Pastor-Gutierrez, J.M. (José Martín)
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- Advanced Boolean modeling of biological networks applied to systems pharmacology(2017) Pastor-Gutierrez, J.M. (José Martín); Gómez-Mantilla, J.D. (José David); Fernández-de-Trocóniz, J.I. (José Ignacio); Irurzun-Arana, I. (Itziar)Motivation Literature on complex diseases is abundant but not always quantitative. Many molecular pathways are qualitatively well described but this information cannot be used in traditional quantitative mathematical models employed in drug development. Tools for analysis of discrete networks are useful to capture the available information in the literature but have not been efficiently integrated by the pharmaceutical industry. We propose an expansion of the usual analysis of discrete networks that facilitates the identification/validation of therapeutic targets. Results In this article, we propose a methodology to perform Boolean modeling of Systems Biology/Pharmacology networks by using SPIDDOR (Systems Pharmacology for effIcient Drug Development On R) R package. The resulting models can be used to analyze the dynamics of signaling networks associated to diseases to predict the pathogenesis mechanisms and identify potential therapeutic targets.
- Flow and clogging of a sheep herd passing through a bottleneck(2015) Zuriguel-Ballaz, Í. (Íker); Martín-Gómez, C. (César); Pastor-Gutierrez, J.M. (José Martín); Ferrer, L.M. (Luis Miguel); Garcimartín-Montero, Á. (Ángel); Ramos, J.J. (J.J.)We present an experimental study of a flock passing through a narrow door. Video monitoring of daily routines in a farm has enabled us to collect a sizable amount of data. By measuring the time lapse between the passage of consecutive animals, some features of the flow regime can be assessed. A quantitative definition of clogging is demonstrated based on the passage time statistics. These display broad tails, which can be fitted by power laws with a relatively large exponent. On the other hand, the distribution of burst sizes robustly evidences exponential behavior. Finally, borrowing concepts from granular physics and statistical mechanics, we evaluate the effect of increasing the door size and the performance of an obstacle placed in front of it. The success of these techniques opens new possibilities regarding their eventual extension to the management of human crowds.
- Effect of obstacle position in the flow of sheep through a narrow door(2016) Zuriguel-Ballaz, Í. (Íker); Martín-Gómez, C. (César); Pastor-Gutierrez, J.M. (José Martín); Olivares, J. (Jorge); Ferrer, L.M. (Luis Miguel); Garcimartín-Montero, Á. (Ángel); Ramos, J.J. (J.J.)In a recent work Phys. Rev. E 91, 022808 (2015)PLEEE81539-375510.1103/PhysRevE.91.022808] it was reported that placing an obstacle in front of a gate has a beneficial effect in the flow of sheep through it. Here, we extend such results by implementing three different obstacle positions. We have observed that the flow is improved in two cases, while it worsens in the other one; the last instance happens when the obstacle is too close to the door. In this situation, the outcomes suggest that clogging develops between the doorjamb and the obstacle, contrary to the cases when the obstacle is farther, in which case clogging always occurs at the very door. The effectiveness of the obstacle (a strategy put forward to alleviate clogging in emergency exits) is therefore quite sensitive to its location. In addition, the study of the temporal evolution of the flow rate as the test develops makes evident a steady behavior during the entire duration of the entrance. This result is at odds with recent findings in human evacuation tests where the flow rate varies over time, therefore challenging the fairness of straightforward comparisons between pedestrian behavior and animal experimental observations.
- Redefining the role of obstacles in pedestrian evacuation(2018) Parisi, D.R. (D. R.); Zuriguel-Ballaz, Í. (Íker); Gómez, C. (Carlos); Pastor-Gutierrez, J.M. (José Martín); Maza-Ozcoidi, D. (Diego); Garcimartín-Montero, Á. (Ángel)The placement of obstacles in front of doors is believed to be an effective strategy to increase the flow of pedestrians, hence improving the evacuation process. Since it was first suggested, this counter-intuitive feature is considered a hallmark of pedestrian flows through bottlenecks. Indeed, despite the little experimental evidence, the placement of an obstacle has been hailed as the panacea for solving evacuation problems. In this work, we challenge this idea and experimentally demonstrate that the pedestrians flow rate is not necessarily altered by the presence of an obstacle. This result-which is at odds with recent demonstrations on its suitability for the cases of granular media, sheep and mice- differs from the outcomes of most of existing numerical models, and warns about the risks of carelessly extrapolating animal behaviour to humans. Our experimental findings also reveal an unnoticed phenomenon in relation with the crowd movement in front of the exit: in competitive evacuations, an obstacle attenuates the development of collective transversal rushes, which are hazardous as they might cause falls.
- Time resolved particle dynamics in granular convection(2007) Zuriguel-Ballaz, Í. (Íker); Pastor-Gutierrez, J.M. (José Martín); Maza-Ozcoidi, D. (Diego); Garcimartín-Montero, Á. (Ángel); Boudet, J.F. (Jean-Français)We present an experimental study of the movement of individual particles in a layer of vertically shaken granular material. High-speed imaging allows us to investigate the motion of beads within one vibration period. This motion consists mainly of vertical jumps, and a global ordered drift. The analysis of the system movement as a whole reveals that the observed bifurcation in the flight time is not adequately described by the Inelastic Bouncing Ball Model. Near the bifurcation point, friction plays an important role, and the branches of the bifurcation do not diverge as the control parameter is increased. By fitting the grains trajectories near the wall it is possible to quantify the effective acceleration acting on them. A comparison of the mass centre flying time and the flying time determined for the grains near the wall exposes the underlying mechanism that causes the downward flow.
- The flow rate of granular materials through an orifice(2007) Zuriguel-Ballaz, Í. (Íker); Pastor-Gutierrez, J.M. (José Martín); Mankoc, C. (C.); Arevalo, R. (Roberto); Maza-Ozcoidi, D. (Diego); Janda, A. (Álvaro); Garcimartín-Montero, Á. (Ángel)The flow rate of grains through large orifices is known to be dependent on its diameter to a 5/2 power law. This relationship has been checked for big outlet sizes, whereas an empirical fitting parameter is needed to reproduce the behavior for small openings. In this work, we provide experimental data and numerical simulations covering a wide span of outlet sizes, both in three- and two-dimensions. This allows us to showthat the laws that are usually employed are satisfactory only if a small range of openings is considered. We propose a new law for the mass flow rate of grains that correctly reproduces the data for all the orifice sizes, including the behaviors for very large and very small outlet sizes.
- Experimental evidence of the ‘Faster Is Slower’ effect(Elsevier, 2014) Parisi, D.R. (D. R.); Zuriguel-Ballaz, Í. (Íker); Martín-Gómez, C. (César); Pastor-Gutierrez, J.M. (José Martín); Garcimartín-Montero, Á. (Ángel)The Faster-Is-Slower effect (Helbing et al (2000)) is an important instance of self-organized phenomenon in pedestrian dynamics. Despite this, an experimental demonstration is still lacking. We present controlled tests where a group of students are asked to exit a room through a door. Instead of just measuring the evacuation times, we have analyzed the probability distribution of the time lapses between consecutive individuals. We show how it displays a power-law tail. This method displays clearly the Faster Is Slower effect, and also allows to assess the impact of several tactics that can be put in place to alleviate the problem.
- Experimental proof of faster-is-slower in systems of frictional particles flowing through constrictions(2015) Pugnaloni, L.A. (Luis A.); Parisi, D.R. (D. R.); Zuriguel-Ballaz, Í. (Íker); Peralta, J.P. (Juan Pablo); Martín-Gómez, C. (César); Pastor-Gutierrez, J.M. (José Martín); Ferrer, L.M. (Luis Miguel); Maza-Ozcoidi, D. (Diego); Garcimartín-Montero, Á. (Ángel); Gago, P.A. (Paula A.)The “faster-is-slower” (FIS) effect was first predicted by computer simulations of the egress of pedestrians through a narrow exit [D. Helbing, I. J. Farkas, and T. Vicsek, Nature (London) 407, 487 (2000)]. FIS refers to the finding that, under certain conditions, an excess of the individuals’ vigor in the attempt to exit causes a decrease in the flow rate. In general, this effect is identified by the appearance of a minimum when plotting the total evacuation time of a crowd as a function of the pedestrian desired velocity. Here, we experimentally show that the FIS effect indeed occurs in three different systems of discrete particles flowing through a constriction: (a) humans evacuating a room, (b) a herd of sheep entering a barn, and (c) grains flowing out a 2D hopper over a vibrated incline. This finding suggests that FIS is a universal phenomenon for active matter passing through a narrowing.
- Vibrot, a simple device for the conversion of vibration into rotation mediated by friction: preliminary evaluation(2013) Zuriguel-Ballaz, Í. (Íker); Pastor-Gutierrez, J.M. (José Martín); Maza-Ozcoidi, D. (Diego); Altshuler, E. (E.); Garcimartín-Montero, Á. (Ángel)While ‘‘vibrational noise’’ induced by rotating components of machinery is a common problem constantly faced by engineers, the controlled conversion of translational into rotational motion or vice-versa is a desirable goal in many scenarios ranging from internal combustion engines to ultrasonic motors. In this work, we describe the underlying physics after isolating a single degree of freedom, focusing on devices that convert a vibration along the vertical axis into a rotation around this axis. A typical Vibrot (as we label these devices) consists of a rigid body with three or more cantilevered elastic legs attached to its bottom at an angle. We show that these legs are capable of transforming vibration into rotation by a ‘‘ratchet effect’’, which is caused by the anisotropic stick-slip-flight motion of the leg tips against the ground. Drawing an analogy with the Froude number used to classify the locomotion dynamics of legged animals, we discuss the walking regime of these robots. We are able to control the rotation frequency of the Vibrot by manipulating the shaking amplitude, frequency or waveform. Furthermore, we have been able to excite Vibrots with acoustic waves, which allows speculating about the possibility of reducing the size of the devices so they can perform tasks into the human body, excited by ultrasound waves from the outside.
- Jamming during the discharge of granular matter from a silo(2005) Pugnaloni, L.A. (Luis A.); Zuriguel-Ballaz, Í. (Íker); Pastor-Gutierrez, J.M. (José Martín); Maza-Ozcoidi, D. (Diego); Garcimartín-Montero, Á. (Ángel)In this work, we present an experimental study of the jamming that stops the free flow of grains from a silo discharging by gravity. When the outlet size is not much bigger than the beads, granular material jams the outlet of the container due to the formation of an arch. Statistical data from the number of grains fallen between consecutive jams are presented. The information that they provide can help one to understand the jamming phenomenon. As the ratio between the size of the orifice and the size of the beads is increased, the probability that an arch blocks the outlet decreases. We show here that there is a power-law divergence of the mean avalanche size for a finite critical radius. Beyond this critical radius, no jamming can occur and the flow is never stopped. The dependence of the arch formation on the shape and the material of the grains has been explored. It has been found that the material properties of the grains do not affect the arch formation probability. On the contrary, the shape of the grains deeply influences it. A simple model to interpret the results is also discussed.