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Simulation and modelling Lab


Fundamental cell Biophysics

We model different types of biological processes occurring in the interior of living cells using techniques previously developed in physics and mathematics.  We consider problems at different scales, from the stochastic behaviour of individual ion gates to the spatial particularities of coupled opposite enzymatic reactions or the viscoelastic properties of the cytoskeleton of cells. Analytic calculations together with the use of numerical simulations permit to reveal some of the mechanisms involved in the biological processes inside of the cells and their relation with the external responses to small perturbations like cell excitations of neurons  or cell locomotion.
Contact: Laureano Ramirez, Sergio Alonso 


Computational neuroscience

The analysis of brain function encompasses multiple scales, from understanding the behavior of single neurons to the global  patterns of electric activity in the brain. Related with this, it is the behavioral manifestation of these patterns with potential applications to understanding debilitating diseases like Alzheimer's. We are interested in simulating intermediate scales in order to stablish a link between the aggregate of neurons and the behavior of specific regions in the brain. To do so, we perform simulations of networks fo neurons which are grown in-vitro and expect to deal soon with the simulation of cortical areas in the brain. Regarding the first issue, neuronal cultures in vitro spontaneously reach a coherent state of collective firing in a pattern of nearly periodic global bursts. Although understanding the spontaneous activity of neuronal networks is of chief importance in neuroscience, the origin and nature of that pulsation has remains elusive. We have studied how the propagation of waves nucleate randomly in a set of points that is specific to each culture and is selected by a non-trivial interplay between dynamics and topology. The phenomenon was explained by the noise focusing effect—a strong spatio-temporal localization of the noise dynamics that originates in the complex structure of avalanches of spontaneous activity. Understanding how to obtain information from the local network in cortical areas is the second goal in this area that we are just starting to work on. Ready to join?
Contact: Enric Alvarez


Complex fluids

Complex fluids have an internal structure that provides them with new and interesting properties. They include a large number of fluids of biological and industrial interest.
A case in which we are interested is constituted by bubbly flows in microgravity, of large technological interest in space industry, and whose behaviour is very different from the usual case with gravity. We have done several experimental microgravity campaigns to study the generation and dynamics of such flows. The results will be relevant both from the fundamental point of view and for application for heat management in space.
Another situation of interest corresponds to viscoelastic fluids, which present a dynamical behavior depending on the frequency of the forcing. For a shear-thinning fluid, experiments show instabilities, first of shear banding, later of the laminar regime to more complex, 3d solutions. We study this problem theoretically, using models that introduce additional nonlinearities.


Chemical reaction-diffusion systems

Spatially extended chemical reactions are systems where the observation of linear instabilities and different types of pattern formation in non-linear reaction-diffusion equations is well-controlled. The combination of reactions with different instabilities together with advection may produce new pattern formation mechanisms. It permits the study of multi-scale problems where two instabilities appear simultaneously in a co-dimensional point at different scales. On the other hand, chemical waves in extended chemical excitable media, e.g. the Belousov-Zhabotinsky reaction or catalytic oxidation in metal surfaces, are particularly dynamic and under certain conditions, their instabilities remain some of the particularities of electrical wave propagation in cardiac tissue, in particular the generation of cardiac arrhythmias.

Contact: Sergio Alonso



The study of the phase transitions produced in superconductors is relevant both for fundamental and applied physics.  Such studies are hampered by the complex diamagnetic interactions occurring when superconductors are present in the system, due to the Meissner effect. This requires the development of new numerical algorithms. We study by means of numerical simulations the transitions in large ensembles of metastable superconducting granules, in the presence of external magnetic fields and and also under the action of incident radiation. These studies have applications in low-energy particle detectors but can also answer fundamental questions in solid state physics or in astrophysics.