Network resilience

Many systems on our planet are known to shift abruptly and irreversibly from one state to another when they are forced across a "tipping point," such as mass extinctions in ecological networks, cascading failures in infrastructure systems, and social convention changes in human and animal networks. Such a regime shift demonstrates a system's resilience that characterizes the ability of a system to adjust its activity to retain its basic functionality in the face of internal disturbances or external environmental changes. In the past 50 years, attention was almost exclusively given to low dimensional systems and calibration of their resilience functions and indicators of early warning signals without considerations for the interactions between the components. Only in recent years, taking advantages of the network theory and lavish real data sets, network scientists have directed their interest to the real-world complex networked multidimensional systems and their resilience function and early warning indicators. This report is devoted to a comprehensive review of resilience function and regime shift of complex systems in different domains, such as ecology, biology, social systems and infrastructure. We cover the related research about empirical observations, experimental studies, mathematical modeling, and theoretical analysis. We also discuss some ambiguous definitions, such as robustness, resilience, and stability.Comment: Review chapter

A Skin Microbiome Model with AMP interactions and Analysis of Quasi-Stability vs Stability in Population Dynamics

The skin microbiome plays an important role in the maintenance of a healthy skin. It is an ecosystem, composed of several species, competing for resources and interacting with the skin cells. Imbalance in the cutaneous microbiome, also called dysbiosis, has been correlated with several skin conditions, including acne and atopic dermatitis. Generally, dysbiosis is linked to colonization of the skin by a population of opportunistic pathogenic bacteria. Treatments consisting in non-specific elimination of cutaneous microflora have shown conflicting results. In this article, we introduce a mathematical model based on ordinary differential equations, with 2 types of bacteria populations (skin commensals and opportunistic pathogens) and including the production of antimicrobial peptides to study the mechanisms driving the dominance of one population over the other. By using published experimental data, assumed to correspond to the observation of stable states in our model, we reduce the number of parameters of the model from 13 to 5. We then use a formal specification in quantitative temporal logic to calibrate our model by global parameter optimization and perform sensitivity analyses. On the time scale of 2 days of the experiments, the model predicts that certain changes of the environment, like the elevation of skin surface pH, create favorable conditions for the emergence and colonization of the skin by the opportunistic pathogen population, while the production of human AMPs has non-linear effect on the balance between pathogens and commensals. Surprisingly, simulations on longer time scales reveal that the equilibrium reached around 2 days can in fact be a quasi-stable state followed by the reaching of a reversed stable state after 12 days or more. We analyse the conditions of quasi-stability observed in this model using tropical algebraic methods, and show their non-generic character in contrast to slow-fast systems. These conditions are then generalized to a large class of population dynamics models over any number of species.Comment: arXiv admin note: substantial text overlap with arXiv:2206.1022

Applying the Free-Energy Principle to Complex Adaptive Systems

The free energy principle is a mathematical theory of the behaviour of self-organising systems that originally gained prominence as a unified model of the brain. Since then, the theory has been applied to a plethora of biological phenomena, extending from single-celled and multicellular organisms through to niche construction and human culture, and even the emergence of life itself. The free energy principle tells us that perception and action operate synergistically to minimize an organism’s exposure to surprising biological states, which are more likely to lead to decay. A key corollary of this hypothesis is active inference—the idea that all behavior involves the selective sampling of sensory data so that we experience what we expect to (in order to avoid surprises). Simply put, we act upon the world to fulfill our expectations. It is now widely recognized that the implications of the free energy principle for our understanding of the human mind and behavior are far-reaching and profound. To date, however, its capacity to extend beyond our brain—to more generally explain living and other complex adaptive systems—has only just begun to be explored. The aim of this collection is to showcase the breadth of the free energy principle as a unified theory of complex adaptive systems—conscious, social, living, or not

Electric Light: Automating the Carceral State During the Quantification of Everything

This dissertation traces the rise of digitally-driven policing technologies in order to make sense of how prevailing logics of governance are transformed by ubiquitous computing technology. Beginning in the early 1990s, police departments and theorists began to rely on increasingly detailed sets of metrics to evaluate performance. The adoption of digital technology to streamline quantitative evaluation coincided with a steep decline in measured crime that served as a proof-of-concept for the effectivity of digital police surveillance and analytics systems. During the turbulent first two decades of the 21st century, such digital technologies were increasingly associated with reform projects designed to improve the transparency and accountability of police departments. This dissertation challenges that assertion, and argues that digitization functions to make “numerical” and “mathematical” racial and sexual violence that is internal to policing neoliberal political economy. Rather than transparency and accountability, this dissertation posits that the effect of digitally-driven police technology is the accelerative disentangling of the “human” from “life” and “life” from government. The consequence has been the ossification of a racialized carceral under the aegis of putatively anti-racist technocratic governance

Physics of Microswimmers - Single Particle Motion and Collective Behavior

Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.Comment: 54 pages, 59 figures, review article, Reports of Progress in Physics (to appear

Lipid Bilayers on Deformable Elastic Substrates

In this thesis an experimental model for the interface between the cell membrane and the supporting cytoskeleton has been developed and analysed. The experimental platform is a novel approach to the design of supported membrane based devices and technologies. The system consists of a single component lipid bilayer coupled to an elastic substrate, the area of which can be reversibly increased and decreased. We uncover three independent mechanisms that the membrane may use to respond to changes in substrate area. If the elastic support is partially hydrophilic, the area of the planar portion of the membrane is strongly coupled to the substrate area. The membrane responds to increasing substrate area by absorbing lipid protrusions, and when the substrate area is decreased the excess membrane area is projected back out in the form of lipid tubes. This mechanical remodelling of the membrane occurs above the plane of the support and mimics the passive means of membrane area regulation recently uncovered in live cells. In contrast, when the surface support is completely hydrophilic, two further mechanisms of substrate stress relaxation are uncovered. When the pH of the solu- tion is greater than 7 the membrane is able to slide over the expanding and contract- ing substrate. This membrane sliding motion occurs in the plane of the support and is dynamic. The effectiveness at which membrane tension is relaxed is dependent on the rate at which the substrate area is changed. When the pH is reduced below pH 7, the membrane area becomes strongly coupled to that of the support and the membrane dramatically ruptures, opening large circular pores, in response to substrate deformation. The pores exhibit a dynamic area change, revealing a complex flow of membrane across the support to equilibrate stress. This novel supported membrane behaviour reveals the rich physics possessed by supported lipid systems, that may assist in the design of new supported lipid based technologies