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http://hdl.handle.net/2445/8482
Mon, 22 Oct 2018 21:37:33 GMT2018-10-22T21:37:33ZNonlinear amplitude dynamics in flagellar beating
http://hdl.handle.net/2445/125495
Title: Nonlinear amplitude dynamics in flagellar beating
Author: Oriola Santandreu, David; Gadêlha, Hermes; Casademunt i Viader, Jaume
Abstract: The physical basis of flagellar and ciliary beating is a major problem in biology which is still far from completely understood. The fundamental cytoskeleton structure of cilia and flagella is the axoneme, a cylindrical array of microtubule doublets connected by passive cross-linkers and dynein motor proteins. The complex interplay of these elements leads to the generation of self-organized bending waves. Although many mathematical models have been proposed to understand this process, few attempts have been made to assess the role of dyneins on the nonlinear nature of the axoneme. Here, we investigate the nonlinear dynamics of flagella by considering an axonemal sliding control mechanism for dynein activity. This approach unveils the nonlinear selection of the oscillation amplitudes, which are typically either missed or prescribed in mathematical models. The explicit set of nonlinear equations are derived and solved numerically. Our analysis reveals the spatio-temporal dynamics of dynein populations and flagellum shape for different regimes of motor activity, medium viscosity and flagellum elasticity. Unstable modes saturate via the coupling of dynein kinetics and flagellum shape without the need of invoking a nonlinear axonemal response. Hence, our work reveals a novel mechanism for the saturation of unstable modes in axonemal beating.Mon, 22 Oct 2018 14:22:46 GMThttp://hdl.handle.net/2445/1254952018-10-22T14:22:46ZDerivation of nearest-neighbor DNA parameters in magnesium from single-molecule experiments
http://hdl.handle.net/2445/125475
Title: Derivation of nearest-neighbor DNA parameters in magnesium from single-molecule experiments
Author: Huguet, J. M.; Ribezzi-Crivellari, M.; Bizarro, C. V.; Ritort Farran, Fèlix
Abstract: DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections.Fri, 19 Oct 2018 17:31:48 GMThttp://hdl.handle.net/2445/1254752018-10-19T17:31:48ZRelationship between nonadiabaticity and damping in permalloy studied by current induced spin structure transformations
http://hdl.handle.net/2445/125427
Title: Relationship between nonadiabaticity and damping in permalloy studied by current induced spin structure transformations
Author: Heyne, L.; Kläui, M.; Backes, D.; Moore. T. A.; Krzyk, S.; Rüdiger, U.; Heyderman, L. J.; Fraile Rodríguez, Arantxa; Nolting, F.; Mentes, T. O.; Niño, M.A.; Locatelli, A.; Kirsch, K.; Mattheis, R.
Abstract: By direct imaging we determine spin structure changes in Permalloy wires and disks due to spin transfer torque as well as the critical current densities for different domain wall types. Periodic domain wall transformations from transverse to vortex walls and vice versa are observed, and the transformation mechanism occurs by vortex core displacement perpendicular to the wire. The results imply that the nonadiabaticity parameter β does not equal the damping α, in agreement with recent theoretical predictions. The vortex core motion perpendicular to the current is further studied in disks revealing that the displacement in opposite directions can be attributed to different polarities of the vortex core.Thu, 18 Oct 2018 10:15:49 GMThttp://hdl.handle.net/2445/1254272018-10-18T10:15:49ZExperimental test of ensemble inequivalence and the fluctuation theorem in the force ensemble in DNA pulling experiments
http://hdl.handle.net/2445/125334
Title: Experimental test of ensemble inequivalence and the fluctuation theorem in the force ensemble in DNA pulling experiments
Author: Martínez Monge, Álvaro; Mañosas Castejón, María; Ritort Farran, Fèlix
Abstract: We experimentally test the validity of the Crooks fluctuation theorem (CFT) in the force ensemble by pulling DNA hairpins, first with magnetic tweezers, next with optical tweezers using force feedback. The CFT holds when using the definition of work Wf=−∫xdf, where x is the molecular extension and f is the force. In contrast, it does not hold when using the usual definition, appropriate for the constant extension ensemble, Wx=∫fdx, showing the importance of the contribution of boundary terms to the full entropy production in a clear example of statistical ensemble inequivalence in small systems. We also evaluate the differences in the average dissipated work in the force ensemble as compared to the extension ensemble, highlighting ensemble inequivalence also at the level of molecular kinetics.Tue, 16 Oct 2018 11:44:04 GMThttp://hdl.handle.net/2445/1253342018-10-16T11:44:04ZModel for probing membrane-cortex adhesion by micropipette aspirations and fluctuation spectroscopy
http://hdl.handle.net/2445/125302
Title: Model for probing membrane-cortex adhesion by micropipette aspirations and fluctuation spectroscopy
Author: Alert Zenón, Ricard; Casademunt i Viader, Jaume; Brugués, Jan; Sens, Pierre
Abstract: We propose a model for membrane-cortex adhesion which couples membrane deformations, hydrodynamics and kinetics of membrane-cortex ligands. In its simplest form, the model gives explicit predictions for the critical pressure for membrane detachment and for the value of adhesion energy. We show that these quantities exhibit a significant dependence on the active acto-myosin stresses. The model provides a simple framework to access quantitative information on cortical activity by means of micropipette experiments. We also extend the model to incorporate fluctuations and show that detailed information on the stability of membrane-cortex coupling can be obtained by a combination of micropipette aspiration and fluctuation spectroscopy measurements.Mon, 15 Oct 2018 11:30:44 GMThttp://hdl.handle.net/2445/1253022018-10-15T11:30:44ZFolding and unfolding of a triple-branch DNA molecule with four conformational states
http://hdl.handle.net/2445/124806
Title: Folding and unfolding of a triple-branch DNA molecule with four conformational states
Author: Engel, Sandra; Alemany i Arias, Anna; Forns Fradera, Núria; Maass, Philipp; Ritort Farran, Fèlix
Abstract: Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational states by pulling experiments with optical tweezers and theoretical modelling. Three distinct force rips associated with different transitions between the conformational states are observed in the folding and unfolding trajectories. By applying transition rate theory to a free energy model of the molecule, probability distributions for the first rupture forces of the different transitions are calculated. Good agreement of the theoretical predictions with the experimental findings is achieved. Furthermore, due to our specific design of the molecule, we found a useful method to identify permanently frayed molecules by estimating the number of opened basepairs from the measured force jump values.Tue, 25 Sep 2018 15:51:33 GMThttp://hdl.handle.net/2445/1248062018-09-25T15:51:33ZA complex network framework to model cognition: unveiling correlation structures from connectivity
http://hdl.handle.net/2445/124564
Title: A complex network framework to model cognition: unveiling correlation structures from connectivity
Author: Rosell-Tarragó, Gemma; Cozzo, Emanuele; Díaz Guilera, Albert
Abstract: Several approaches to cognition and intelligence research rely on statistics-based model testing, namely, factor analysis. In the present work, we exploit the emerging dynamical system perspective putting the focus on the role of the network topology underlying the relationships between cognitive processes. We go through a couple of models of distinct cognitive phenomena and yet find the conditions for them to be mathematically equivalent. We find a nontrivial attractor of the system that corresponds to the exact definition of a well-known network centrality and hence stresses the interplay between the dynamics and the underlying network connectivity, showing that both of the two are relevant. Correlation matrices evince there must be a meaningful structure underlying real data. Nevertheless, the true architecture regarding the connectivity between cognitive processes is still a burning issue of research. Regardless of the network considered, it is always possible to recover a positive manifold of correlations. Furthermore, we show that different network topologies lead to different plausible statistical models concerning the correlation structure, ranging from one to multiple factor models and richer correlation structures.Fri, 14 Sep 2018 10:39:22 GMThttp://hdl.handle.net/2445/1245642018-09-14T10:39:22ZBiophysics of active vesicle transport, an intermediate step that couples excitation and exocytosis of serotonin in the neuronal soma
http://hdl.handle.net/2445/124525
Title: Biophysics of active vesicle transport, an intermediate step that couples excitation and exocytosis of serotonin in the neuronal soma
Author: De-Miguel, Francisco F.; Santamaría Holek, Iván; Noguez, Paula; Bustos, Carlos; Hernández-Lemus, Enrique; Rubí Capaceti, José Miguel
Abstract: Transmitter exocytosis from the neuronal soma is evoked by brief trains of high frequency electrical activity and continues for several minutes. Here we studied how active vesicle transport towards the plasma membrane contributes to this slow phenomenon in serotonergic leech Retzius neurons, by combining electron microscopy, the kinetics of exocytosis obtained from FM1-43 dye fluorescence as vesicles fuse with the plasma membrane, and a diffusion equation incorporating the forces of local confinement and molecular motors. Electron micrographs of neurons at rest or after stimulation with 1 Hz trains showed cytoplasmic clusters of dense core vesicles at 1.5±0.2 and 3.7±0.3 µm distances from the plasma membrane, to which they were bound through microtubule bundles. By contrast, after 20 Hz stimulation vesicle clusters were apposed to the plasma membrane, suggesting that transport was induced by electrical stimulation. Consistently, 20 Hz stimulation of cultured neurons induced spotted FM1-43 fluorescence increases with one or two slow sigmoidal kinetics, suggesting exocytosis from an equal number of vesicle clusters. These fluorescence increases were prevented by colchicine, which suggested microtubule-dependent vesicle transport. Model fitting to the fluorescence kinetics predicted that 52-951 vesicles/cluster were transported along 0.60-6.18 µm distances at average 11-95 nms−1 velocities. The ATP cost per vesicle fused (0.4-72.0), calculated from the ratio of the ΔGprocess/ΔGATP, depended on the ratio of the traveling velocity and the number of vesicles in the cluster. Interestingly, the distance-dependence of the ATP cost per vesicle was bistable, with low energy values at 1.4 and 3.3 µm, similar to the average resting distances of the vesicle clusters, and a high energy barrier at 1.6-2.0 µm. Our study confirms that active vesicle transport is an intermediate step for somatic serotonin exocytosis by Retzius neurons and provides a quantitative method for analyzing similar phenomena in other cell types.Thu, 13 Sep 2018 14:17:50 GMThttp://hdl.handle.net/2445/1245252018-09-13T14:17:50ZGeometric frustration in a hexagonal lattice of plasmonic nanoelements
http://hdl.handle.net/2445/124484
Title: Geometric frustration in a hexagonal lattice of plasmonic nanoelements
Author: Conde-Rubio, Ana; Fraile Rodríguez, Arantxa; Borrisé, Xavier; Pérez-Murano, Francesc; Batlle Gelabert, Xavier; Labarta, Amílcar
Abstract: We introduce the concept of geometric frustration in plasmonic arrays of nanoelements. In particular, we present the case of a hexagonal lattice of Au nanoasterisks arranged so that the gaps between neighboring elements are small and lead to a strong near-field dipolar coupling. Besides, far-field interactions yield higher-order collective modes around the visible region that follow the translational symmetry of the lattice. However, dipolar excitations of the gaps in the hexagonal array are geometrically frustrated for interactions beyond nearest neighbors, yielding the destabilization of the low energy modes in the near infrared. This in turn results in a slow dynamics of the optical response and a complex interplay between localized and collective modes, a behavior that shares features with geometrically frustrated magnetic systems.Wed, 12 Sep 2018 11:48:31 GMThttp://hdl.handle.net/2445/1244842018-09-12T11:48:31ZSynchronization invariance under network structural transformations
http://hdl.handle.net/2445/124143
Title: Synchronization invariance under network structural transformations
Author: Arola-Fernández, Lluís; Díaz Guilera, Albert; Arenas, Àlex
Abstract: Synchronization processes are ubiquitous despite the many connectivity patterns that complex systems can show. Usually, the emergence of synchrony is a macroscopic observable; however, the microscopic details of the system, as, e.g., the underlying network of interactions, is many times partially or totally unknown. We already know that different interaction structures can give rise to a common functionality, understood as a common macroscopic observable. Building upon this fact, here we propose network transformations that keep the collective behavior of a large system of Kuramoto oscillators invariant. We derive a method based on information theory principles, that allows us to adjust the weights of the structural interactions to map random homogeneous in-degree networks into random heterogeneous networks and vice versa, keeping synchronization values invariant. The results of the proposed transformations reveal an interesting principle; heterogeneous networks can be mapped to homogeneous ones with local information, but the reverse process needs to exploit higher-order information. The formalism provides analytical insight to tackle real complex scenarios when dealing with uncertainty in the measurements of the underlying connectivity structure.Mon, 27 Aug 2018 10:11:42 GMThttp://hdl.handle.net/2445/1241432018-08-27T10:11:42Z