Màster Oficial - Biofísica

URI permanent per a aquesta col·leccióhttps://hdl.handle.net/2445/5761

Projectes finals del Màster Oficial de Biofísica de la UB .

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A Lattice-Boltzmann simulation of a bead-polymer complex
(2009-10-02T06:45:48Z) Panadès i Guinart, Carles; Pagonabarraga Mora, Ignacio
A complex composed of a polymer and a colloid coupled together and immersed in a fluid, is simulated by means of the Lattice-Boltzmann Method and Molecular Dynamics. The system dynamics is character-ized using dimensionless numbers. Unravelling the properties of the complex might have severe implications in single molecule experiments or in any system similar to a polymer attached to rigid ob ject, such as some molecular machines or the novel polymer-protein hybrid materials. In addition, the adhesion of the colloid to one of the edges of the polymer creates a unique frame for the latter in the sense that many new properties may arise due to the shear effects induced near the colloid and the symmetry breaking that its presence represents for the polymer.
Fluid fronts in hydrophilic and hydrophobic microchannels
(2009-09-30T06:58:28Z) Queralt Martín, María; Hernández Machado, Aurora
An experimental setup is designed and experimental studies are done in order to investigate the behavior of fluid fronts in different microchannels. Different levels of hydrophobicity and pressure are explored, getting very different results for hydrophobic and hydrophilic microchannels. For hydrophilic microchannels and any driving pressure difference the distribution of velocities corresponds to a Gaussian distribution and the front advances with h ~ tv with the classical Washburn exponent v = 0.5 for hydrophilic microchannels. The same results are obtained for hydrophobic microchannels at large driving pressure differences. For hydrophobic microchannels and when the pressure di¿erence is decreased, the distribution of velocities corresponds to a Gumbel distribution that correctly characterizes rare events like avalanches and the front advances with an exponent v as small as 0.38.
Mechanochemical alterations in lung cells during fibrogenesis
(2009-09-21T09:17:33Z) Pavelescu, Irina; Alcaraz Casademunt, Jordi
Idiopath pulmonary fibrosis (IPF) is a usually fatal disease associated with hardening of the lung tissue, epithelial injury and abnormal wound healing. Myo_broblasts are cells with smooth muscle like features and are believed to promote abnormal extracellular matrix (ECM) deposition, perpetuated scarring and loss of tissue function during fibrosis. These cells seem to arise either from epithelial cells via transforming growth factor (TGFß1) induced epithelial to mesenchymal transition (EMT) or from the activation of resident fibroblasts through TGFß1 mediated fibroblast to myofibroblast transition (FMT). We treated with TGFß1 three human lung epithelial cell lines (H441, A549, H1975) and primary lung fibroblasts from three healthy patients and from three IPF patients. We used immunouorescence techniques in order to quantify the expression of various cytoskeletal proteins (F-actin, alpha smooth muscle actin and vimentin) in both treated and untreated cells. We also used atomic force microscopy to measure the Young modulus of the cells. When treated with TGFß1, epithelial cells adopted a mesenchymal morphology and displayed indicators of EMT. TGFß1 stimulated fibroblasts acquired a myofibroblast phenotype, supporting the hypothesis of resident fibroblast activation through TGFß1 induced FMT.
Rheology of complex fluids. Stochastic switches in the galactose signalling network
(2009-05-06T08:25:37Z) Casanellas Vilageliu, Laura; Ortín, Jordi, 1959-; Ibañes Miguez, Marta
Part I: Many biological fluids are complex fluids. Complex fluids present a particular mesoscopic structure which provides them viscoelastic effects, among others. These fluids can show viscous or solid behavior depending on the time-scale in which they are operating. These properties can have a major influence on the biological processes in which the fluids are involved. Rheological techniques can be applied in order to characterize these fluids. In the present work experiments using a cone-plane geometry rheometer will be done on a complex fluid with worm-like chain micellar structure, CPyCl-NaSal [100:60], in order to present a complete rheological characterization. In addition, a particular example of biorheology applied to blood samples will be presented. Part II: Bistability is observed in many biological processes and in particular in processes involved in cellular differentiation. It can arise from positive feedback transcription networks and can be found in a colony of cells by the coexistence of two populations with different stable concentration of a specific protein. In M. Acar, A. Becskei, A. van Oudenaarden, ¿Enhancement of cellular memory by reducing stochastic transitions¿, Letters to nature 435, 228 (2005), Yeast Saccharomyces cerevisiae cells were found to switch from one stable state to another one of the Galactose-signalling network. This network is mainly governed by a positive feedback loop and the switching rate depended on the state from which cells came. In order to describe such phenomena a deterministic model based on positive feedback loops is not sufficient. The aim of the present work is to understand from a theoretical point of view how these transitions are originated and predict the rate at which they jump between different stable states. For this purpose numerical simulations have been done based on Langevin equations with multiplicative noise and later compared to theoretical predictions derived from Fokker-Plank equations. In order to become familiar with the required numerical and theoretical techniques the Ginzburg-Landau model has been previously studied. Our results show that fluctuations in the maximal transcription rate can be responsible for this phenomenon. For the galactose network, our results predict that fluctuations in the levels of proteins Gal4p and Gal80 are crucial.
Study of a two-state model for a membrane channel
(2009-02-24T15:05:40Z) Gómez Orlandi, Javier; Sancho, José M.
We explore biological transport across membrane channels from a physical point of view. The main objective is to use the tools available to a physicist from non-equilibrium thermodynamics and apply them to a concrete biological problem. In this case, we focus our attention in trying to build simple physical models, yet not trivial, that match the behavior of real channels, or ones that can be synthetically accomplished. We start with a brief review of the results we obtained for a model with multiplicative noise and proceed to study a dichotomous model, introducing a more realistic description of channel gating, both analytically and numerically. We also introduce a new different simulation framework that allows more flexibility in parameter exploration than the one previously used.
Modelling the F1-ATPase
(2008-12-30T08:17:48Z) Pérez Carrasco, Rubén; Sancho, José M.
ATPase is a rotator molecular machine which synthesizes ATP out of a proton gradient. The F1 subunit is the part of the motor in charge of catalyzing the ATP synthesis out of a rotatory motion induced by the F0 subunit. F1 can also work as a motor itself by reversing its working regime hydrolyzing ATP and inducing a rotatory motion (F1-ATPase). Because of the noisy media in which the F1-ATPase works, herein we have studied its rotatory dynamics through the Langevin formalism. In order to understand the physical description, the main energy sources acting in the F1-ATPase have been studied. Including not only the intrinsic energetic of the system but also those sources corresponding to external physical manipulations done in experiments. All these elements are introduced in a simple model in order to understand how the different parts of the motor act together and which is their relevance.
Resonant spike propagation in coupled neurons with subthreshold activity
(2008-12-29T12:11:42Z) Sancristóbal Alonso, Belén; Sancho, José M.; García Ojalvo, Jordi
Chemical coupling between neurons is only active when the presynaptic neuron is firing, and thus it does not allow for the propagation of subthreshold activity. Electrical coupling via gap junctions, on the other hand, is also ubiquitous and, due to its diffusive nature, transmits both subthreshold and suprathreshold activity between neurons. We study theoretically the propagation of spikes between two neurons that exhibit subthreshold oscillations, and which are coupled via both chemical synapses and gap junctions. Due to the electrical coupling, the periodic subthreshold activity is synchronized in the two neurons, and affects propagation of spikes in such a way that for certain values of the delay in the synaptic coupling, propagation is not possible. This effect could provide a mechanism for the modulation of information transmission in neuronal networks.
Biological transport: membrane channels, a white noise flashing ratchet model
(2008-12-29T13:34:05Z) Gómez Orlandi, Javier; Sancho, José M.
We explore biological transport across membrane channels from a physical point of view. The main objective is to use the tools available to a physicist from non-equilibrium thermodynamics and apply them to a concrete biological problem. In this case, we focus our attention in trying to build simple physical models, yet not trivial, that match the behavior of real channels, or ones that can be synthetically accomplished. The model of a channel studied in here consists on a symmetric sawtooth potential with multiplicative noise. The introduction of multiplicative noise into the system makes it dramatically change its behavior, yet it remains analytically solvable. We also present a simulation framework applicable to more complex and realistic models for channels that can be easily mapped to real experiments and does not require cumbersome theoretical developments.

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