their dynamics. Given
these associations, it is feasible to apply their particular methods at different levels. Based on existing work synergies, our proposal will
facilitate the flow of methods between the different scales and discuss transversal aspects of bioprocesses modeling, in the context of an
interdisciplinary team. This setting will permit to study questions related to the concurrent use of different modeling approaches, such as
the interaction between reaction-diffusion equations and agent-based models. As a result, a common methodology for the study of
complex biophysical systems will emerge.
The project counts on some international team members that have wide expertise on some of the bioprocesses studied. In addition, the
research team closely collaborates with external investigators that will provide experimental data, when needed. At present, 3 PhD
students are being supervised by our group and will participate in some of the tasks.
Scope
Adm. Estat
Plan
Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020
Call year
2019
Funcding program
Programa Estatal de Generación de Conocimiento y Fortalecimiento Científico y Tecnológico del Sistema de I+D+i
Funding subprogram
Subprograma Estatal de Generación de Conocimiento
Funding call
Proyectos de I+D de generación de conocimiento (antigues EXC)
Grant institution
Agencia Estatal De Investigacion

Participants