Leticia Ribeiro Paiva, Sidiney Geraldo Alves, Og DeSouza, Octavio Miramontes
{"title":"Emergent dynamical phases and collective motion in termites.","authors":"Leticia Ribeiro Paiva, Sidiney Geraldo Alves, Og DeSouza, Octavio Miramontes","doi":"10.1098/rsif.2025.0097","DOIUrl":"10.1098/rsif.2025.0097","url":null,"abstract":"<p><p>Termites which are able to forage in the open can be often seen, in the field or in the laboratory: (i) wandering around, forming no observable pattern, (ii) clustering themselves in a dense and almost immobile pack, or (iii) milling about in a circular movement. Despite being well reported patterns, they are normally regarded as independent phenomena whose specific traits have never been properly quantified. Evidence, however, favours the hypothesis that these are interdependent patterns, arising from self-organized interactions and movement among workers. After all, termites are a form of active matter where blind cooperative individuals are self-propelled and lack the possibility of visual cues to spatially orientate and align. It follows that their non-trivial close-contact patterns could generate motion-collision-induced phase separations. This would then trigger the emergence of these three patterns (disorder, clustering, milling) as parts of the same continuum. By inspecting termite groups confined in arenas, we could quantitatively describe each one of these patterns in detail. We identified disorder, clustering and milling spatial patterns. These phases and their transitions are characterized aiming to offer refinements in the understanding of these aspects of self-propelled particles in active matter where close-range contacts and collisions are important.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20250097"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12187419/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144484830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nina Baldy, Marmaduke Woodman, Viktor K Jirsa, Meysam Hashemi
{"title":"Dynamic causal modelling in probabilistic programming languages.","authors":"Nina Baldy, Marmaduke Woodman, Viktor K Jirsa, Meysam Hashemi","doi":"10.1098/rsif.2024.0880","DOIUrl":"10.1098/rsif.2024.0880","url":null,"abstract":"<p><p>Understanding the intricate dynamics of brain activities necessitates models that incorporate causality and nonlinearity. Dynamic causal modelling (DCM) presents a statistical framework that embraces causal relationships among brain regions and their responses to experimental manipulations, such as stimulation. In this study, we perform Bayesian inference on a neurobiologically plausible generative model that simulates event-related potentials observed in magneto/encephalography data. This translates into probabilistic inference of latent and observed states of a system driven by input stimuli, described by a set of nonlinear ordinary differential equations (ODEs) and potentially correlated parameters. We provide a guideline for reliable inference in the presence of multimodality, which arises from parameter degeneracy, ultimately enhancing the predictive accuracy of neural dynamics. Solutions include optimizing the hyperparameters, leveraging initialization with prior information and employing weighted stacking based on predictive accuracy. Moreover, we implement the inference and conduct comprehensive model comparison in several probabilistic programming languages to streamline the process and benchmark their efficiency. Our investigation shows that model inversion in DCM extends beyond variational approximation frameworks, demonstrating the effectiveness of gradient-based Markov chain Monte Carlo methods. We illustrate the accuracy and efficiency of posterior estimation using a self-tuning variant of Hamiltonian Monte Carlo and the automatic Laplace approximation, effectively addressing parameter degeneracy challenges. This technical endeavour holds the potential to advance the inversion of state-space ODE models, and contribute to neuroscience research and applications in neuroimaging through automatic DCM.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20240880"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133347/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ellen Juel Pørtner, Anna Mularski, Tobias William Jarrett, Stine Lauritzen Sønder, Jesper Nylandsted, Adam Cohen Simonsen
{"title":"Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology.","authors":"Ellen Juel Pørtner, Anna Mularski, Tobias William Jarrett, Stine Lauritzen Sønder, Jesper Nylandsted, Adam Cohen Simonsen","doi":"10.1098/rsif.2024.0885","DOIUrl":"10.1098/rsif.2024.0885","url":null,"abstract":"<p><p>Cell nuclei are commonly isolated for mechanobiology studies although isolated nuclei may display viscoelastic properties differing from those of live cells. Nuclear mechanics is generally dependent on the time scale of the applied load and cannot accurately be assessed by a simple elasticity parameter. Active microrheology with an atomic force microscope (AFMMR) is a versatile tool for probing nuclear mechanics and we employ the technique for exploring isolated and live-cell nuclei in MCF7 cells, including the significance of actin depolymerization. We successfully validate the method using polyacrylamide hydrogels with correction for cantilever drag in the fluid. The AFMMR results reveal that isolated and live-cell nuclei are equivalent to within a scaling factor, in their frequency-dependent modulus, with isolated nuclei being softer. The loss tangent reveals a transition from solid- to liquid-like behaviour occurring at higher frequency in isolated than in live-cell nuclei. Viscoelastic modelling using the Jeffreys model describes the frequency-dependent modulus of all measured nuclei. Model parameters display sensitivity to nuclei isolation and to actin depolymerization in live cells. Sections of the Jeffreys circuit can potentially be assigned to internal and external nucleus structures, respectively, thereby establishing a minimal mechanistic framework for interpreting microrheology data on cell nuclei.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20240885"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Optimal switching strategies for navigation in stochastic settings.","authors":"Francesco Mori, L Mahadevan","doi":"10.1098/rsif.2024.0677","DOIUrl":"10.1098/rsif.2024.0677","url":null,"abstract":"<p><p>When navigating complex environments, animals often combine multiple strategies to mitigate the effects of external disturbances. These modalities often correspond to different sources of information, leading to speed - accuracy trade-offs. Inspired by the intermittent reorientation strategy seen in the behaviour of the dung beetle, we consider the problem of the navigation strategy of a correlated random walker moving in two dimensions. We assume that the heading of the walker can be reoriented to the preferred direction by paying a fixed cost as it tries to maximize its total displacement in a fixed direction. Using optimal control theory, we derive analytically and confirm numerically the strategy that maximizes the walker's speed, and show that the average time between reorientations scales inversely with the magnitude of the environmental noise. We then extend our framework to describe execution errors and sensory acquisition noise. As a result, we provide a range of testable predictions and suggest new experimental directions. Our approach may be amenable to other navigation problems involving multiple sensory modalities that require switching between egocentric and geocentric strategies.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20240677"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexander E Zarebski, Antoine Zwaans, Bernardo Gutierrez, Louis du Plessis, Oliver G Pybus
{"title":"Estimating epidemic dynamics with genomic and time series data.","authors":"Alexander E Zarebski, Antoine Zwaans, Bernardo Gutierrez, Louis du Plessis, Oliver G Pybus","doi":"10.1098/rsif.2024.0632","DOIUrl":"10.1098/rsif.2024.0632","url":null,"abstract":"<p><p>Accurately estimating the prevalence and transmissibility of an infectious disease is an important task in genetic infectious disease epidemiology. However, generating accurate estimates of these quantities, that make use of both epidemic time series and pathogen genome sequence data, is a challenging problem. Phylogenetic birth-death processes are a popular choice for modelling the transmission of infectious diseases, but it is difficult to estimate the prevalence of infection with them. Here, we extended our approximate likelihood approach, which combines phylogenetic information from sampled pathogen genomes and epidemiological information from a time series of case counts, to estimate historical prevalence in addition to the effective reproduction number. We implement this new method in a BEAST2 package called Timtam. In a simulation study our approximation is seen to be well-calibrated and recovers the parameters of simulated data. To demonstrate how Timtam can be applied to real datasets, we carried out empirical analyses of data from two infectious disease outbreaks: the outbreak of SARS-CoV-2 onboard the <i>Diamond Princess</i> cruise ship in early 2020 and poliomyelitis in Tajikistan in 2010. In both cases we recover estimates consistent with previous analyses.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20240632"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tom Carrard, Elham Nourani, Lukas Jansing, Tim Zimmermann, Petra Sumasgutner, Matthias Tschumi, David Jenny, Martin Wikelski, Kamran Safi, Michael Sprenger, Martina Scacco
{"title":"Golden eagles regularly use gravity waves to soar: new insights from high-resolution weather data.","authors":"Tom Carrard, Elham Nourani, Lukas Jansing, Tim Zimmermann, Petra Sumasgutner, Matthias Tschumi, David Jenny, Martin Wikelski, Kamran Safi, Michael Sprenger, Martina Scacco","doi":"10.1098/rsif.2024.0891","DOIUrl":"10.1098/rsif.2024.0891","url":null,"abstract":"<p><p>Soaring flight allows birds to reduce the metabolic cost of flight by harnessing energy from the atmosphere. The study of soaring behaviour has been significantly constrained by the low resolution of available atmospheric data, limiting our ability to accurately describe the conditions enabling soaring and its adaptability to different updraught types. For instance, while the use of thermals and orographic lifting updraughts are well described in the literature, the role of gravity waves has remained largely unexplored. Advancements in high-resolution atmospheric modelling, with hourly output available at the kilometre-scale grid spacing, offer new opportunities to investigate the flexibility of soaring flight in response to complex atmospheric dynamics, including gravity waves. In this study, we used a combination of a high-resolution atmospheric analysis and high-resolution global positioning system tracking data to characterize the updraught sources used by golden eagles, <i>Aquila chrysaetos</i>, in the European Alps. Our findings reveal that golden eagles repeatedly used gravity waves, with at least 19% of the inspected soaring segments involving this updraught source. Thermals remained the primary energy source for soaring, but during winter, when thermals were more scarce, the quasi-totality of soaring events were powered by gravity waves or orographic lifting. Our results provide a new perspective on the environmental energy available to soaring birds and on landscape connectivity in topographically complex regions.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20240891"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bohan Wu-Zhang, Peixin Zhang, Renaud Baillou, Anke Lindner, Eric Clement, Gerhard Gompper, Dmitry A Fedosov
{"title":"Run-and-tumble dynamics of <i>Escherichia coli</i> is governed by its mechanical properties.","authors":"Bohan Wu-Zhang, Peixin Zhang, Renaud Baillou, Anke Lindner, Eric Clement, Gerhard Gompper, Dmitry A Fedosov","doi":"10.1098/rsif.2025.0035","DOIUrl":"10.1098/rsif.2025.0035","url":null,"abstract":"<p><p>The huge variety of microorganisms motivates fundamental studies of their behaviour with the possibility to construct artificial mimics. A prominent example is the <i>Escherichia coli</i> bacterium, which employs several helical flagella to exhibit a motility pattern that alternates between run (directional swimming) and tumble (change in swimming direction) phases. We establish a detailed <i>E. coli</i> model, coupled to fluid flow described by the dissipative particle dynamics method, and investigate its run-and-tumble behaviour. Different <i>E. coli</i> characteristics, including body geometry, flagella bending rigidity, the number of flagella and their arrangement at the body, are considered. Experiments are also performed to directly compare with the model. Interestingly, in both simulations and experiments, the swimming velocity is nearly independent of the number of flagella. The rigidity of a hook (the short part of a flagellum that connects it directly to the motor), polymorphic transformation (spontaneous change in flagella helicity) of flagella and their arrangement at the body surface strongly influence the run-and-tumble behaviour. Mesoscale hydrodynamics simulations with the developed model help us better understand physical mechanisms that govern <i>E. coli</i> dynamics, yielding the run-and-tumble behaviour that compares well with experimental observations. This model can further be used to explore the behaviour of <i>E. coli</i> and other peritrichous bacteria in more complex realistic environments.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20250035"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yoko Matsumura, Shayan Ramezanpour, Thomas van de Kamp, Stanislav Gorb, Alexander Kovalev, Hamed Rajabi
{"title":"Correlated evolution of elaborate intromission mechanics during copulation between the sexes in leaf beetles.","authors":"Yoko Matsumura, Shayan Ramezanpour, Thomas van de Kamp, Stanislav Gorb, Alexander Kovalev, Hamed Rajabi","doi":"10.1098/rsif.2025.0155","DOIUrl":"10.1098/rsif.2025.0155","url":null,"abstract":"<p><p>Diverse female and male genitalia have evolved. Although the evolutionary mechanisms behind this phenomenon have been studied extensively, the mechanical interactions between female and male genitalia are much less understood. Here, we provide an in-depth biomechanical study on the intromission of elongated tube-like female and male genitalia, termed the spermathecal duct and flagellum, in tortoise leaf beetles. Our findings reveal that this seemingly straightforward penetration mechanism is underpinned by structural and material specializations of the genitalia. We employed synchrotron-based micro-computed tomography and confocal laser scanning microscopy (CLSM) to visualize the precise mechanical interactions between female and male genitalia. Mechanical tests revealed a stiffness gradient within the flagellum and correlated stiffness variations between the sexes. Combining CLSM and cryo-microtome techniques, we characterized a heterogeneous material distribution at the flagellum tip; this specialization was more remarkable in the species with a more sclerotized spermathecal duct. Finite element analyses incorporating the observed material properties demonstrated that the observed material distribution reduced the penetration force required tremendously and dispersed the stress at the flagellum tip. This study unveils that structural and material adaptations in female and male genitalia have probably coevolved and highlights the importance of biomechanics in genital studies.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20250155"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Generative design as a tool to analyse the uncertain loading regimes of intricate skeletal structures.","authors":"John Michael Racy, Bart Boom, Adam Summers","doi":"10.1098/rsif.2025.0023","DOIUrl":"10.1098/rsif.2025.0023","url":null,"abstract":"<p><p>The morphology of a skeletal structure is driven in part by the forces it endures over evolutionary time. We demonstrate that generative design, an iterative engineering tool, can yield insight into the loading regimes of complex skeletal elements. With only a simple model of the spatial constraints and potential forces seen by a skeletal element, we generated analogous structures. We used this technique to provide insights into the specialization of the radial elements of batoid pectoral fins, a case that would be challenging to analyse by conventional means. Particular configurations of generative designs resulted in structures with a morphology remarkably similar to that of real radials. We suggest that these cases reveal the loading configurations that the real radials have evolved to withstand.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20250023"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yisen Guo, Keelin Quirk, Douglas H Kelley, John H Thomas
{"title":"Advection and diffusion in perivascular and extracellular spaces in the brain.","authors":"Yisen Guo, Keelin Quirk, Douglas H Kelley, John H Thomas","doi":"10.1098/rsif.2025.0010","DOIUrl":"10.1098/rsif.2025.0010","url":null,"abstract":"<p><p>Knowledge of the relative importance of advection and diffusion in clearing waste from the brain has been elusive, especially concerning the extracellular space (ECS). With local and global computational models of the mouse brain, we explore how the presence or absence of advection in the ECS affects solute transport. Without advection in the ECS, clearance would occur by diffusion into flowing cerebrospinal fluid in perivascular spaces (PVSs) or elsewhere, but we find this process to be severely limited by build-up of solute in the PVSs. We simulate flow in the ECS driven by a pressure drop between arteriole and venule PVSs, which enhances clearance considerably. To assess the relative importance of advection and diffusion, we introduce a <i>local</i> Péclet number [Formula: see text], a dimensionless scalar field. For our simulations, [Formula: see text] through much of the ECS but [Formula: see text] near PVSs near the brain surface. This local dominance of advection in the ECS establishes a clearance mechanism markedly different from that produced by diffusion alone. In network simulations that explore different parameter values and efflux routes, the pressures needed to drive the PVS flows measured <i>in vivo</i> are unrealistically large for most cases lacking ECS flow. Collectively, our models indicate that a flow in the ECS is necessary to explain experimental measurements and maintain homeostasis.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20250010"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12092104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}