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Dynamical and collective properties of active and passive particles in Single File
Get PDFParticles motion inside complex, irregular or crowded environments is a common phenomenon ranging from microscopic to macroscopic scales. It can be involved in everyday practical problems, like traffic, in fundamental biological mechanisms, like growth and reproduction of cells, and in important industrial or chemical applications, like oil catalysis. In many cases, transport in crowded environments is guided by 'active' elements, i.e. units that consume energy in order to produce motion. Among systems belonging in this class, the diffusion of hard-core particles in a channel so narrow they cannot pass each other, known as Single File Diffusion, has assumed a particular role. Single File Diffusion is responsible for the transport of ions in membrane channels, the diffusion in nano- and micro-porous materials and has been observed in many other natural and artificial systems.
Aim of this thesis is to investigate Single File system of passive (purely diffusive) or active (self propelled) particles, focusing on the effects of the activity on the Single File motion and on the Single File properties in the presence of absorbing boundaries. Most of the work has been carried out developing analytical and numerical tools within the framework of the Stochastic Processes. By using single particle techniques in a microfluidic approach, we obtained an excellent comparison between experimental data and numerical model of particles emptying a Single File channel with open ends.
In this thesis, after a brief introduction in the framework of confined diffusion processes, we will review the most relevant works in the theoretical and experimental literature of Single File Diffusion, with particular attention to an analytical technique, the Reflection Principle Method, which will be extensively used in this thesis. We will investigate the properties of Single File systems of diffusing particles in presence of two absorbing boundaries, with particular interest to the survival probability, i.e. the probability to find a particle between the boundaries at time t. We will provide an analytical solution of the emptying process, i.e. we calculate the probability characterizing the progressive decrease of the number of particles in the presence of absorbing boundaries, and for the survival probability of a Tagged Particle within the file, either in the presence or in the absence of a constant external force. We also characterize the trend of the characteristic survival times (also called Mean First Passage Times) as function of the system size and of the initial number of particles. We also investigate numerically the case when only the central particle is affected by the absorbing boundaries. We find an exponential decay of the survival probability, as it happens for normal diffusive processes, even in the presence of overcrowding. We will then introduce activity in a Single File system, through a Self-Propelled Particle model, for which we will provide a detailed characterization. In particular, within this model, particles can be either runners or tumblers, if their motion is dominated by straight runs or by changes of direction, respectively. Under Single File conditions, runners tend to form dynamical aggregates: these clusters are continuously formed and disassembled due to random fluctuations of the activity. For tumblers, the survival probabilities are still well described by the analytical theory developed for passive diffusing particles. Conversely, the formation of dynamical clusters enhances anomalous behaviours in the characteristic survival times of runners and induces a remarkable capacity to overcome the action of an external force.Il moto di particelle in mezzi irregolari, complessi o affollati è un fenomeno comune, dalla scala microscopica a quella macroscopica. Lo si può incontrare tanto in situazioni comuni, come il traffico, quanto in meccanismi biologici, come la riproduzione e la crescita delle cellule, e in importanti processi chimici e tecnologici, come la catalisi di idrocarburi. In molti casi, il trasporto in mezzi confinati o affollati è guidato da elementi 'attivi', cioè unità che consumano energia per sostenere il loro stato di moto. Fra i diversi sistemi soggetti a confinamento, particolare rilevanza è rivestita dalla diffusione di sfere impenetrabili in un canale così stretto da non permettere il passaggio di più di una particella alla volta, conosciuto come diffusione in Single File. La diffusione in Single File è il meccanismo responsabile del trasporto di ioni attraverso la membrana cellulare, della diffusione in materiali micro e nanoporosi ed è stata osservata in molti altri sistemi naturali ed artificiali.
Scopo di questa tesi è lo studio su scala mesoscopica di particelle passive (diffusive) o attive (auto-propellenti) in condizioni di Single File, con particolare attenzione all'effetto dell'attività sulla dinamica e sulle proprietà delle particelle nel caso siano presenti condizioni al contorno assorbenti. Gran parte del lavoro è stato svolto nello sviluppo di risultati analitici e numerici nel contesto dei Processi Stocastici. Inoltre, mediante tecniche di manipolazione ottica di singola particella in canali microfluidici, abbiamo ottenuto una eccellente confronto fra dati sperimentali e numerici per il processo di svuotamento di un sistema di particelle in condizioni di Single File.
In questa tesi, dopo una breve introduzione ai processi diffusivi fortemente confinati, passeremo in rassegna i lavori più rilevanti della letteratura teorica e sperimentale sulla Single File Diffusion, con particolare attenzione ad un formalismo matematico, il Reflection Principle Method, che sarà applicato in maniera estensiva nel corso della tesi. Studieremo poi le proprietà di un sistema di particelle diffusive in Single File in presenza di condizioni al contorno assorbenti, concentrandoci sulla survival probability, cioè la probabilità di trovare una particella fra gli estremi del sistema al tempo t. Mostreremo come, in condizioni di Single File, abbiamo ottenuto una soluzione analitica per il processo di svuotamento, cioè calcoleremo la probabilità che caratterizza la progressiva diminuzione del numero di particelle in presenza di condizioni al contorno assorbenti, e per la survival probability di una particella 'marcata' all'interno della Single File sia in presenza che in assenza di una forza esterna costante. Caratterizzeremo gli andamenti dei tempi caratteristici di sopravvivenza, chiamati Tempi Medi di Primo Passaggio, in funzione della taglia del canale e del numero iniziale di particelle. Indagheremo inoltre numericamente il caso in cui solo la particella centrale del sistema in Single File subisce l'effetto delle condizioni al contorno assorbenti. Osserviamo un decadimento esponenziale della survival probability, come accade nell'usuale moto Browniano, anche in presenza di estremo confinamento. Introdurremo l'attività nella Single File attraverso un modello di particelle Self-Propelled, di cui descriveremo le proprietà in dettaglio. In particolare in questo modello le particelle possono essere o runners o tumblers, a seconda che la loro traiettoria sia dominata da lunghi tratti rettilinei o da cambi di direzione. In condizioni di Single File, i runners tendono a formare aggregati dinamici: questi cluster vengono continuamente formati e distrutti dalle fluttuazioni casuali della forza propulsiva. Per i tumblers, le probabilità di sopravvivenza sono ben descritte dalla teoria analitica sviluppata per le particelle passive. Per contro, la formazione di cluster dinamici accresce i comportamenti anomali nei tempi caratteristici di sopravvivenza dei runners e ne induce una notevole capacità di opporsi all'azione di un campo esterno
Conformation and dynamics of partially active linear polymers
Get PDFWe perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along the chain determines the conformational and dynamical properties of the system. Notably, one can modulate the diffusion coefficient of the polymer from active-like to passive-like just by changing the position of the active block. Further, we show that a slight modification of the self-propulsion rule may give rise to an enhancement of diffusion under certain conditions, despite a decrease of the overall polymer activity. Our findings may help in the modelisation of active biophysical systems, such as filamentous bacteria or worms.We study isolated, partially active polymers, i.e. a fraction of the monomers are subject to tangential propulsion. We show that, if the active monomers are contiguous, their position along the chain sets the conformation and dynamics of the polymer
Condensation and Demixing in Solutions of DNA Nanostars and Their Mixtures
No full textWe present a numerical/theoretical approach to efficiently evaluate the
phase diagram of self-assembling DNA nanostars. Combining input
information based on a realistic coarse-grained DNA potential with the
Wertheim association theory, we derive a parameter-free thermodynamic
description of these systems. We apply this method to investigate the
phase behavior of single components and mixtures of DNA nanostars with
different numbers of sticky arms, elucidating the role of the system
functionality and of salt concentration. Specifically, we evaluate the
propensity to demix, the gas liquid phase boundaries and the location of
the critical points. The predicted critical parameters compare very well
with existing experimental results for the available compositions. The
approach developed here is very general, easily extensible to other
all-DNA systems, and provides guidance for future experiments
Self-Organized States from Solutions of Active Ring Polymers in Bulk and under Confinement
No full text: In the present work, we study, by means of numerical simulations, the structural and dynamical behavior of a suspension of active ring polymers in bulk and under lateral confinement. At high activity, when changing the distance between the confining planes and the polymers' density, we identify the emergence of a self-organized dynamical state, characterized by the coexistence of slowly diffusing clusters of rotating disks and faster rings moving in between them. We further assess that self-organization is robust in a range of polymer sizes, and we identify a critical value of the activity, necessary to trigger cluster formation. This system has distinctive features resembling at the same time polymers, liquid crystals, and active systems, where the interplay between activity, topology, and confinement leads to a spontaneous segregation in an initially one-component solution
Active Brownian particles escaping a channel in single file
No full textActive particles may happen to be confined in channels so narrow that they cannot overtake each other (single-file conditions). This interesting situation reveals nontrivial physical features as a consequence of the strong interparticle correlations developed in collective rearrangements. We consider a minimal two-dimensional model for active Brownian particles with the aim of studying the modifications introduced by activity with respect to the classical (passive) single-file picture. Depending on whether their motion is dominated by translational or rotational diffusion, we find that active Brownian particles in single file may arrange into clusters that are continuously merging and splitting (active clusters) or merely reproduce passive-motion paradigms, respectively. We show that activity conveys to self-propelled particles a strategic advantage for trespassing narrow channels against external biases (e.g., the gravitational field)
An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids
Get PDFWe present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, the Wertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest-order virial expansion and on a nearest-neighbor DNA model, can provide, in an undemanding way, a parameter-free thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of the scheme are as accurate as those obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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