1,720,959 research outputs found
Le fluttuazioni su scala statistica - dalla teoria fisica statistica alle applicazioni biologiche
No full textFluctuations at different scales arise naturally as a result of coarse-graining dynamics at smaller spatial levels. In this thesis, we will see how tools from statistical physics can help analyse fluctuations in different systems and the resulting effects, especially in a biological context. We move from theoretical computations in non equilibrium statistical mechanics and numerical simulations of biological examples to brief experimental verifications through microbial communities to understand such stochasticity at different spatiotemporal scales.
We begin initially with techniques to understand fluctuations of non equilibrium currents in a stochastic process. We focus on entropy production which is a significant marker of out-of-equilibrium regime, and propose a simple and graphical method to compute its various moments, not just in a discrete example of interest, but also in general spatially continuous systems. From non-equilibrium produced by heat baths at different temperatures, we pivot to present another kind of out-of-equilibrium processes due to sink-driven boundary dynamics. Such processes, found in systems with absorbing boundaries invalidate standard relations between fluctuations and dissipations. We propose a generalization of powerful fluctuation-dissipation theorems to include the effect of such boundary driven effects, and apply the results to strongly biologically motivated examples of birth-death forest dynamics and DNA target search on proteins. Here, we compute responses of previously infeasible quantities which point to strong ecological considerations.
Boundary effects due to sinks in a local setting is significantly different from a spatially structured system. This necessitates an explicit incorporation of information of the landscape structure into biological models, offered through the lens of metapopulation theory. We present a first principles derivation of classical theoretical models and demonstrate additional benefits that this statistical mechanics route offers, including the ability to incorporate heterogeneous landscape and dispersal network information. In such systems, close to extinction, demographic fluctuations become significant. Contrarily, at the opposite spatial scale, in a laboratory environment, this regime is hardly reached, with minimum population of microbes being in tens to hundreds of thousands of individuals. Nevertheless, a natural setting involves constant environmental variability, captured through stochasticity in parameters in theoretical models. Specifically, serial dilution, a common experimental technique, gets represented as a periodic fluctuation in the dynamics of species and resources. Incorporating the different aspects of this technique through theoretical methods demonstrates a relation between different associated parameters which enable a sensible comparison across different dilution frequencies, opening the doors to further analysis of effects of environmental variability in microscale biological systems.
Techniques developed for specific processes yield specific results whose scope remain limited. However, generalizations open up new paths of investigation into extended systems offering novel findings. Through investigations of systems at different levels using generalizing methods, we not only understand the specific process, but also observe the potential patterns of non-equilibrium across scales. Such results serve to underscore the importance of fluctuations, either thermal or externally driven, in determining different observed behaviours. This not only aids in the search for general non-equilibrium principles, which is inspired by biological systems, but also motivates further interdisciplinary research
Fluctuations of entropy production of a run-and-tumble particle
Full text linkOut-of-equilibrium systems continuously generate entropy, with its rate of production being a fingerprint of nonequilibrium conditions. In small-scale dissipative systems subject to thermal noise, fluctuations of entropy production are significant. Hitherto, mean and variance have been abundantly studied, even if higher moments might be important to fully characterize the system of interest. Here, we introduce a graphical method to compute any moment of entropy production for a generic discrete-state system. Then, we focus on a paradigmatic model of active particles, i.e., run-and-tumble dynamics, which resembles the motion observed in several micro-organisms. Employing our framework, we compute the first three cumulants of the entropy production for a discrete version of this model. We also compare our analytical results with numerical simulations. We find that as the number of states increases, the distribution of entropy production deviates from a Gaussian. Finally, we extend our framework to a continuous state-space run-and-tumble model, using an appropriate scaling of the transition rates. The approach presented here might help uncover the features of nonequilibrium fluctuations of any current in biological systems operating out-of-equilibrium.LB
Emergent encoding of dispersal network topologies in spatial metapopulation models
Full text link: We address a generalization of the concept of metapopulation capacity for trees and networks acting as the template for ecological interactions. The original measure had been derived from an insightful phenomenological model and is based on the leading eigenvalue of a suitable landscape matrix. It yields a versatile predictor of metapopulation persistence through a threshold value of the eigenvalue determined by ecological features of the focal species. Here, we present an analytical solution to a fundamental microscopic model that incorporates key ingredients of metapopulation dynamics and explicitly distinguishes between individuals comprising the "settled population" and "explorers" seeking colonization. Our approach accounts for general network characteristics (in particular graph-driven directional dispersal which is known to significantly constrain many ecological estimates) and yields a generalized version of the original model, to which it reduces for particular cases. Through examples, including real landscapes used as the template, we compare the predictions from our approach with those of the standard model. Results suggest that in several cases of practical interest, differences are significant. We also examine, with both models, how changes in habitat fragmentation, including removal, addition, or alteration in size, affect metapopulation persistence. The current approach demonstrates a high level of flexibility, enabling the incorporation of diverse "microscopic" elements and their impact on the resulting biodiversity landscape pattern
Landscape and environmental heterogeneity support coexistence in competitive metacommunities
Full text linkMetapopulation models have been instrumental in quantifying the ecological impact of landscape structure on the survival of a focal species. However, extensions to multiple species with arbitrary dispersal networks often rely on phenomenological assumptions that inevitably limit their scope. Here, we propose a multilayer network model of competitive dispersing metacommunities to investigate how spatially structured environments impact species coexistence and ecosystem stability. We introduce the concept of landscape-mediated fitness, quantifying how fit a species is in a given environment in terms of colonization and extinction. We show that, when all environments are equivalent, one species excludes all the others—except the marginal case where species fitnesses are in exact trade-off. However, we prove that stable coexistence becomes possible in sufficiently heterogeneous environments by introducing spatial disorder in the model and solving it exactly in the mean-field limit. Crucially, coexistence is supported by the spontaneous localization of species through the emergence of ecological niches. We show that our results remain qualitatively valid in arbitrary dispersal networks, where topological features can improve species coexistence by buffering competition. Finally, we employ our model to study how correlated heterogeneity promotes spatial ecological patterns in realistic terrestrial and riverine landscapes. Our work provides a framework to understand how landscape structure enables coexistence in metacommunities by acting as the substrate for ecological interactions.ECH
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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