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  • 1.
    Bottinelli, Arianna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Tillämpad matematik och statistik.
    Modelling collective movement and transport network formation in living systems2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The emergence of collective patterns from repeated local interactions between individuals is a common feature to most living systems, spanning a variety of scales from cells to animals and humans. Subjects of this thesis are two aspects of emergent complexity in living systems: collective movement and transport network formation. For collective movement, this thesis studies the role of movement-mediated information transfer in fish decision-making. The second project on collective movement takes inspiration from granular media and soft mode analysis and develops a new approach to describe the emergence of collective phenomena from physical interactions in extremely dense crowds. As regards transport networks, this thesis proposes a model of network growth to extract simple, biologically plausible rules that reproduce topological properties of empirical ant trail networks.  In the second project on transport networks, this thesis starts from the simple rule of “connecting each new node to the closest one”, that describes ants building behavior, to study how balancing local building costs and global maintenance costs influences the growth and topological properties of transport networks. These projects are addressed through a modeling approach and with the aim of identifying minimal sets of basic mechanisms that are most likely responsible of large-scale complex patterns. Mathematical models are always based on empirical observations and are, when possible, compared to experimental data.

    Delarbeid
    1. Local cost minimization in ant transport networks: from small-scale data to large-scale trade-offs
    Åpne denne publikasjonen i ny fane eller vindu >>Local cost minimization in ant transport networks: from small-scale data to large-scale trade-offs
    2015 (engelsk)Inngår i: Journal of the Royal Society Interface, ISSN 1742-5689, E-ISSN 1742-5662, Vol. 12, nr 112, artikkel-id 20150780Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Transport networks distribute resources and information in many human and biological systems. Their construction requires optimization and balance of conflicting criteria such as robustness against disruptions, transport efficiency and building cost. The colonies of the polydomous Australian meat ant Iridomyrmex purpureus are a striking example of such a decentralized network, consisting of trails that connect spatially separated nests. Here we study the rules that underlie network construction in these ants. We find that a simple model of network growth, which we call the minimum linking model (MLM), is sufficient to explain the growth of real ant colonies. For larger networks, the MLM shows a qualitative similarity with a Euclidean minimum spanning tree, prioritizing cost and efficiency over robustness. We introduce a variant of our model to show that a balance between cost, efficiency and robustness can be also reproduced at larger scales than ant colonies. Remarkably, such a balance is influenced by a parameter reflecting the specific features of the modelled transport system. The extended MLM could thus be a suitable source of inspiration for the construction of cheap and efficient transport networks with non-zero robustness, suggesting possible applications in the design of human-made networks.

    Emneord
    transport networks, network growth model, graph theory, ant collective behaviour, ant colony, network optimization
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-268402 (URN)10.1098/rsif.2015.0780 (DOI)000363987900009 ()
    Tilgjengelig fra: 2015-12-09 Laget: 2015-12-04 Sist oppdatert: 2017-12-01bibliografisk kontrollert
    2. Emergent Structural Mechanisms for High-Density Collective Motion Inspired by Human Crowds
    Åpne denne publikasjonen i ny fane eller vindu >>Emergent Structural Mechanisms for High-Density Collective Motion Inspired by Human Crowds
    2016 (engelsk)Inngår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 117, nr 22, artikkel-id 228301Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Collective motion of large human crowds often depends on their density. In extreme cases like heavy metal concerts and black Friday sales events, motion is dominated by physical interactions instead of conventional social norms. Here, we study an active matter model inspired by situations when large groups of people gather at a point of common interest. Our analysis takes an approach developed for jammed granular media and identifies Goldstone modes, soft spots, and stochastic resonance as structurally driven mechanisms for potentially dangerous emergent collective motion.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-303941 (URN)10.1103/PhysRevLett.117.228301 (DOI)000388630000032 ()
    Tilgjengelig fra: 2016-09-27 Laget: 2016-09-27 Sist oppdatert: 2017-11-21bibliografisk kontrollert
    3. How Do Fish Use the Movement of Other Fish to Make Decisions?: From Individual Movement to Collective Decision Making
    Åpne denne publikasjonen i ny fane eller vindu >>How Do Fish Use the Movement of Other Fish to Make Decisions?: From Individual Movement to Collective Decision Making
    2013 (engelsk)Inngår i: Proceedings of the European Conference on Complex Systems 2012 / [ed] Thomas Gilbert, Markus Kirkilionis, Gregoire Nicolis, 2013, Vol. V, s. 591-606Konferansepaper, Publicerat paper (Annet vitenskapelig)
    Serie
    Springer Proceedings in Complexity, ISSN 2213-8684
    Emneord
    Collective animal behaviour, Decision making, SPP models, Fish
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-301517 (URN)10.1007/978-3-319-00395-5_73 (DOI)9783319003948 (ISBN)9783319003955 (ISBN)
    Konferanse
    European Conference on Complex Systems 2012
    Tilgjengelig fra: 2016-08-23 Laget: 2016-08-23 Sist oppdatert: 2016-10-04bibliografisk kontrollert
    4. Balancing building and maintenance costs in growing transport networks
    Åpne denne publikasjonen i ny fane eller vindu >>Balancing building and maintenance costs in growing transport networks
    2017 (engelsk)Inngår i: Physical revview E, ISSN 2470-0045, Vol. 96, nr 3, artikkel-id 032316Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The costs associated to the length of links impose unavoidable constraints to the growth of natural and artificial transport networks. When future network developments cannot be predicted, the costs of building and maintaining connections cannot be minimized simultaneously, requiring competing optimization mechanisms. Here, we study a one-parameter nonequilibrium model driven by an optimization functional, defined as the convex combination of building cost and maintenance cost. By varying the coefficient of the combination, the model interpolates between global and local length minimization, i.e., between minimum spanning trees and a local version known as dynamical minimum spanning trees. We show that cost balance within this ensemble of dynamical networks is a sufficient ingredient for the emergence of tradeoffs between the network's total length and transport efficiency, and of optimal strategies of construction. At the transition between two qualitatively different regimes, the dynamics builds up power-law distributed waiting times between global rearrangements, indicating a point of nonoptimality. Finally, we use our model as a framework to analyze empirical ant trail networks, showing its relevance as a null model for cost-constrained network formation.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-303938 (URN)10.1103/PhysRevE.96.032316 (DOI)000411991200004 ()
    Tilgjengelig fra: 2016-09-27 Laget: 2016-09-27 Sist oppdatert: 2017-12-20bibliografisk kontrollert
  • 2.
    Bottinelli, Arianna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Analys och tillämpad matematik.
    Bassetti, B.
    Lagomarsino, M. C.
    Gherardi, M.
    Influence of homology and node age on the growth of protein-protein interaction networks2012Inngår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 86, nr 4, s. 041919-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so the dynamics of the two objects are intrinsically linked. Here we first introduce a statistical model describing the joint growth of the network and the partitioning of nodes into classes, which is studied through a combined mean-field and simulation approach. We then employ this unified framework to address the specific issue of the age dependence of protein interactions through the definition of three different node wiring or divergence schemes. A comparison with empirical data indicates that an age-dependent divergence move is necessary in order to reproduce the basic topological observables together with the age correlation between interacting nodes visible in empirical data. We also discuss the possibility of nontrivial joint partition and topology observables.

  • 3.
    Bottinelli, Arianna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Tillämpad matematik och statistik.
    Perna, Andrea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Tillämpad matematik och statistik.
    Ward, Ashley
    The University of Sydney, NSW, Australia.
    Sumpter, David TJ
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Tillämpad matematik och statistik.
    How Do Fish Use the Movement of Other Fish to Make Decisions?: From Individual Movement to Collective Decision Making2013Inngår i: Proceedings of the European Conference on Complex Systems 2012 / [ed] Thomas Gilbert, Markus Kirkilionis, Gregoire Nicolis, 2013, Vol. V, s. 591-606Konferansepaper (Annet vitenskapelig)
  • 4.
    Bottinelli, Arianna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Tillämpad matematik och statistik.
    Sumpter, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Tillämpad matematik och statistik.
    Silverberg, Jesse
    Wyss Institute for Biologically Inspired Engineering, Harvard University.
    Emergent Structural Mechanisms for High-Density Collective Motion Inspired by Human Crowds2016Inngår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 117, nr 22, artikkel-id 228301Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Collective motion of large human crowds often depends on their density. In extreme cases like heavy metal concerts and black Friday sales events, motion is dominated by physical interactions instead of conventional social norms. Here, we study an active matter model inspired by situations when large groups of people gather at a point of common interest. Our analysis takes an approach developed for jammed granular media and identifies Goldstone modes, soft spots, and stochastic resonance as structurally driven mechanisms for potentially dangerous emergent collective motion.

  • 5.
    Bottinelli, Arianna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Tillämpad matematik och statistik.
    van Wilgenburg, E.
    Fordham Univ, Dept Biol Sci, Bronx, NY 10458 USA..
    Sumpter, David J. T.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Tillämpad matematik och statistik.
    Latty, T.
    Univ Sydney, Sch Biol Sci, Sydney, NSW 2006, Australia..
    Local cost minimization in ant transport networks: from small-scale data to large-scale trade-offs2015Inngår i: Journal of the Royal Society Interface, ISSN 1742-5689, E-ISSN 1742-5662, Vol. 12, nr 112, artikkel-id 20150780Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Transport networks distribute resources and information in many human and biological systems. Their construction requires optimization and balance of conflicting criteria such as robustness against disruptions, transport efficiency and building cost. The colonies of the polydomous Australian meat ant Iridomyrmex purpureus are a striking example of such a decentralized network, consisting of trails that connect spatially separated nests. Here we study the rules that underlie network construction in these ants. We find that a simple model of network growth, which we call the minimum linking model (MLM), is sufficient to explain the growth of real ant colonies. For larger networks, the MLM shows a qualitative similarity with a Euclidean minimum spanning tree, prioritizing cost and efficiency over robustness. We introduce a variant of our model to show that a balance between cost, efficiency and robustness can be also reproduced at larger scales than ant colonies. Remarkably, such a balance is influenced by a parameter reflecting the specific features of the modelled transport system. The extended MLM could thus be a suitable source of inspiration for the construction of cheap and efficient transport networks with non-zero robustness, suggesting possible applications in the design of human-made networks.

1 - 5 of 5
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