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Article ; Online: Sandpile cascades on oscillator networks: The BTW model meets Kuramoto.

Mikaberidze, Guram / D'Souza, Raissa M

2022 Volume 32, Issue 5, Page(s) 53121

Abstract: Cascading failures abound in complex systems and the Bak-Tang-Weisenfeld (BTW) sandpile model provides a theoretical underpinning for their analysis. Yet, it does not account for the possibility of nodes having oscillatory dynamics, such as in power ... ...

Abstract	Cascading failures abound in complex systems and the Bak-Tang-Weisenfeld (BTW) sandpile model provides a theoretical underpinning for their analysis. Yet, it does not account for the possibility of nodes having oscillatory dynamics, such as in power grids and brain networks. Here, we consider a network of Kuramoto oscillators upon which the BTW model is unfolding, enabling us to study how the feedback between the oscillatory and cascading dynamics can lead to new emergent behaviors. We assume that the more out-of-sync a node is with its neighbors, the more vulnerable it is and lower its load-carrying capacity accordingly. Also, when a node topples and sheds load, its oscillatory phase is reset at random. This leads to novel cyclic behavior at an emergent, long timescale. The system spends the bulk of its time in a synchronized state where load builds up with minimal cascades. Yet, eventually, the system reaches a tipping point where a large cascade triggers a "cascade of larger cascades," which can be classified as a dragon king event. The system then undergoes a short transient back to the synchronous, buildup phase. The coupling between capacity and synchronization gives rise to endogenous cascade seeds in addition to the standard exogenous ones, and we show their respective roles. We establish the phenomena from numerical studies and develop the accompanying mean-field theory to locate the tipping point, calculate the load in the system, determine the frequency of the long-time oscillations, and find the distribution of cascade sizes during the buildup phase.
MeSH term(s)	Brain
Language	English
Publishing date	2022-06-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1472677-4
ISSN	1089-7682 ; 1054-1500
ISSN (online)	1089-7682
ISSN	1054-1500
DOI	10.1063/5.0095094
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: What you have, not who you know: food-enhanced social capital and changes in social behavioural relationships in a non-human primate.

Blersch, Rosemary / Vandeleest, Jessica J / Nathman, Amy C / Pósfai, Márton / D'Souza, Raissa / McCowan, Brenda / Beisner, Brianne A

Royal Society open science

2024 Volume 11, Issue 1, Page(s) 231460

Abstract: Social network position in non-human primates has far-reaching fitness consequences. Critically, social networks are both heterogeneous and dynamic, meaning an individual's current network position is likely to change due to both intrinsic and extrinsic ... ...

Abstract	Social network position in non-human primates has far-reaching fitness consequences. Critically, social networks are both heterogeneous and dynamic, meaning an individual's current network position is likely to change due to both intrinsic and extrinsic factors. However, our understanding of the drivers of changes in social network position is largely confined to opportunistic studies. Experimental research on the consequences of
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2787755-3
ISSN	2054-5703
ISSN	2054-5703
DOI	10.1098/rsos.231460
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Article ; Online: Curtailing cascading failures.

D'Souza, Raissa M

Science (New York, N.Y.)

2017 Volume 358, Issue 6365, Page(s) 860–861

Language	English
Publishing date	2017--17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aaq0474
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.MG 77: Show issues

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Book ; Online: Sandpile cascades on oscillator networks

Mikaberidze, Guram / D'Souza, Raissa M.

the BTW model meets Kuramoto

2021

Abstract: Cascading failures abound in complex systems and the BTW sandpile model provides a theoretical underpinning for their analysis. Yet, it does not account for the possibility of nodes having oscillatory dynamics such as in power grids and brain networks. ... ...

Abstract	Cascading failures abound in complex systems and the BTW sandpile model provides a theoretical underpinning for their analysis. Yet, it does not account for the possibility of nodes having oscillatory dynamics such as in power grids and brain networks. Here we consider a network of Kuramoto oscillators upon which the BTW model is unfolding, enabling us to study how the feedback between the oscillatory and cascading dynamics can lead to new emergent behaviors. We assume that the more out-of-sync a node is with its neighbors the more vulnerable it is and lower its load-carrying capacity accordingly. And when a node topples and sheds load, its oscillatory phase is reset at random. This leads to novel cyclic behavior at an emergent, long timescale. The system spends the bulk of its time in a synchronized state where load builds up with minimal cascades. Yet, eventually the system reaches a tipping point where a large cascade triggers a "cascade of larger cascades," which can be classified as a Dragon King event. The system then undergoes a short transient back to the synchronous, build-up phase. The coupling between capacity and synchronization gives rise to endogenous cascade seeds in addition to the standard exogenous ones, and we show their respective roles. We establish the phenomena from numerical studies and develop the accompanying mean-field theory to locate the tipping point, calculate the load in the system, determine the frequency of the long-time oscillations and find the distribution of cascade sizes during the build-up phase. Comment: 13 pages, 11 figures
Keywords	Nonlinear Sciences - Adaptation and Self-Organizing Systems ; Condensed Matter - Disordered Systems and Neural Networks ; Mathematics - Dynamical Systems ; Nonlinear Sciences - Chaotic Dynamics
Subject code	612 ; 515
Publishing date	2021-11-30
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Cluster synchronization on hypergraphs

Salova, Anastasiya / D'Souza, Raissa M.

2021

Abstract: We develop the formalism to analyze cluster synchronization for dynamical elements coupled via hypergraphs beyond pairwise interactions. We introduce the notion of edge partitions and show how node and edge partitions allow us to identify admissible ... ...

Abstract	We develop the formalism to analyze cluster synchronization for dynamical elements coupled via hypergraphs beyond pairwise interactions. We introduce the notion of edge partitions and show how node and edge partitions allow us to identify admissible cluster synchronization states and simplify their linear stability calculations. The analysis in terms of node and edge partitions provides a principled way to track dynamics on hypergraphs, and the projected Laplacian matrices based on each edge cluster are essential to block diagonalizing the Jacobian in order to reduce the dimensionality of the stability analysis. Our work enables detailed analysis of patterns of synchronization beyond full synchronization and beyond dyadic interactions. Comment: 7 pages, 3 figures; updated content, figures, and references
Keywords	Nonlinear Sciences - Adaptation and Self-Organizing Systems ; Condensed Matter - Disordered Systems and Neural Networks ; Mathematics - Dynamical Systems ; Nonlinear Sciences - Chaotic Dynamics
Subject code	612
Publishing date	2021-01-14
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Unified framework for hybrid percolation transitions based on microscopic dynamics

Choi, Hoyun / Cho, Y. S. / D'Souza, Raissa / Kertész, János / Kahng, B.

2023

Abstract: A hybrid percolation transition (HPT) exhibits both discontinuity of the order parameter and critical behavior at the transition point. Such dynamic transitions can occur in two ways: by cluster pruning with suppression of loop formation of cut links or ... ...

Abstract	A hybrid percolation transition (HPT) exhibits both discontinuity of the order parameter and critical behavior at the transition point. Such dynamic transitions can occur in two ways: by cluster pruning with suppression of loop formation of cut links or by cluster merging with suppression of the creation of large clusters. While the microscopic mechanism of the former is understood in detail, a similar framework is missing for the latter. By studying two distinct cluster merging models, we uncover the universal mechanism of the features of HPT-s at a microscopic level. We find that these features occur in three steps: (i) medium-sized clusters accumulate due to the suppression rule hindering the growth of large clusters, (ii) those medium size clusters eventually merge and a giant cluster increases rapidly, and (iii) the suppression effect becomes obsolete and the kinetics is governed by the Erd\H{o}s-R\'enyi type of dynamics. We show that during the second and third period, the growth of the largest component must proceed in the form of a Devil's staircase. We characterize the critical behavior by two sets of exponents associated with the order parameter and cluster size distribution, which are related to each other by a scaling relation. Extensive numerical simulations are carried out to support the theory where a specific method is applied for finite-size scaling analysis to enable handling the large fluctuations of the transition point. Our results provide a unified theoretical framework for the HPT. Comment: 15 pages, 14 figures, 4 tables
Keywords	Condensed Matter - Statistical Mechanics
Subject code	612
Publishing date	2023-07-07
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mutualistic networks emerging from adaptive niche-based interactions.

Cai, Weiran / Snyder, Jordan / Hastings, Alan / D'Souza, Raissa M

Nature communications

2020 Volume 11, Issue 1, Page(s) 5470

Abstract: Mutualistic networks are vital ecological and social systems shaped by adaptation and evolution. They involve bipartite cooperation via the exchange of goods or services between actors of different types. Empirical observations of mutualistic networks ... ...

Abstract	Mutualistic networks are vital ecological and social systems shaped by adaptation and evolution. They involve bipartite cooperation via the exchange of goods or services between actors of different types. Empirical observations of mutualistic networks across genres and geographic conditions reveal correlated nested and modular patterns. Yet, the underlying mechanism for the network assembly remains unclear. We propose a niche-based adaptive mechanism where both nestedness and modularity emerge simultaneously as complementary facets of an optimal niche structure. Key dynamical properties are revealed at different timescales. Foremost, mutualism can either enhance or reduce the network stability, depending on competition intensity. Moreover, structural adaptations are asymmetric, exhibiting strong hysteresis in response to environmental change. Finally, at the evolutionary timescale we show that the adaptive mechanism plays a crucial role in preserving the distinctive patterns of mutualism under species invasions and extinctions.
MeSH term(s)	Animals ; Biological Evolution ; Computational Biology ; Ecology/methods ; Ecosystem ; Food Chain ; Models, Theoretical ; Symbiosis
Language	English
Publishing date	2020-10-29
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-19154-5
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Article ; Online: Talent and experience shape competitive social hierarchies.

Pósfai, Márton / D'Souza, Raissa M

Physical review. E

2018 Volume 98, Issue 2-1, Page(s) 20302

Abstract: The hierarchy of social organization is a ubiquitous property of animal and human groups, linked to resource allocation, collective decisions, individual health, and even to social instability. Experimental evidence shows that both the intrinsic ... ...

Abstract	The hierarchy of social organization is a ubiquitous property of animal and human groups, linked to resource allocation, collective decisions, individual health, and even to social instability. Experimental evidence shows that both the intrinsic abilities of individuals and social reinforcement processes impact hierarchies; existing mathematical models, however, focus on the latter. Here, we develop a rigorous model that incorporates both features and explore their synergistic effect on stability and the structure of hierarchy. For pairwise interactions, we show that there is a trade-off between relationship stability and having the most talented individuals in the highest ranks. Extending this to open societies, where individuals enter and leave the population, we show that important societal effects arise from the interaction between talent and social processes: (i) Despite a positive global correlation between talent and rank, paradoxically, local correlation is negative, and (ii) the removal of an individual can induce a series of rank reversals. We show that the mechanism underlying the latter is the removal of an older individual of limited talent, who nonetheless was able to suppress the rise of younger, more talented individuals.
MeSH term(s)	Animals ; Aptitude ; Hierarchy, Social ; Humans ; Models, Theoretical
Language	English
Publishing date	2018-09-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.98.020302
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Article: Multi-scale phase separation by explosive percolation with single-chromatin loop resolution.

Sengupta, Kaustav / Denkiewicz, Michał / Chiliński, Mateusz / Szczepińska, Teresa / Mollah, Ayatullah Faruk / Korsak, Sevastianos / D'Souza, Raissa / Ruan, Yijun / Plewczynski, Dariusz

Computational and structural biotechnology journal

2022 Volume 20, Page(s) 3591–3603

Abstract: The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, ... ...

Abstract	The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical human genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis of chromatin features. We also include dynamics of loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds in 3D space into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that at least 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our
Language	English
Publishing date	2022-07-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.06.063
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

Sengupta, Kaustav / Denkiewicz, Michał / Chiliński, Mateusz / Szczepińska, Teresa / Mollah, Ayatullah Faruk / Korsak, Sevastianos / D'Souza, Raissa / Ruan, Yijun / Plewczynski, Dariusz

Computational and Structural Biotechnology Journal. 2022, v. 20

2022

Abstract	The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical human genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis of chromatin features. We also include dynamics of loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds in 3D space into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that at least 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our in-silico model integrates the high-throughput 3D genome interaction experimental data with the novel theoretical concept of phase separation, which allows us to model event-based time dynamics of chromatin loop formation and folding trajectories.
Keywords	DNA ; biotechnology ; chromatin ; computer simulation ; discriminant analysis ; epigenome ; extrusion ; fibroblasts ; genomics ; humans ; mathematical theory ; models ; separation ; stem cells ; topology
Language	English
Size	p. 3591-3603.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.06.063
Database	NAL-Catalogue (AGRICOLA)

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