Extreme flow simulations reveal skeletal adaptations of deep-sea sponges.

Since its discovery1,2, the deep-sea glass sponge Euplectella aspergillum has attracted interest in its mechanical properties and beauty. Its skeletal system is composed of amorphous hydrated silica and is arranged in a highly regular and hierarchical cylindrical lattice that begets exceptional flexibility and resilience to damage3-6. Structural analyses dominate the literature, but hydrodynamic fields that surround and penetrate the sponge have remained largely unexplored. Here we address an unanswered question: whether, besides improving its mechanical properties, the skeletal motifs of E. aspergillum underlie the optimization of the flow physics within and beyond its body cavity. We use extreme flow simulations based on the 'lattice Boltzmann' method7, featuring over fifty billion grid points and spanning four spatial decades. These in silico experiments reproduce the hydrodynamic conditions on the deep-sea floor where E. aspergillum lives8-10. Our results indicate that the skeletal motifs reduce the overall hydrodynamic stress and support coherent internal recirculation patterns at low flow velocity. These patterns are arguably beneficial to the organism for selective filter feeding and sexual reproduction11,12. The present study reveals mechanisms of extraordinary adaptation to live in the abyss, paving the way towards further studies of this type at the intersection between fluid mechanics, organism biology and functional ecology.

Fame through surprise: How fame-seeking mass shooters diversify their attacks.

Mass shootings are becoming more frequent in the United States, as we routinely learn from the media about attempts that have been prevented or tragedies that destroyed entire communities. To date, there has been limited understanding of the modus operandi of mass shooters, especially those who seek fame through their attacks. Here, we explore whether the attacks of these fame-seeking mass shooters were more surprising than those of others and clarify the link between fame and surprise in mass shootings. We assembled a dataset of 189 mass shootings from 1966 to 2021, integrating data from multiple sources. We categorized the incidents in terms of the targeted population and shooting location. We measured "surprisal" (often known as "Shannon information content") with respect to these features, and we scored fame from Wikipedia traffic data-a commonly used metric of fame. Surprisal was significantly higher for fame-seeking mass shooters than non-fame-seeking ones. We also registered a significant positive correlation between fame and surprisal controlling for the number of casualties and injured victims. Not only do we uncover a link between fame-seeking behavior and surprise in the attacks but also we demonstrate an association between the fame of a mass shooting and its surprise.

Adapting to the Abyss: Passive Ventilation in the Deep-Sea Glass Sponge Euplectella aspergillum.

We analyze the flow physics inside the body cavity and downstream the deep-sea glass sponge Euplectella aspergillum. We provide evidence that the helical skeletal motifs of the sponge give rise to a rich fluid dynamic field, allowing the organism to scavenge flow from the bottom of the sea and promoting a spontaneous, organized vertical flow within its body cavity toward the osculum. Our analysis points at a functional adaptation of the organism, which can passively divert flow through the osculum in unfavorable, low ambient currents, with no need for active pumping, with potential repercussions in functional ecology, as well as the design of chemical reactors, air-treatment units, and civil and aeronaval structures.

Modeling State Firearm Law Adoption Using Temporal Network Models.

Policy Points Promoting healthy public policies is a national priority, but state policy adoption is driven by a complex set of internal and external factors. This study employs new social network methods to identify underlying connections among states and to predict the likelihood of new firearm-related policy adoption given changes to this interstate network. This approach could be used to assess the likelihood that a given state will adopt a specific new firearm-related law and to identify points of influence that could either inhibit or promote wider diffusion of specific laws. CONTEXT: US states are largely responsible for the regulation of firearms within their borders. Each state has developed a different legal environment with regard to firearms based on different values and beliefs of citizens, legislators, governors, and other stakeholders. Predicting the types of firearm laws that states may adopt is therefore challenging. METHODS: We propose a parsimonious model for this complex process and provide credible predictions of state firearm laws by estimating the likelihood they will be passed in the future. We employ a temporal exponential-family random graph model to capture the bipartite state law-state network data over time, allowing for complex interdependencies and their temporal evolution. Using data on all state firearm laws over the period 1979-2020, we estimate these models' parameters while controlling for factors associated with firearm law adoption, including internal and external state characteristics. Predictions of future firearm law passage are then calculated based on a number of scenarios to assess the effects of a given type of firearm law being passed in the future by a given state. FINDINGS: Results show that a set of internal state factors are important predictors of firearm law adoption, but the actions of neighboring states may be just as important. Analysis of scenarios provide insights into the mechanics of how adoption of laws by specific states (or groups of states) may perturb the rest of the network structure and alter the likelihood that new laws would become more (or less) likely to continue to diffuse to other states. CONCLUSIONS: The methods used here outperform standard approaches for policy diffusion studies and afford predictions that are superior to those of an ensemble of machine learning tools. The proposed framework could have applications for the study of policy diffusion in other domains.

Dipole- and vortex sheet-based models of fish swimming.

Elucidating the hydrodynamics of fish swimming is critical to identifying the processes underlying fish orientation and schooling. Due to their mathematical tractability, models based on potential flow are preferred in the study of bidirectional interactions of fish with their surroundings. Dipole-based models that assimilate fish to pairs of vortices are particularly enticing, but yet to be thoroughly validated. Here, we embark on a computational fluid dynamics (CFD) campaign informed by experimental data to validate the accuracy of dipole-based models. The locomotory patterns of a fish undergoing carangiform swimming are reconstructed from existing experimental data, which are used as inputs to CFD simulations of a fish swimming in a channel flow. We demonstrate that dipole-based models are accurate in capturing key features of the fluid flow, but cannot predict the elongated flow streamlines around the fish that are evident in CFD. To address this issue, we propose an alternative model that replaces each vortex in the pair with a sheet along the fish length. Using a pair of vortex sheets that span approximately 80% of the fish body length with a separation distance of approximately 50% of the body width, the model is successful in predicting the fluid flow around the swimming fish for a range of background flow speeds and channel widths. The proposed model shows improved accuracy at the cost of a mildly increased computational effort, thereby constituting an ideal basis for research on fish hydrodynamics.

Correction: Modeling multi-sensory feedback control of zebrafish in a flow.

[This corrects the article DOI: 10.1371/journal.pcbi.1008644.].

Beyond the Bristol book: Advances and perspectives in non-smooth dynamics and applications.

Non-smooth dynamics induced by switches, impacts, sliding, and other abrupt changes are pervasive in physics, biology, and engineering. Yet, systems with non-smooth dynamics have historically received far less attention compared to their smooth counterparts. The classic "Bristol book" [di Bernardo et al., Piecewise-smooth Dynamical Systems. Theory and Applications (Springer-Verlag, 2008)] contains a 2008 state-of-the-art review of major results and challenges in the study of non-smooth dynamical systems. In this paper, we provide a detailed review of progress made since 2008. We cover hidden dynamics, generalizations of sliding motion, the effects of noise and randomness, multi-scale approaches, systems with time-dependent switching, and a variety of local and global bifurcations. Also, we survey new areas of application, including neuroscience, biology, ecology, climate sciences, and engineering, to which the theory has been applied.

Modeling multi-sensory feedback control of zebrafish in a flow.

Understanding how animals navigate complex environments is a fundamental challenge in biology and a source of inspiration for the design of autonomous systems in engineering. Animal orientation and navigation is a complex process that integrates multiple senses, whose function and contribution are yet to be fully clarified. Here, we propose a data-driven mathematical model of adult zebrafish engaging in counter-flow swimming, an innate behavior known as rheotaxis. Zebrafish locomotion in a two-dimensional fluid flow is described within the finite-dipole model, which consists of a pair of vortices separated by a constant distance. The strength of these vortices is adjusted in real time by the fish to afford orientation and navigation control, in response to of the multi-sensory input from vision, lateral line, and touch. Model parameters for the resulting stochastic differential equations are calibrated through a series of experiments, in which zebrafish swam in a water channel under different illumination conditions. The accuracy of the model is validated through the study of a series of measures of rheotactic behavior, contrasting results of real and in-silico experiments. Our results point at a critical role of hydromechanical feedback during rheotaxis, in the form of a gradient-following strategy.

Urban Determinants of COVID-19 Spread: a Comparative Study across Three Cities in New York State.

The ongoing pandemic is laying bare dramatic differences in the spread of COVID-19 across seemingly similar urban environments. Identifying the urban determinants that underlie these differences is an open research question, which can contribute to more epidemiologically resilient cities, optimized testing and detection strategies, and effective immunization efforts. Here, we perform a computational analysis of COVID-19 spread in three cities of similar size in New York State (Colonie, New Rochelle, and Utica) aiming to isolate urban determinants of infections and deaths. We develop detailed digital representations of the cities and simulate COVID-19 spread using a complex agent-based model, taking into account differences in spatial layout, mobility, demographics, and occupational structure of the population. By critically comparing pandemic outcomes across the three cities under equivalent initial conditions, we provide compelling evidence in favor of the central role of hospitals. Specifically, with highly efficacious testing and detection, the number and capacity of hospitals, as well as the extent of vaccination of hospital employees are key determinants of COVID-19 spread. The modulating role of these determinants is reduced at lower efficacy of testing and detection, so that the pandemic outcome becomes equivalent across the three cities.

The detection matrix as a model-agnostic tool to estimate the number of degrees of freedom in mechanical systems and engineering structures.

Estimating the number of degrees of freedom of a mechanical system or an engineering structure from the time-series of a small set of sensors is a basic problem in diagnostics, which, however, is often overlooked when monitoring health and integrity. In this work, we demonstrate the applicability of the network-theoretic concept of detection matrix as a tool to solve this problem. From this estimation, we illustrate the possibility to identify damage. The detection matrix, recently introduced by Haehne et al. [Phys. Rev. Lett. 122, 158301 (2019)] in the context of network theory, is assembled from the transient response of a few nodes as a result of non-zero initial conditions: its rank offers an estimate of the number of nodes in the network itself. The use of the detection matrix is completely model-agnostic, whereby it does not require any knowledge of the system dynamics. Here, we show that, with a few modifications, this same principle applies to discrete systems, such as spring-mass lattices and trusses. Moreover, we discuss how damage in one or more members causes the appearance of distinct jumps in the singular values of this matrix, thereby opening the door to structural health monitoring applications, without the need for a complete model reconstruction.

Spatiotemporal patterns of firearm acquisition in the United States in different presidential terms.

This study develops mathematical tools and approaches to investigate spatiotemporal patterns of firearm acquisition in the U.S. complemented by hypothesis testing and statistical analysis. First, state-level and nation-level instant background check (BC) data are employed as proxy of firearm acquisition corresponding to 1999-2021. The relative-phase time-series of BC in each U.S. state is recovered and utilized to calculate the time-series of the U.S. states' synchronization degree. We reveal that U.S. states present a high-level degree of synchronization except in 2010-2011 and after 2018. Comparing these results with respect to a sitting U.S. president provides additional information: specifically, any two presidential terms are characterized by statistically different synchronization degrees except G. W. Bush's first term and B. H. Obama's second term. Next, to detail variations of BC, short-time Fourier transform, dimensionality reduction techniques, and diffusion maps are implemented within a time-frequency representation. Firearm acquisition in the high frequency band is described by a low-dimensional embedding, in the form of a plane with two embedding coordinates. Data points on the embedding plane identify separate clusters that signify state transitions in the original BC data with respect to different time windows. Through this analysis, we reveal that the frequency content of the BC data has a time-dependent characteristic. By comparing the diffusion map at hand with respect to a presidential term, we find that at least one of the embedding coordinates presents statistically significant variations between any two presidential terms except B. H. Obama's first term and D. J. Trump's pre-COVID term. The results point at a possible interplay between firearm acquisition in the U.S. and a presidential term.

Inversion of Solvent Migration in Charged Membranes.

We theoretically demonstrate the possibility of inversion of solvent migration in charged membranes, opposing osmosis. Inversion of solvent migration is ascribed to the finite volume of ions in the solution permeating the membrane, a quantity that has been neglected in the literature so far. We propose a model of the electrochemistry in the proximity of an electrode, illustrating the range of the molar volume of ions that can yield the inversion of solvent migration. This study poses the basis for novel applications in microfluidics, nanofluidics, and electrochemistry, along with new inquiries in biology.

Solvation-Driven Electrochemical Actuation.

We demonstrate a novel principle of contactless actuation for ionic membranes in salt solution based on solvation. Actuation is driven by differential swelling of the sides of the membrane, due to comigrating water in the solvation shells of mobile ions. We validate our theory through a series of experiments, which unravel a strong dependence of membrane deflection on the hydration numbers of mobile ions in the external solution and membrane. Our study suggests a critical role of solvation in the chemoelectromechanics of natural and artificial selectively permeable membranes.

How adherence to public health measures shapes epidemic spreading: A temporal network model.

The COVID-19 pandemic has laid bare the importance of non-pharmaceutical interventions in the containment of airborne infectious diseases. Social distancing and mask-wearing have been found to contain COVID-19 spreading across a number of observational studies, but a precise understanding of their combined effectiveness is lacking. An underdeveloped area of research entails the quantification of the specific role of each of these measures when they are differentially adopted by the population. Pursuing this research allows for answering several pressing questions like: how many people should follow public health measures for them to be effective for everybody? Is it sufficient to practice social distancing only or just wear a mask? Here, we make a first step in this direction, by establishing a susceptible-exposed-infected-removed epidemic model on a temporal network, evolving according to the activity-driven paradigm. Through analytical and numerical efforts, we study epidemic spreading as a function of the proportion of the population following public health measures, the extent of social distancing, and the efficacy of masks in protecting the wearer and others. Our model demonstrates that social distancing and mask-wearing can be effective in preventing COVID-19 outbreaks if adherence to both measures involves a substantial fraction of the population.

Validity and Limitations of the Detection Matrix to Determine Hidden Units and Network Size from Perceptible Dynamics.

Determining the size of a network dynamical system from the time series of some accessible units is a critical problem in network science. Recent work by Haehne et al. [Phys. Rev. Lett. 122, 158301 (2019).PRLTAO0031-900710.1103/PhysRevLett.122.158301] has presented a model-free approach to address this problem, by studying the rank of a detection matrix that collates sampled time series of perceptible nodes from independent experiments. Here, we unveil a profound connection between the rank of the detection matrix and the control-theoretic notion of observability, upon which we conclude when and how it is feasible to exactly infer the size of a network dynamical system.

Data-driven modeling of zebrafish behavioral response to acute caffeine administration.

Over the last thirty years, we have witnessed a dramatic rise in the use of zebrafish in preclinical research. Every year, more than 5000 technical papers are published about zebrafish, many of them seeking to explain the underpinnings of anxiety through animal testing. In-silico experiments could significantly contribute to zebrafish research and welfare, by offering new means to support the 3Rs principles of replacement, reduction, and refinement. Here, we propose a data-driven modeling framework to predict the anxiety-related behavioral response of zebrafish to acute caffeine administration. The modeling framework unfolds along a two-time-scale dichotomy to capture freezing behavior along a slow temporal scale and burst-and-coast locomotion at a fast time-scale. Anchored in the theory of Markov chains and stochastic differential equations, we demonstrate a parsimonious, yet robust, modeling framework to accurately simulate experimental observations of zebrafish treated at different caffeine concentrations. Our results complement recent modeling efforts, laying the foundations for conducting in-silico experiments in zebrafish behavioral pharmacology.

Collective Pulsing in Xeniid Corals: Part I-Using Computer Vision and Information Theory to Search for Coordination.

Xeniid corals (Cnidaria: Alcyonacea), a family of soft corals, include species displaying a characteristic pulsing behavior. This behavior has been shown to increase oxygen diffusion away from the coral tissue, resulting in higher photosynthetic rates from mutualistic symbionts. Maintaining such a pulsing behavior comes at a high energetic cost, and it has been proposed that coordinating the pulse of individual polyps within a colony might enhance the efficiency of fluid transport. In this paper, we test whether patterns of collective pulsing emerge in coral colonies and investigate possible interactions between polyps within a colony. We video recorded different colonies of Heteroxenia sp. in a laboratory environment. Our methodology is based on the systematic integration of a computer vision algorithm (ISOMAP) and an information-theoretic approach (transfer entropy), offering a vantage point to assess coordination in collective pulsing. Perhaps surprisingly, we did not detect any form of collective pulsing behavior in the colonies. Using artificial data sets, however, we do demonstrate that our methodology is capable of detecting even weak information transfer. The lack of a coordination is consistent with previous work on many cnidarians where coordination between actively pulsing polyps and medusa has not been observed. In our companion paper, we show that there is no fluid dynamic benefit of coordinated pulsing, supporting this result. The lack of coordination coupled with no obvious fluid dynamic benefit to grouping suggests that there may be non-fluid mechanical advantages to forming colonies, such as predator avoidance and defense.

Improving on transfer entropy-based network reconstruction using time-delays: Approach and validation.

Transfer entropy constitutes a viable model-free tool to infer causal relationships between two dynamical systems from their time-series. In an information-theoretic sense, transfer entropy associates a cause-and-effect relationship with directed information transfer, such that one may improve the prediction of the future of a dynamical system from the history of another system. Recent studies have proposed the use of transfer entropy to reconstruct networks, but the inherent dyadic nature of this metric challenges the development of a robust approach that can discriminate direct from indirect interactions between nodes. In this paper, we seek to fill this methodological gap through the cogent integration of time-delays in the transfer entropy computation. By recognizing that information transfer in the network is bound by a finite speed, we relate the value of the time-delayed transfer entropy between two nodes to the number of walks between them. Upon this premise, we lay out the foundation of an alternative framework for network reconstruction, which we illustrate through closed-form results on three-node networks and numerically validate on larger networks, using examples of Boolean models and chaotic maps.

Model-based feedback control of live zebrafish behavior via interaction with a robotic replica.

The possibility of regulating the behavior of live animals using biologically-inspired robots has attracted the interest of biologists and engineers for over twenty-five years. From early work on insects to recent endeavors on mammals, we have witnessed fascinating applications that have pushed forward our understanding of animal behavior along new directions. Despite significant progress, most of the research has focused on open-loop control systems, in which robots execute predetermined actions, independent of the animal behavior. We integrate mathematical modeling of social behavior toward the design of realistic feedback laws for robots to interact with a live animal. In particular, we leverage recent advancements in data-driven modeling of zebrafish behavior. Ultimately, we establish a novel robotic platform that allows real-time actuation of a biologically-inspired 3D-printed zebrafish replica to implement model-based control of animal behavior. We demonstrate our approach through a series of experiments, designed to elucidate the appraisal of the replica by live subjects with respect to conspecifics and to quantify the biological value of closed-loop control.