60f Franzese, G. (Giancarlo) [WorldCat Identities]
WorldCat Identities

Franzese, G. (Giancarlo)

Works: 27 works in 54 publications in 4 languages and 565 library holdings
Genres: Conference papers and proceedings 
Roles: Editor, Contributor, htt, Other, Opponent, Author
Classifications: QH505, 571.4
Publication Timeline
Most widely held works by G Franzese
Aspects of physical biology : biological water, protein solutions, transport and replication by W Beiglböck( )

17 editions published in 2008 in English and held by 531 WorldCat member libraries worldwide

The application to Biology of the methodologies developed in Physics is attracting an increasing interest from the scientific community. It has led to the emergence of a new interdisciplinary field, called Physical Biology, with the aim of reaching a better understanding of the biological mechanisms at molecular and cellular levels. Statistical Mechanics in particular plays an important role in the development of this new field. For this reason, the XXth session of the famous Sitges Conference on Statistical Physics was dedicated to "Physical Biology: from Molecular Interactions to Cellular Behavior". As is by now tradition, a number of lectures were subsequently selected, expanded and updated for publication as lecture notes, so as to provide both a state-of-the-art introduction and overview to a number of subjects of broader interest and to favor the interchange and cross-fertilization of ideas between biologists and physicists. The present volume focuses on three main subtopics (biological water, protein solutions as well as transport and replication), presenting for each of the them the on-going debates on recent results. The role of water in biological processes, the mechanisms of protein folding, the phases and cooperative effects in biological solutions, the thermodynamic description of replication, transport and neural activity, all are subjects that are revised in this volume, based on new experiments and new theoretical interpretations
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces by Valentino Bianco( )

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

Water is commonly associated with life. This substance affects the living beings in countless aspects and length scales, ranging from molecular biology to climatology. Water exhibits a long series of anomalous behaviors. These anomalies can be rationalized as a consequence of a second critical point in the supercooled region of the liquid phase. Nevertheless, the large part of the phase diagram of supercooled water is to date experimentally inaccessible for the inevitable crystallization of the bulk liquid. Confinement of water in nano-structures is a possible way to prevent the crystallization of molecules. In this thesis we present a coarse-grain model to describe the physical behavior of water at hydrophobic interfaces. The essential feature of the model is the description of water-water interaction via directional and cooperative components of the hydrogen bond (HB). We explore the phase diagram of supercooled water nano-confined between hydrophobic walls. Our results, grounded in statistical physics methods and Monte Carlo simulations, show the presence of a line of first order phase transition in the temperature-pressure plane separating two liquid phases and ending in a liquid-liquid critical point (LLCP). The LLCP universality class approaches the one of the Ising model in two dimensions in the thermodynamic limit, while large deviations are observed for strong confinement. Below the LLCP we find the locus of maxima of correlation length (the Widom line) of the system. Near the LLCP we find a large increase of the thermodynamic response functions consistent with the anomalous behaviors of water. These predictions are confirmed by a percolation description of water molecules based on the definition of cluster of correlated degrees of freedom. Along the phase transition line and the Widom line we recover a power law cluster distribution. At the LLCP the scaling of the percolation quantities agree with the Ising critical exponents. The density, energy and entropy fluctuations that are at the base of the anomalies of water and the existence of its LLCP have also consequences in the context of protein stability. General thermodynamic prediction asserts the existence of a close stability region (SR) in temperature-pressure plane for the native folded state of a protein. Experimental evidences support this theory showing hot-, cold- and pressure-denaturation. Water behavior at the protein interface is expected to be the driving force for the folding-unfolding process. To shed light on this mechanism we study the SR of a folded hydrophobic polymer solvated in the coarse-grain water. Tuning the water-water interaction at the interface and the density of the hydration shell we find an elliptic protein SR in the temperature-pressure plane, qualitatively consistent with available experimental data. Our work contributes to the ongoing debate about the role of hydration water in stabilizing the native protein state. We show here that the physics of water, and in particular its energy, density and entropy fluctuations are sufficient to rationalize the existence of a protein SR with respect to temperature and pressure
Forces and flows in cells and tissue : Blebs, active gels, and collective cell migration by Ricard Alert Zenón( Book )

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

"In this thesis, we have studied mechanical aspects of some biological processes in cells and tissues, which we addressed by developing theoretical models based on the physics of soft active matter. The thesis contains three parts that focus on different biological systems. In Part I, we study the adhesion between the plasma membrane and the actin cortex of eukaryotic cells. We propose a continuum model for membrane-cortex adhesion that couples the mechanics and hydrodynamics of the membrane to the force-dependent binding kinetics of the linker proteins. We predict the critical pressure difference that causes membrane-cortex detachment, and we discuss how cortical tension can be inferred from micropipette suction experiments. Then, we study the fluctuations of an adhered membrane, and suggest ways in which our predictions could allow probing membrane-cortex adhesion in fluctuation spectroscopy experiments. Then, we employ the proposed model to study the nucleation of blebs, which are balloon-like membrane protrusions arising from a local membrane-cortex detachment. We show that bleb nucleation is governed by membrane peeling, the fracture propagation process whereby adjacent membrane-cortex bonds break sequentially. Through this mechanism, bleb nucleation is not determined by the energy of a local detachment like in the classical nucleation picture, but rather by the kinetics of membrane-cortex linkers. We predict the critical radius for bleb nucleation through membrane peeling and the corresponding effective energy barrier. Finally, we simulate a fluctuating adhered membrane to obtain the probability distribution of bleb nucleation times. In Part II, we study the dynamics of active polar gels, which are soft materials, usually transiently-crosslinked polymeric networks, that are maintained out of equilibrium by internal processes that continuously transduce energy. We derive the constitutive equations of an active polar gel from a mesoscopic model for the dynamics of the molecules that crosslink the polar elements of the system. This way, we establish a connection between the molecular properties and the macroscopic behaviour of active polar gels. Specifically, we explicitly obtain the transport coefficients in terms of molecular parameters, showing that all transport coefficients have an active contribution that stems from breaking detailed balance for the crosslinker binding kinetics. In Part III, we study cell colonies and tissues, focusing in collective cell migration and tissue morphology. First, we propose a particle-based description of cell colonies to study how the different organizations of cells in tissues emerge from intercellular interactions. The model intends to capture generic cellular behaviours such as cell migration, adhesion, and cell-cell overlapping. In addition, it models the so-called contact inhibition of locomotion (CIL), which repolarizes cell migration away from cell-cell contacts, as a torque on the migration direction. We show how CIL yields an effective repulsion between cells, which allows to predict transitions between non-cohesive, cohesive, and 3D tissues. We conclude that, at low cell-cell adhesion, CIL hinders the formation of cohesive tissues. Yet, in continuous cell monolayers, CIL gives rise to self-organized collective motion, ensures tensile stresses in the monolayer, and opposes cell extrusion, thereby hindering the collapse of the monolayer into a 3D aggregate. Then, we focus on the spreading of epithelial monolayers, which we address by means of a continuum model based on the theory of active polar gels. First, we concentrate on the wetting transition of epithelial tissues, which separates monolayer spreading from retraction towards a 3D aggregate — namely the equivalent of a fluid droplet. We show that a critical radius exists for the wetting transition, which does not exist in the classical wetting picture. Thus, we show how the wetting properties of tissues emerge from active cellular forces, evidencing that the wetting transition has an active nature. Finally, we study the morphological stability of the front of a spreading monolayer. The model predicts that traction forces cause a long-wavelength instability of the monolayer front, whereas tissue contractility has a stabilizing effect. The predicted instability can explain the formation of finger-like multicellular protrusions observed during epithelial spreading. It can also explain the symmetry breaking of tissue shape observed during monolayer dewetting. By fitting the predictions to experimental data, we infer the monolayer viscosity and the noise intensity of tissue shape fluctuations, which we suggest to have an active origin." -- TDX
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
L'experiment d'Stern i Gerlach en el seu context teòric la història d'una reorientació by Blai Pié i Valls( Book )

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

L'experiment d'Stern-Gerlach (SG) és considerat un dels més importants de la història de la teoria quàntica, i sovint s'utilitza en llibres de text de Mecànica Quàntica per il·lustrar el concepte d'espín i, fins i tot, els postulats de la teoria. Aquest ús didàctic tan estès ha fet que moltes vegades es confongui el rol que l'SG va jugar en el desenvolupament de la teoria quàntica: no és rar trobar fonts que afirmen que els resultats de l'SG es van rebre amb estupefacció o que van comportar el descobriment de l'espín. Si busquem estudis historiogràfics sobre aquest episodi tan important, ens trobarem davant d'una mancança completa de fonts especialitzades. La majoria de publicacions contenen poc més que algunes anècdotes entorn de l'experiment i algunes fins i tot perpetuen les interpretacions incorrectes que hem esmentat. Segurament l'únic estudi historiogràfic complet de l'experiment d'SG es pot trobar a la recent tesi de Wolfgang Trageser ("L'efecte Stern-Gerlach. Gènesi, desenvolupament i reconstrucció d'un dels experiments fonamentals de la teoria quàntica entre 1916 i 1926"--En alemany), presentada el 2011 a la Johann Wolfgang Goethe-Universität a Frankfurt am Main. L'autor tracta en detall el treball experimental d'Otto Stern i Walther Gerlach, però passa per sobre els comentaris sobre la motivació teòrica de l'experiment, així com les seves conseqüències teòriques. Analitzant en detall el context teòric que envoltava l'SG, intentarem recuperar la interpretació correcta del seu rol en el desenvolupament de la teoria quàntica; no ens ha de sorprendre trobar un relat completament nou amb importants conseqüències en l'àmbit didàctic. En aquesta tesi comencem revisant l'estat de la qüestió de la Teoria Quàntica Antiga (TQA) durant la dècada dels 1910, posant especial èmfasi en les teories de Niels Bohr i Arnold Sommerfeld. És important tenir clars els principis fonamentals d'aquesta teoria per interpretar correctament l'SG. Traçant les motivacions que van portar a l'experiment, estudiem l'efecte Zeeman i la quantització espacial. L'efecte Zeeman es pot considerar una de les principals guies dels desenvolupaments portats a terme per Bohr i Sommerfeld durant la construcció de les seves respectives teories. Precisament, una d'aquestes hipòtesis teòriques destinades a expilcar parcialment l'efecte Zeeman és la quantització espacial, proposada per Sommerfeld a mitjans 1916 i que ràpidament va ser adoptada per Bohr i incorporada a la teoria. La conveniència d'aquesta hipòtesi, però, va ser posada en dubte en repetides ocasions, i algunes de les seves prediccions experimentals no podien ser verificades. És per això que el 1921 Stern va proposar un dràstic experiment per confirmar-la (o falsar-la) d'una vegada per totes. Amb l'ajuda de Gerlach, els dos físics van trigar gairebé un any a obtenir el resultat buscat, confirmant la quantització espacial i aportant també un cert artibtratge a certs debats que s'havien establert entre Bohr i Sommerfeld sobre el nombre d'orientacions que podia atènyer un àtom immers en un camp magnètic. Malgrat aquest experiment, l'experiment d'Stern-Gerlach, sovint es postula com una pedra angular de la TQA, topem amb una contradicció històrica quan estudiem les seves conseqüències històriques. L'única reacció significativa és un article d'Einstein i Ehrenfest que posava de manifest les immenses contradiccions amb què topava la teoria si s'intentava fer un càlcul acurat de les observacions d'Stern i Gerlach. Malgrat el caire catastròfic d'aquest article, la seva publicació va obtenir una minsa resposta: breus discussions es van establir entre els dos autors i Bohr, Smekal, Born i Heisenberg. En cap es es pot considerar, però, que aquesta problemàtica s'incorporés a la naixent crisi que la TQA va patir durant el 1923-1924
Human collective behavior models: language, cooperation and social conventions by Roberta Amato( Book )

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

The topics dealt with in this thesis are all part of the general problem of social consensus, namely how a convention flourish and decay and what motivates people to conform to it. Examples range from driving on the right side of the street, to language, rules of courtesy or moral judgments. Some conventions arise directly from the need to coordinate or conform, such as fashion or speaking the same language, others, instead, apply to situations where there is a tension between individual and collective interest, such as cooperation, reciprocity, etc. This thesis is developed around three main questions still open in the research field of collective human behavior: how coexistence of concurrent conventions is possible, why cooperation in real systems is more common than predicted and how a population undergoes collective behavioral change, namely how an initially minority norm can supplant a majority ones. In the first work, we study the impact of concurrent social pressures in consensus processes. We propose a model of opinion competition where individuals participate in different social networks and receive conflicting social influences. The dynamics take place in two distinct domains, which we model as layers of a multiplex network. The novelty of our study lies to the fact that individuals can have different options in the different layers. This naturally reflects a common situation where an individual can possess some different opinions in different social contexts as a result of consensus with other individuals in the one context but not in the other. Our analysis shows that the latter property enriches the system's dynamics and allows not only for consensus into a single state for both layers, but also for active dynamical states of coexistence of both options. In the second model, we analyze the influence of opinion dynamic in competitive strategical games. Cooperation between humans is quite common and stable behavior even in situations where both game theory and experiments predict defection prevalence. One of the reasons could be just the fact that individuals engaging in strategic interactions are also exposed to social influence and, consequently, to the spread of opinions. We present a new evolutionary game model where game and opinions dynamics take place in different layers of a multiplex network. We show that the coupling between the two dynamical processes can lead to cooperation in scenarios where the pure game dynamics predicts defection and, in some particular setting, gives rise to a metastable state in which nodes that adopt the same strategy self-organize into local groups. In the last work, we present the first extensive quantitative analysis of the phenomenon of norm change by looking at 2,365 orthographic and lexical norms shifts occurred in English and Spanish over the last two centuries as recorded by millions of digitized books. We are able to identify three distinct patterns in the data depending on the nature of the norm shift. Furthermore, we propose a simple evolutionary model that captures all the identified mechanisms and reproduces quantitatively the transitions between norms. This work advances the current understanding of norm shifts in language change, most often limited to qualitative illustrations (e.g., the observation that adoption curve of the new norm follows an ‘S-shaped' behavior
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
Structural properties of water confined by phospholipid membranes by Fausto Martelli( )

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

A geometric approach to the structure of complex networks by Guillermo García Pérez( Book )

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

Complex networks are mathematical representations of the interaction patterns of complex systems. During the last 20 years of Network Science, it has been recognized that networks from utterly different domains exhibit certain universal properties. In particular, real complex networks present heterogeneous, and usually scale-free, degree distributions, a large amount of triangles, or high clustering coefficient, a very short diameter, and a clear community structure. Among the vast set of models proposed to explain the structure of real networks, geometric models have proven to be particularly promising. This thesis is developed in the framework of hidden metric spaces, in which the high level of clustering observed in real networks emerges from underlying geometric spaces encoding the similarity between nodes. Besides providing an intuitive explanation to the observed clustering coefficient, geometric models succeed at reproducing the structure of complex networks with high accuracy. Furthermore, they can be used to obtain embeddings of networks, that is, maps of real systems enabling their geometric analysis and efficient navigation. This work introduces the main concepts in the hidden metric spaces approach and presents a thorough description of the main models and embedding procedures. We generalize these models to generate networks with soft communities, that is, with correlated positions of nodes in the underlying metric space. We also explore one of the models in higher similarity-space dimensions, and show that the maximum clustering coefficient attainable decreases with the dimension, which allows us to conclude that real-world networks must have low-dimensional similarity spaces as a consequence of their high clustering coefficient. The thesis also includes a detailed geometric analysis of the international trade system. After reconstructing a yearly sequence of world trade networks covering 14 decades, we embed them into hyperbolic space to obtain a series of maps, which we named The World Trade Atlas 1870-2013. In these maps, the likelihood for two countries to be connected by a significant trade channel depends on the distance among them in the underlying space, which encodes the different factors influencing trade interactions. Our analysis of the networks and their maps reveals that the world is being shaped by three different forces acting simultaneously: globalization, localization and hierarchization. The hidden metric spaces approach can be exploited beyond network metrics. We show that similarity space defines a notion of scale in real-world networks. We present a Geometric Renormalization Group transformation that unveils a previously unknown self-similarity of real networks. Remarkably, the phenomenon is explained by the congruency of real systems with our model. This renormalization transformation provides us with two immediate applications: a method to construct high-fidelity smaller-scale replicas of real networks and a multiscale navigation protocol in hyperbolic space that outperforms single-scale versions. The geometric origin of real networks is not restricted to their binary structure, but it affects their weighted organization as well. We provide empirical evidence for this claim and propose a geometric model with the capability to reproduce the weighted features of real systems from many different domains. We also present a method to infer the level of coupling of real networks with the underlying metric space, which is generally found to be high in real systems
Studying protein-ligand interactions using a Monte Carlo procedure by Daniel Lecina Casas( Book )

2 editions published between 2017 and 2018 in English and held by 2 WorldCat member libraries worldwide

Biomolecular simulations have been widely used in the study of protein-ligand interactions; comprehending the mechanisms involved in the prediction of binding affinities would have a significant repercussion in the pharmaceutical industry. Notwithstanding the intrinsic difficulty of sampling the phase space, hardware and methodological developments make computer simulations a promising candidate in the resolution of biophysically relevant problems. In this context, the objective of the thesis is the development of a protocol that permits studying protein-ligand interactions, in view to be applied in drug discovery pipelines. The author contributed to the rewriting PELE, our Monte Carlo sampling procedure, using good practices of software development. These involved testing, improving the readability, modularity, encapsulation, maintenance and version control, just to name a few. Importantly, the recoding resulted in a competitive cutting-edge software that is able to integrate new algorithms and platforms, such as new force fields or a graphical user interface, while being reliable and efficient. The rest of the thesis is built upon this development. At this point, we established a protocol of unbiased all-atom simulations using PELE, often combined with Markov (state) Models (MSM) to characterize the energy landscape exploration. In the thesis, we have shown that PELE is a suitable tool to map complex mechanisms in an accurate and efficient manner. For example, we successfully conducted studies of ligand migration in prolyl oligopeptidases and nuclear hormone receptors (NHRs). Using PELE, we could map the ligand migration and binding pathway in such complex systems in less than 48 hours. On the other hand, with this technique we often run batches of 100s of simulations to reduce the wall-clock time. MSM is a useful technique to join these independent simulations in a unique statistical model, as individual trajectories only need to characterize the energy landscape locally, and the global characterization can be extracted from the model. We successfully applied the combination of these two methodologies to quantify binding mechanisms and estimate the binding free energy in systems involving NHRs and tyorsinases. However, this technique represents a significant computational effort. To reduce the computational load, we developed a new methodology to overcome the sampling limitations caused by the ruggedness of the energy landscape. In particular, we used a procedure of iterative simulations with adaptive spawning points based on reinforcement learning ideas. This permits sampling binding mechanisms at a fraction of the cost, and represents a speedup of an order of magnitude in complex systems. Importantly, we show in a proof-of-concept that it can be used to estimate absolute binding free energies. Overall, we hope that the methodologies presented herein help streamline the drug design process
Prospects of microwave spectrometry for vascular stent monitoring : towards a non-invasive and non-ionizing follow-up alternative by Gianluca Arauz Garofalo( Book )

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

"Throughout this thesis we have assessed the prospects of microwave spectrometry (MWS) as a non-ionizing non-invasive monitoring alternative for stented patients in a very early proof-of-concept stage. In Chapter 1 we have provided a generalist retrospective medical background along with a state-of-the-art summary of existing microwave-based stent monitoring approaches. First, we have introduced cardiovascular diseases in general, and ischemic heart disease in particular. Next we have reviewed how percutaneous coronary interventions addressed the medical problem represented by atherosclerosis, giving a special emphasis to balloon angioplasty, bare-metal stenting and drug-eluting stenting. We have further exposed how the outcomes of such revolutionary strategies were compromised by the high rates of post-procedural complications, making unavoidable the invasive and ionizing follow-up of stented patients. Finally, we have summarized existing non-invasive and non-ionizing stent monitoring alternatives based in microwave techniques. In Chapter 2 we have introduced the working principle of our MWS setup. We have first presented how this arrangement can obtain the absorbance of a stent as a function of the frequency and the incidence angle of the microwave fields. We have also shown how these data are combined in a single two-dimensional chart, and how we recognize therein the characteristic resonance frequencies of stents at a glance. As an example, we have presented a typical absorbance diagram to illustrate the general features of such resonances. In particular we have highlighted that these resonances are discrete and have multi-lobed angular patterns. In Chapter 3 we have characterized many stents having a wide variety of nominal sizes to better understand their characteristic resonances in terms of microwave scattering. First, we have found that the resonance frequency obeys a reciprocal dependence on the stent length. This has allowed us to obtain an empirical expression for such relationship just by adjusting two fitting parameters. However, we have not been able to find an analogous expression for the dependence on the stent diameter. In any case, while investigating the latter, we have unexpectedly uncovered how the particular stent architecture influences the corresponding resonance frequencies. By gathering all these individual results we have finally suggested a straightforward half-theoretical half-empirical model linking the resonance frequencies of stents with their structural integrity (through their length), with their particular architecture (through the scaling factor), as well as with their surrounding medium (through the dielectric permittivity and the magnetic permeability). We have also theoretically estimated the resonance frequencies of implanted stents from their corresponding values in free space conditions, showing that in vivo resonance frequencies should be around one order of magnitude smaller than their free space counterparts. Finally, in Chapters 4 and 5 we have explored the potential diagnostic capabilities of MWS in two possible scenarios: stent fracture (SF) and in-stent neoatherosclerosis (ISNA). We have started both chapters reviewing the incidence, the medical implications, and the mechanism of these two stent-related complications. SF has been evaluated in Chapter 4 by means of two "fracture tests" consisting in a successive series of strut cuts. We have shown that MWS provides qualitative indicators for single and multiple strut fractures (downshift of the fundamental resonance frequency), and also quantitative indicators for single or multiple complete transverse linear SFs (split and upshift of that frequency). ISNA has been evaluated in Chapter 6 by means of four ̀̀cholesterol tests'' consisting in a gradual process of increasing cholesterol deposition. We have shown that MWS provides an indicator for a growing presence of cholesterol around a stent (downshift of the fundamental resonance frequency). We have concluded this chapter calculating the theoretical evolution of the resonance frequencies along a cholesterol deposition process, estimating the upper limit for the resonance frequency displacement. Taking together the results we have reported in Chapters 5 and 6, we have shown that MWS could potentially warn about SF and ISNA." -- TDX
Behaviour of the anomalous regions of the Continuos Shouldered Well isotropic soft-core potential by Pol Vilaseca Mainar( )

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

Using molecular dynamics we simulate a system of particles interacting through a continuous isotropic pairwise coresoftened potential, proposed by Giancarlo Franzese, consisting on a repulsive shoulder and an attractive well. The model is known to display a phase diagram with three fuid phases with a gas-liquid critical point and liquid-liquid critical point and to present density, diffusion and structural anomalies, in the same hierarchy that characterizes water. In this work we increase systematically the slope of the repulsive shouder to study the effect on the anomalies. We find that the different anomalous regions are sensible to the changes and get narrow as the slope increases. While diffusion and density anomalous regions tend to colapse into one single point in the T - [rho] plane, structural anomalous region tends asimptotically to a fixed value

1 edition published in 2001 in Italian 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
'A cullanella by Franco Calone( Recording )

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

Dynamics and Effective Connectivity in Bi- and Three-dimensional Neuronal Cultures : from Self-organization to Engineering by Estefanía Estévez Priego( )

1 edition published in 2020 in English and held by 1 WorldCat member library worldwide

"This thesis was part of the European consortium MESOBRAIN, a team of 5 organizations that joined efforts in nanofabrication, cell culturing, imaging and data analysis to build tailored human 3D networks. The thesis timing was limited to 3 years, and several of the resources needed for its development were built from scratch. The main objective of this Ph.D. thesis was to explore complex characteristics of cortical neuronal cultures in terms of effective connectivity and exhaustive network analyses. This objective comprised four research lines: (i) The evaluation of neuronal network resilience and emerging plasticity mechanisms, (ii) the characterization of functional development to underline crucial timepoints in healthy neuronal networks, (iii) the study of 3D network interactions of neurons embedded inside an ECM--like environment, and (iv) the design, construction and viability inspection of neurons seeded on tiny 3D nanoprinted solid scaffold structures as a first step towards recreating cortical columns in vitro.For these multiple lines, we used either primary rat cultures (i,iii,iv) or human--derived neurons (ii). The former group corresponds to cultures with long established protocols that have been thoroughly studied in the field. The latter group corresponds to human neurons derived from iPSCs, a relatively novel model with promising and thrilling applications in regenerative medicine. Despite the increasing use of stem cells in neuroscience, complex systems and medicine, they still lack a thorough exploration in terms of neuronal and circuit formation as well as the properties of the emergent activity patterns. With either primary or stem cells, we explored the formation of neuronal circuits in 2D and 3D, characterized the effective connectivity and rendered a number of network traits. This Thesis combines experiments of highly difficult implementation with detailed data analysis. It was necessary to develop brand new protocols for culturing 3D neuronal networks and for human-derived neurons, the use of different microscopy setups the programming of object detection and tracking software and advance the analysis toolbox of calcium fluorescence data. First, resilience experiments on primary clustered neuronal cultures consisted on progressive perturbations through chemical receptor antagonists. This study represents an inspiring numerical--experimental model to comprehend the impact of plasticity mechanisms in the spontaneous activity of neuronal circuits. The results showed that, upon progressive connectivity blockade through chemical receptors' antagonists, only--excitatory neuronal networks displayed a surprising hyper--efficiency (HE) state for early--onset doses. As plasticity mechanisms influence the response of effective connectivity in the presence of perturbations, these compensatory mechanisms, usually disregarded, must be included in biological modeling as accurately as possible. Otherwise, episodes of functional rewiring and synaptic strengthening could mask important phenomena during experiments that alter channel communication. A simple algorithm that hypothesized an effective synaptic scaling was able to capture the hyper--efficiency state seen in experimental data, while percolation models wrongly predicted a progressive decay.The second research line was a sum of engineering efforts within the MESOBRAIN consortium, the European adventure to build 3D neuronal cultures embedded in hydrogels and with the presence of scaffolds. After several months of biomaterials testing, the candidate D--Clear resulted suitable for the construction of scaffolds, both with primary rat cells and hiPSCs, due to its good optical properties, manageability and biocompatibility. To our knowledge, D--Clear was never used before outside the orthodontic field and could provide a new catalogue of interesting designs for support and guidance of neuronal assemblies. Using this material, we developed a series of designs to offer support and guidance to cortical neurons in a 3D platform.The third research line focused on the study of neuronal development and cell-to-cell interactions in a semi-synthetic hydrogel that resembles the extracellular matrix of the brain. These hydrogel cultures keep the advantages of in vitro models while achieving an effective connectivity and architecture closer to in vivo. Finally, the fourth line of research applied cortical neurons from human-derived pluripotent stem cells to study key developmental stages and characterize the healthy maturation of these cells in vitro. As this technology has tremendous potential for regenerative medicine and to model neuronal diseases, it is urgent to consolidate the capacity of these human neuronal networks to reproduce efficient activity patterns of healthy patients, and explore the differences against the results obtained with animal models." -- TDX
Revealing DNA dynamics from atomistic to genomic level by multiscale computational approaches by Jürgen Walther( )

1 edition published in 2019 in English and held by 1 WorldCat member library worldwide

"The study of DNA from atomistic to mesoscopic level and connecting different resolution levels constitutes a major challenge since the new millennium. In the early 2000s, experiments could resolve for the first time the structure of the nucleosome in high detail or capture physical contacts in the genome of segments far apart in sequence. At around the same time, the force field development for atomistic nucleic acid simulations reached a peak with parmbsc0 in 2007 and coarse grain nucleosome fiber models emerged. The first decade ended with a remarkable experimental advance in visualizing the whole genome, Hi-C. In the current decade, almost ten years after Hi-C was invented, the structure of the cell nucleus is still a very hot topic. We can now harvest the fruits of the pioneers in the first decade of multi-scale investigation of DNA and connect the different resolution levels to obtain a complete picture of DNA from electron orbitals to genome folding. In this work, we use computational approaches to dissect the different resolution levels, from atomistic MD simulations to mesoscopic secondary chromatin structure modeling. We developed a force-field (parmbsc1) for the accurate description of atomistic DNA dynamics based on quantum mechanical simulations. With the accuracy of parmbsc1, sequence-dependent effects of B-DNA flexibility beyond the base pair level were described and used as a starting point to parametrize a novel helical coarse grain model which shows similar accuracy to the DNA dynamics obtained by atomistic MD, but at much lower computational cost. In a newly developed nucleosome fiber model the coarse grain DNA algorithm is used for the linker DNA description and alongside with a simple mesoscopic characterization of the nucleosome chromatin dynamics can be probed at kilobase scale with a DNA model whose roots lie in the quantum mechanical regime. On top of that, to meet current standards of accessibility and usability of tools, the developed coarse grain DNA and nucleosome fiber model are freely available as stand-alone versions or integrated in a single webserver or large-scale online research environment platform." -- TDX
Io t'aspetto by Franco Calone( Recording )

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

Free energy and information-content measurements in thermodynamic and molecular ensembles by Álvaro Martínez Monge( )

1 edition published in 2019 in English and held by 1 WorldCat member library worldwide

"Single-molecule experiments have emerged as a powerful tool that allow researchers to investigate the physical behavior of individual molecules with unprecedented resolution. The feasibility exerting forces at the piconewton scale (10̂-12 N) and measuring nanometric displacements in the sub-millisecond scale, offer a widespread range of exciting possibilities. The major part of this thesis is devoted to address fundamental topics of statistical physics using single-molecule experiments. In particular, in the first part of the thesis, we aimed to study one of the eldest questions in statistical mechanics: the issue of ensemble inequivalence. By performing single- molecule experiments on a well-known molecule (the CD4 DNA hairpin), we have been able of exploring two conjugate ensembles: the fixed-extension and the force-fixed ensemble. Both ensembles are conjugate with respect to energy since the product force times extension equals has energy dimensions. We carried out experiments in the fixed-force ensemble using both optical tweezers and magnetic tweezers, and in the fixed-extension using optical tweezers. We have found that these two conjugate ensembles are not equivalent at the level of thermodynamics nor in kinetics. Moreover, we showed that the often-neglected boundary terms in the definition of the thermodynamic work are essential to the validity of the fluctuation theorem. The second part of this thesis is also merely theoretical. Recent single-molecule assays confirmed the connection between information theory and statistical physics. Single- molecule experiments have turned out to be the perfect playground to explore the thermodynamic implications of having --or lacking-- information. It is worthwhile to mention the experimental realization of the Szilard engine and the experimental verification of Landauer's limit. With the current existing results, the information-to- energy connection is well established. We have been able to experimentally demonstrate, for the first time, the reversed implication. We have been able to quantify the information-content of neutral molecular ensembles by means of thermodynamic measurements. That is, we experimentally demonstrated the energy- to-information conversion. Our works are built on what we call ensemble force spectroscopy, a systematic procedure capable of obtaining a robust characterization of molecular ensembles in the best tradition of statistical physics, by measuring few tens of molecules. In the final part of the thesis we aimed to measure the specific binding energy of a metallic ion to the tertiary structure of a three-way RNA junction belonging to the central domain of the 16S ribosomal RNA (rRNA). From the physics perspective, to the best of our knowledge, first time we have been able to discern the free energy contribution due to the specific binding of magnesium ions to an RNA substrate by means of single-molecule assays. On the other hand, such molecule is able to form, besides its native conformation, a force-induced misfolded state. Despite this fact was already pointed out in previous single-molecule studies, there was a lack of knowledge regarding the molecular kinetics and the folding pathway. Aiming to fill this gap, we performed a thorough study of the three-helix RNA junction using dynamic force spectroscopy. As a result, we have characterized the full folding pathway of the molecule, including both the native and the misfolded structure. Furthermore, we have experimentally confirmed the fact that the presence of magnesium promotes the stabilization of the native structure and we have measured this contribution. We have found that magnesium is able to rescue the native structure from the misfolded structure via electrostatic interactions due to magnesium binding. This fact is biologically relevant, since we have been able to characterize the conditions in which a misfolded molecule is able to recover its native conformation." -- TDX
Statistical thermodynamics of long-range interacting systems and near-field thermal radiation by Ivan Latella( )

1 edition published in 2016 in English and held by 1 WorldCat member library worldwide

Two main topics are examined in this thesis: classical systems with long-range interactions and thermal radiation in the near-field regime. In the first part, we present a thermodynamic approach describing systems with long-range interactions which takes into account the intrinsic nonadditivity in these systems. The basic concept behind this approach is to consider a large ensemble of replicas of the system where the standard formulation of thermodynamics can be naturally applied and the properties of a single system can be consequently inferred. The formulation of the thermodynamic for these systems is in close connection with Hill's thermodynamics of systems with small number of particles. It is shown that systems with long-range interactions can attain equilibrium configurations in the unconstrained ensemble. In this statistical ensemble, the control parameters are the temperature, pressure, and chemical potential, while the energy, volume, and number of particles fluctuate. We consider a solvable model as a concrete example of a system that achieves stable equilibria in this ensemble. We also give a complete description of the phase-diagram of the Thirring model in both the microcanonical and the canonical ensemble, highlighting the main features of ensemble inequivalence. I the second part, we study energy and entropy fluxes of near-field thermal radiation in many-body systems, with application to energy-conversion processes. It is shown that the maximum work that can be obtained from the thermal radiation emitted by two planar sources in the near-field regime is much larger than that corresponding to the blackbody limit. This quantity as well as an upper bound for the efficiency of the process are computed from the formulation of thermodynamics in the near-field regime. The case when the difference of temperatures of the hot source and the environment is small, relevant for energy harvesting, is studied in detail. We also show that thermal radiation energy conversion can be more efficient in the near-field regime. Moreover, by analyzing the thermodynamic performance of three-body near-field heat engines, we demonstrate that the power they supply can be substantially larger than that of two-body systems, showing their strong potential for energy harvesting. Theoretical limits for energy and entropy fluxes in three-body systems are discussed and compared with their corresponding two-body counterparts. Such considerations confirm that the thermodynamic availability in energy-conversion processes driven by three-body photon tunneling can exceed the thermodynamic availability in two-body systems
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Aspects of physical biology : biological water, protein solutions, transport and replication
Alternative Names
Franzese, G.

Giancarlo Franzese researcher

Giancarlo Franzese wetenschapper