60f Pagonabarraga Mora, Ignacio [WorldCat Identities]
WorldCat Identities

Pagonabarraga Mora, Ignacio

Overview
Works: 16 works in 30 publications in 2 languages and 29 library holdings
Roles: Author
Publication Timeline
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Most widely held works by Ignacio Pagonabarraga Mora
New mechanisms in the adsorption of colloidal suspensions by Ignacio Pagonabarraga Mora( Book )

4 editions published between 1995 and 2010 in English and held by 4 WorldCat member libraries worldwide

Facing the environment : hydrodynamics and confinement modulate molecular motors dynamics by Paolo Malgaretti( )

3 editions published between 2013 and 2014 in English and held by 3 WorldCat member libraries worldwide

In this thesis we characterize the behavior of molecular motors when the properties of the cytoplasm they displace through are not homogeneous or isotropic. Anisotropies in the cytoplasm can be induced, for example, by net fluxes that can be generated by the displacement of motors themselves as well by other mechanism such as remodeling of the overall cell shape. In the cytoplasm there are many molecules, proteins, vesicles and organelles in suspension. Such a crowded environment develop inhomogeneities in the local properties of the cytoplasm. The different length scales that characterize such inhomogeneities might led to different interplays according to the size of the cargo pulled by motors. For example, suspended particles whose size is much smaller than the cargo size will be experienced by the cargo as an enhancement in the effective viscosity. On the other hand, suspended particles of the same size or bigger than cargoes will develop local structures that affect the space the cargo can explore and will act like a porous medium. In the first chapter we characterize the hydrodynamic coupling generated by an ensemble of molecular motors displacing along a filament. By numerical simulations we show how such a coupling develops. The hydrodynamic coupling between motor relies on the fluid flow generated by motors displacement. We discuss how the hydrodynamic coupling between motors depends upon the boundary conditions provided by different geometries. Motors do not always displace in the same direction, rather cargoes pulled by teams of motors pulling on opposite directions has been observed to undergo a bidirectional motion where the cargo moves back and forth due to the reorganization of the force generated by the motors. In many cases the cargoes motors pull on are vesicles or membrane-embedded organelles. In these cases motors exert force on the cargo by pulling on molecular linkers embedded in the membrane that link the tail of the motors to the membrane. Therefore, the displacement of the linkers in the membrane will lead to a local flow of membrane that can lead to an overall coupling between motors that will sum up to the one generated by the displacement of the motors in the cytoplasm. In the second chapter we develop a coarse grained description of a team of motors pulling on opposite directions that are hydrodynamically coupled. Thanks to our coarse grained model we characterize the overall dynamics of the system and we discuss the peculiar features induced by the hydrodynamic coupling by comparing them against those obtained in the case of rigidly coupled motors. In the third chapter we characterize the dynamics of a single molecular motor displacing in an inhomogeneous environment modeled as a varying section channel. In the limit in which the channel section is smoothly varying it is possible to reduce the overall dynamics to that of a particle moving in a 1D effective potential where the varying confinement enters as an entropic contribution to the overall potential. Using this framework we characterize the dynamics of molecular motors moving according to different schemes. The comparison between the results obtained with the different models allows us to distinguish between general behaviors and model dependent features
Hydrophobicity in capillary flows : dynamics and stability of menisci, thin films and filaments in confined geometries by Rodrigo Andrés Ledesma Aguilar( )

2 editions published in 2009 in English and held by 2 WorldCat member libraries worldwide

Guiding active particles through surface interactions by Jaideep Katuri( Book )

2 editions published in 2018 in English and held by 2 WorldCat member libraries worldwide

Living organisms and systems are continually converting energy, either internally stored or transduced from their surroundings, into motion. This activity and the resulting self-propulsion constantly push these biological systems out of thermal equilibrium. A number of exotic phenomenon result from the intrinsic non-equilibrium nature of these living systems, that are not accessible in a system at thermal equilibrium. In recent years, these ubiquitous non-equilibrium systems have come to be classified as active matter. Active matter, by definition, refers to systems composed of active units, each capable of converting ambient or stored energy into systematic movement. Examples range from the sub-micrometer scale, with microtubules associated with motor proteins in the cytoplasm, to the micrometer length scales of swimming bacteria, and the meter-length scales of greater familiarity, such as that of fish and birds. There are two common themes that run through all these active matter systems. The first is the emergence of correlated collective phenomenon through particle-particle interactions as exemplified in flocking of birds, swarming of bacteria and crystallization of self-propelled particles. And the second is the ability of the active units to interact with their surroundings through self-propulsion. Common examples of this include chemotaxis and rheotaxis, observed in many biological systems. In this thesis, I have focussed on studying the ability of artificial active matter systems to respond to their local environment. As a model active matter system, we use colloidal active particles, that propel due to self-diffusiophoresis. These particles coated with two different materials on each half are referred to as Janus particles. In a solution of H2O2, one of the sides has catalytic properties (Pt), while the other half remains inert (SiO2). This creates a concentration gradient of the reaction product along the surface of the particle and induces a phoretic slip, which propels the particle. We study the dynamics of these self-phoretic particles close to solid surfaces. The particles interact with their surroundings via hydrodynamic and phoretic effects and we observe that when confined closed to a surface, a strong alignment interaction comes into play. This effect can be used to guide micron sized active particles along predetermined pathways. We then exploit this alignment interaction to design micropatterned ratchets capable of generating a strong directional flow of active particles. A different geometry of the same system can also be used to accumulate active particles in confined areas. Finally, we study the influence of an applied external shear flow on the dynamics of active particles near surfaces. We find that a strong directional response emerges for the active particles in the direction perpendicular to the flow direction leading to the cross-stream migration of active particles. This response is dependent on the applied shear flow and the propulsion velocity of the particle, potentially opening up a possibility to sort particles of different activities based on their response to shear flows. Overall, our results indicate that active particles can have a strong directional response in certain environments allowing us to engineer ways of guiding them
Hydrodynamic effects in externally and internally driven particle suspensions : fluctuation-induced forces, active settling and bacterial patterns by Ricard Matas Navarro( )

2 editions published in 2012 in English and held by 2 WorldCat member libraries worldwide

Evolution and ecology of the digital world : a complex systems perspective by Kaj Kolja Kleineberg( Book )

2 editions published between 2016 and 2017 in English and held by 2 WorldCat member libraries worldwide

Online social networks (OSNs) enable researchers to study the social universe at a previously unattainable scale. The worldwide impact and the necessity to sustain their rapid growth emphasize the importance to unravel the laws governing their evolution. We present a quantitative two-parameter model which reproduces the entire topological evolution of a quasi-isolated OSN with unprecedented precision from the birth of the network. This allows us to precisely gauge the fundamental macroscopic and microscopic mechanisms involved. Our findings suggest that the coupling between the real pre-existing underlying social structure, a viral spreading mechanism, and mass media influence govern the evolution of OSNs. The empirical validation of our model, on a macroscopic scale, reveals that virality is four to five times stronger than mass media influence and, on a microscopic scale, individuals have a higher subscription probability if invited by weaker social contacts, in agreement with the "strength of weak ties" paradigm. The simultaneous existence of numerous digital services naturally raises the question under which conditions these services can coexist. In analogy to population dynamics, the digital world is forming a complex ecosystem of interacting networks whose fitnesses depend on their ability to attract and maintain users' attention, which constitutes a limited resource. We introduce an ecological theory of the digital world which exhibits a stable coexistence of several networks as well as the domination of a single one, in contrast to the principle of competitive exclusion. Interestingly, our model also predicts that the most probable outcome is the coexistence of a moderate number of services, in agreement with empirical observations. In addition, we discuss the impact of heterogeneity in network fitnesses induced by competition between an international network, such as Facebook, and local services. To this end, we construct a 1:1000 scale model of the digital world, consisting of the 80 countries with the most Internet users. We show how inter-country social ties induce increased fitness of the international network. Under certain conditions, this leads to the extinction of local networks; whereas under different conditions, local networks can persist and even dominate the international network completely. Finally, we investigate how multiple coexisting networks, which form a so called multiplex system, facilitate search and navigation with only local knowledge. This task is especially important in decentralized architectures. In particular, we show that multiplex systems are not random combinations of single network layers. Instead, they are organized in specific ways dictated by hidden geometric correlations between the individual layers. We find that these correlations are strong in different real multiplexes, and form a key framework for answering many important questions. Specifically, we show that these geometric correlations facilitate: (i) the definition and detection of multidimensional communities, which are sets of nodes that are simultaneously similar in multiple layers; (ii) accurate trans-layer link prediction, where connections in one layer can be predicted by observing the hidden geometric space of another layer; and (iii) efficient targeted navigation in the multilayer system using only local knowledge, which outperforms navigation in the single layers only if the geometric correlations are sufficiently strong. Interestingly, many real systems fulfill these conditions. To conclude, from a system-level perspective, a prospering future in the digital age comprised of a diverse digital landscape with interacting, decentralized architectures is possible, but so is the opposite. It remains a task for society to create sufficient awareness and the correct incentives to create this future we desire
Hydrodynamic effects on active colloidal suspensions by Eloy Navarro Argemí( Book )

2 editions published in 2019 in English and held by 2 WorldCat member libraries worldwide

The goal of this thesis is studying hydrodynamic effects on active colloidal suspensions. Hydrodynamic interaction is propagated through the fluid in which the colloids displace due to the flow they create during their motion. It can lead to the emergence of collective phenomena, such as the self-assembly of more complex structures. Hydrodynamic interactions are not the only present in the system, since other forces may be acting between colloids, or there can be external fields acting on them such as gravity. We present our study for two different systems: magnetic colloids and Janus particles. When applying a circular magnetic field, we can induce a rotation to a particle possessing a magnetic moment. Due to the coupling of the flow with the one created by surrounding particles and with system interfaces, a rotor will eventually self-propel. Two magnetic moments interact with each other through the magnetic dipole-dipole force, which tends to align them into arrays. We study how the balance between hydrodynamic, magnetic and gravitational forces determines the morphology of the structures magnetic colloids can form. Janus particles have two faces with different chemical properties, thus the interaction between them depends on their relative orientation. We study the morphology and order of the structures that can emerge for these particles as a function of the intensity, sign and reach of the interaction between them, as well as the type of flow they create when self-propelling. Methodologically, we have combined the use of far-field theory to draw analytical expressions that have given us qualitative insight on the results we could expect with high-performance computing simulations which have allowed us to extend our study to bigger systems
Red blood cells mechanics : from membrane elasticity to blood rheology by Guillermo Rodríguez Lázaro( )

2 editions published in 2014 in English and held by 2 WorldCat member libraries worldwide

The mechanics and elasticity of red blood cells (RBCs) determine the capability to deform of these cells when passing through the thinnest capillaries, where the delivery of oxygen takes place. The understanding of the elastic properties of RBCs is fundamental for improving our knowledge about microcirculation and it also has important biomedical applications, such as control of blood storage, or cell manipulation for pathology diagnosis. In this Thesis, we study the elasticity of RBCs under different conditions, understanding their mechanical response to different type of perturbations. In a first Part, we study the shape morphologies observed in the disco-echinocyte transition, when the cell is subjected to an imbalance in the membrane asymmetry, for instance after ATP depletion when lipids flip from the inner to the outer leaflet. Affected cells deform, adopting crenated morphologies known as echinocytes. We develop a theoretical study which allows us to identify and quantify the relevant aspects that trigger the shape transition. The lipid bilayer tries to expand its outer leaflet in order to accommodate the excess area, whereas the cytoskeleton opposes resistance to this type of deformations, preserving more compact shapes. The subtle interplay between both membrane structures determines the equilibrium morphology of the cell. The cytoskeleton is fundamental to ensure the stability of the healthy shape, the discocyte, against changes in the membrane composition. However, it is not severely stressed under weak deformations in which low curvatures are involved. Our results show that the energetic scale of these shape transitions is of hundreds of kbT, demonstrating the large stability of these shapes. Based on the knowledge gained from the theoretical study we also analyze a series of experiments in which echinocytes are mechanically perturbed by a AFM tip, inducing shape transitions towards the healthy discocyte in a controlled manner. In the second Part, we derive a phase-field method for membrane modeling. Phase-field methods have been extensively used for the study of interface phenomena, though with few applications to membranes. We present a new model which accounts for the membrane elasticity, and couples the membrane dynamics with an external fluid, whose hydrodynamics is dictated by the Navier-Stokes equation. We derive the expression of the stress tensor which allows us to recover the stress profile of the membrane. We also obtain the membrane equilibrium equations, proving that in the macroscopic limit our phase-field model recovers the correct expressions given by the elastic theory of membranes. In the third Part we make use of this phase-field model to study the behaviour of RBCs in flow in narrow channels, of width similar to that of the cell. We consider pressure-driven flows as they relevant for both in vivo and in vitro circulation. We carry out simulations by means of a lattice-Bolztmann method. Our study highlights the crucial role of the RBC shape, softness and deformability to explain its complex behaviour and rheological properties. RBCs flowing at low concentratrions, when they do not interact with other cells and the dynamics is governed by the interaction with the cell, are shown to migrate lateral towards the wall, avoiding the axial position. The RBC assumes an asymmetric shape and orients with the flow, reducing the viscosity of the fluid which presents a shear-thinning behaviour. The lateral position can be controlled by tuning the channel geometry and flow velocity, and it is also dependent on the shape of the cell, as sherical cells as shown to occupy and axial position. The control of these factors is important for the manipulation of different cell species, such as RBCs and leukocytes, in microfluidic devices. Finally, we study the behaviour of RBC suspensions at intermediate concentrations, when hydrodynamic interactions between RBCs govern the dynamics. The focusing to lateral positions induced by the walls is inhibited and cells are shown to order along the channel section, occupying the core of the channel. RBCs adopt and horizontal inclination, forming a relatively ordered structure of parallel rows. The rheology of the suspension is also affected, as the interactions between cells attenuate the orientation with the flux and higher flow velocities are required to induce the shear-thinning decay of the viscosity. The results presented in this Thesis highlight the delicate dependence of the cell mechanics in the balance of the cell membrane composition and elastic properties. They also demonstrate that the elastic behaviour of the cell, determined by its membrane, is also crucial for the rheological behaviour of blood, and any process of membrane damage or stiffening can substantially alter the correct blood functioning
Computational study of the emergent behavior of micro-swimmer suspensions by Francisco Alarcón Oseguera( Book )

2 editions published between 2015 and 2016 in English and held by 2 WorldCat member libraries worldwide

It is known that active particles induce emerging patterns as a result of their dynamic interactions, giving rise to amazing collective motions, such as swarming or clustering. Here we present a systematic numerical study of self-propelling particles; our main goal is to characterize the collective behavior of suspensions of active particles as a result of the competition among their propulsion activity and the intensity of an attractive pair potential. Active particles are modeled using the squirmer model. Due to its hydrodynamic nature, we are able to classify the squirmer swimmer activity in terms of the stress it generates (referred to as pullers or pushers). We show that these active stresses play a central role in the emergence of collective motion. We have found that hydrodynamics drive the coherent swimming between swimmers while the swimmer direct interactions, modeled by a Lennard-Jones potential, contributes to the swimmers' cohesion. This competition gives rise to two different regimes where giant density fluctuations (GDF) emerge. These two regimes are differentiated by the suspension alignment; one regime has GDF in aligned suspensions whereas the other regime has GDF of suspensions with an isotropic orientated state. All the simulated squirmer suspensions shown in this study were characterized by a thorough analysis of global properties of the squirmer suspensions as well as a complementary cluster analysis. Active matter refers generically to systems composed of self-driven units, active particles, each capable of converting stored or ambient free energy into systematic movement. Examples of active systems are found at all length scales and could be classified in living and nonliving systems such as microorganisms, tissues and organisms, animal groups, self- propelled colloids and artificial nanoswimmers. Specifically, at the micro and nano scale we find an enormous range of interesting systems both biological and artificial; e.g. spermatozoa that fuse with the ovum during fertilization, the bacteria that inhabit our guts, the protozoa in our ponds, the algae in the ocean; these are but a few examples of a wide biological spectrum. In the artificial world we have self- healing colloidal crystals and membranes as well as self- assembled microswimmers and robots. Experiments in this field are now developing at a very rapid pace and new theoretical ideas are needed to bring unity to the field and identify "universal" behavior in these internally driven systems. One important feature of active matter is that their elements can develop emergent, coordinated behavior; collective motion constitutes one of the most common and spectacular example. Collective motion is ubiquitous and at every scale, from herds of large mammals to amoeba and bacteria colonies, down to the cooperative behavior of molecular motors in the cell. The behavior of large fish schools and the dance of starling flocks at dusk are among the most spectacular examples. From a physical perspective collective motion emerges from a spontaneous symmetry breaking that allows for long-range orientational orden The different mechanisms responsible for such symmetry breaking are still not completely understood. We have performed a systematic numerical study of interactive micro-swimmer suspensions building on the squirmer model, introduced by Lighthill. Since the squirmer identifies systematically the hydrodynamic origin of self-propulsion and stress generation it provides a natural scheme to scrutinize the impact that the different features associated to self-propulsion in a liquid medium have in the collective dynamics of squirmer suspensions. In this abstract we describe the simulation scheme and how squirmers are modeled, then some of the main results are discussed and finally we conclude emphasizing the main implications of the results obtained
Hydrodynamic cooperativity in micro-swimmer suspensions by Isaac Llopis Fusté( )

2 editions published in 2008 in English and held by 2 WorldCat member libraries worldwide

Swimmers' Collective Dynamics Modelization by Guillem Ferré Porta( )

1 edition published in 2011 in English and held by 1 WorldCat member library worldwide

Activity mediated interactions in soft matter : emergent structures and phase transitions by Joan Codina Sala( Book )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

In this thesis we asses the phenomena of arising interactions in soft matter in coexistence with soft active matter. As a non-equilibrium bath we introduce ensembles of self-propelled particles, granular shaken beds, and photo active catalytic particles. We start the thesis with a detailed study of the widely used Active Brownian Particle (ABP) model. This model exhibits a non-equilibrium phase transition which has been intensively studied in recent years, we have finally reported that this transition satisfies all features of equilibrium first order phase transitions. Then, we introduce aligning interactions in ABP and characterize the emergent collective phenomena. In parallel, we explore the emergent forces, from mechanical contact forces, in probe particles in suspensions of aligning active particles and horizontally shaken granular beds. We characterize the forces and identify the emergence of long range interactions in both systems, in aligning active particles long range attractive interactions appear as alignment is increased, and in granular shaken media when the pair of particles align in the shaking direction. Finally, we conclude this thesis with the study of emergent interactions in spherically symmetric systems of catalytic active particles. Symmetry does not permit such particles to propell but the symmetry is broken with the addition of neighboring particles. We model the pair interaction in terms of the relative velocity between particles, and proceed to explore the emergent structures in mixtures of catalytic magnetic particles, and passive particles. We have unveiled the formation of clusters of passive particles. The addition of magnetic interactions between active particles leads to the formation of ramified gel-like structures for dense configurations of active particles. In this case, experimentalists have checked the formation of structures with the same morphologies in experiments in the laboratory
Estudio computacional de un medio granular húmedo forzado by Silvio René Morales Suárez( )

2 editions published in 2010 in Spanish and held by 1 WorldCat member library worldwide

Activity Mediated Interactions in Soft Matter. Structure, Interactions, and Phase Transitions by Joan Codina Sala( )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

In this thesis we asses the phenomena of arising interactions in soft matter in coexistence with soft active matter. As a non-equilibrium bath we introduce ensembles of self-propelled particles, granular shaken beds, and photo active catalytic particles. We start the thesis with a detailed study of the widely used Active Brownian Particle (ABP) model. This model exhibits a non-equilibrium phase transition which has been intensively studied in recent years, we have finally reported that this transition satisfies all features of equilibrium first order phase transitions. Then, we introduce aligning interactions in ABP and characterize the emergent collective phenomena. In parallel, we explore the emergent forces, from mechanical contact forces, in probe particles in suspensions of aligning active particles and horizontally shaken granular beds. We characterize the forces and identify the emergence of long range interactions in both systems, in aligning active particles long range attractive interactions appear as alignment is increased, and in granular shaken media when the pair of particles align in the shaking direction. Finally, we conclude this thesis with the study of emergent interactions in spherically symmetric systems of catalytic active particles. Symmetry does not permit such particles to propell but the symmetry is broken with the addition of neighboring particles. We model the pair interaction in terms of the relative velocity between particles, and proceed to explore the emergent structures in mixtures of catalytic magnetic particles, and passive particles. We have unveiled the formation of clusters of passive particles. The addition of magnetic interactions between active particles leads to the formation of ramified gel-like structures for dense configurations of active particles. In this case, experimentalists have checked the formation of structures with the same morphologies in experiments in the laboratory
Protein-protein docking using geometrical arguments by Israel Cabeza de Vaca López( )

1 edition published in 2009 in English and held by 1 WorldCat member library worldwide

This project aims to develop nobels algorithms to model protein-protein complexes, a very important aspect in biophysics. The algorithm presented based only on geometrical arguments, is intended to be a first and fast approach to get the most probable configurations. The algorithm finds the best positions producing only a small number of solutions (over 250 solutions). The method is based on 2D FFT (fast fourier transform) and orthographic projections of the proteins. The method allows us to find solutions around 15 Ǻ of C[alpha] root mean square deviation for proteins with low electrostatic interactions
Modelo híbrido para la simulación de un Superconductor de Tipo-I by Diego Villuendas Pellicero( )

1 edition published in 2008 in Spanish and held by 1 WorldCat member library worldwide

En este trabajo se presenta un modelo para estudiar los superconductores de tipo-I. El objetivo principal es reproducir el estado intermedio, en el que regiones del material han transitado al estado normal mientras el resto sigue en estado superconductor. Reproducir las estructuras encontradas experimentalmente y entender la histéresis que aparece en estos sistemas bajo determinadas condiciones es otro de los objetivos. El sistema a estudio es una lámina delgada sometida a un campo externo perpendicular a la misma y a temperatura nula. Los resultados obtenidos reproducen en gran medida lo esperado, pese a que los ciclos de histéresis no son exactamente los encontrados experimentalmente
 
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Alternative Names
Ignacio Pagonabarraga researcher

Ignacio Pagonabarraga wetenschapper

Pagonabarraga, I. (Ignacio)

Pagonabarraga, Ignacio

Pagonabarraga Mora, Ignasi

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