{"title":"Bayesian Parameter Estimation and Stochastic Extinction Analysis in a Seasonal Bubonic Plague Transmission Model.","authors":"Suman Kumari, Partha Sarathi Mandal","doi":"10.1007/s11538-026-01762-9","DOIUrl":"10.1007/s11538-026-01762-9","url":null,"abstract":"<p><p>Mathematical models of plague dynamics provide insight into zoonotic transmission processes and epidemic persistence but often neglect stochastic effects and seasonal variability. In this study, we examine how seasonal variability influences zoonotic disease transmission through a rat-flea-human plague model. Periodic environmental forcing modulates rat abundance, flea survival, and biting activity, generating time-dependent rates that capture realistic ecological seasonality. To represent demographic randomness, we formulate a continuous-time Markov chain (CTMC) model and apply a multi-type branching process approximation near the disease-free equilibrium (DFE) to derive approximate disease extinction probabilities using probability generating functions (PGFs) and the backward Kolmogorov differential equation (BKDE). Our results show that random fluctuations can prevent an epidemic outbreak even when the seasonal reproduction number satisfies <math> <mrow><msub><mi>R</mi> <mn>0</mn></msub> <mo>></mo> <mn>1</mn></mrow> </math> . We also quantify the spillover probability arising from a single infectious flea, demonstrating that seasonal forcing significantly alters outbreak risk. Along with this, an expression for time to extinction is also derived. To ensure biological understanding, we estimate model parameters from historical data using a Bayesian Markov chain Monte Carlo (MCMC) approach implemented via the Delayed Rejection Adaptive Metropolis (DRAM) algorithm. Through this analysis, we highlight the critical role of seasonality in shaping outbreak risk and demonstrate the limitations of relying solely on deterministic models.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149036505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alberto Tenore, Fabiana Russo, Luigi Frunzo, Maria Rosaria Mattei
{"title":"Modeling Phototaxis and Planktonic Cell Behavior in Phototrophic Biofilms.","authors":"Alberto Tenore, Fabiana Russo, Luigi Frunzo, Maria Rosaria Mattei","doi":"10.1007/s11538-026-01753-w","DOIUrl":"10.1007/s11538-026-01753-w","url":null,"abstract":"<p><p>We propose a continuous multidimensional multispecies model of planktonic cell invasion in phototrophic biofilms that incorporates phototaxis as a key mechanism driving directed movement along light gradients. The biofilm is modeled as a homogeneous, viscous, incompressible fluid, with the velocity field governed by a Darcy-type law. The phototactic behavior of planktonic cells is integrated in the model by considering a reaction-advection-diffusion equation including a diffusive and tactic flux with a volume-filling term. Cell movement toward favorable light conditions and away from harmful ones is modeled through a light-dependent sensitivity function capturing both positive and negative phototaxis. Planktonic cells are attracted to regions with optimal light intensity, where they accumulate as an effect of phototactic behavior, and might switch their phenotype from planktonic to sessile, contributing to biofilm expansion. Numerical simulations highlight the crucial role of phototaxis in biofilm dynamics, showing how the balance between random diffusion and phototactic movement regulates biomass distribution and, consequently, oxygen and organic carbon dynamics. Under high-light stress conditions, photoinhibition reverses phototaxis, causing planktonic cells to move away from the light source, reducing overall biofilm development. Higher biofilm densities increase light attenuation, which, depending on light conditions, either reduces overall phototrophic growth or provides protection against excessive light exposure. Finally, biofilm geometry influences light attenuation and phototrophic growth, with its effects depending on incident light conditions and biofilm density. Overall, the proposed multispecies framework provides a mechanistic tool to investigate how phototactic motility, light conditions, biofilm properties, and microbial interactions jointly regulate phototrophic biofilm development.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13601179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Effect of Climate Warming on Culex Mosquito Population Dynamics in Newfoundland.","authors":"Joseph Baafi, Amy Hurford","doi":"10.1007/s11538-026-01756-7","DOIUrl":"10.1007/s11538-026-01756-7","url":null,"abstract":"<p><p>Mosquitoes are important vectors of infectious diseases affecting humans and animals. In North America, Culex mosquitoes transmit West Nile virus and other arboviruses, while their persistence in temperate regions depends strongly on seasonal processes such as diapause. Temperature, rainfall, and photoperiod jointly regulate mosquito development, survival, reproduction, and seasonal activity, yet many climate-driven models do not explicitly represent diapause or interacting environmental drivers. We develop a mechanistic, stage-structured model for temperate Culex populations that includes eggs, larvae, pupae, active adult females, and diapausing adult females. The model integrates temperature-dependent oviposition and mortality, temperature- and rainfall-dependent maturation, and photoperiod-driven diapause induction and termination. Mathematical analysis establishes positivity and boundedness of solutions and derives a mosquito population replacement threshold that links climate-dependent life-history rates to population persistence. Using historical climate data, stochastic rainfall sampling, and prescribed warming and rainfall scenarios, we examine how climate variability shapes abundance and active season length. Simulations reveal strong nonlinear responses to warming, with active adult female abundance increasing substantially under higher temperature shifts and the active season expanding into early spring and late fall. Rainfall modulates population responses, with dry conditions suppressing abundance, wet conditions producing the largest increases, and erratic rainfall yielding intermediate outcomes. These results show that temperature, rainfall, and photoperiod jointly shape temperate mosquito dynamics and highlight the potential for climate warming to increase vector abundance and extend seasonal windows of activity. The framework provides a basis for evaluating climate-sensitive vector dynamics and informing adaptive mosquito control strategies under environmental change.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pierre-Alexandre Bliman, Manon de la Tousche, Yves Dumont
{"title":"Sterile Insect Technique in a n-patch System with Allee Effect and Mass Trapping: Modelling, Analysis and Simulations.","authors":"Pierre-Alexandre Bliman, Manon de la Tousche, Yves Dumont","doi":"10.1007/s11538-026-01722-3","DOIUrl":"10.1007/s11538-026-01722-3","url":null,"abstract":"<p><p>The sterile insect technique (SIT) is a biological control method aimed at reducing or eliminating populations of pests and disease vectors. This technique involves releasing sterilised insects which, by mating with wild individuals, will reduce the target population. In this study, spatial aspects are incorporated through an explicit metapopulation model, in which both wild and sterile insects disperse across multiple patches. We derive a general sufficient condition ensuring elimination of the wild population in all patches through SIT. When a strong Allee effect is naturally present in each patch, the release programme can be terminated after a finite time, and an upper bound on the required release duration is provided. We then study an optimisation problem aimed at minimising the daily number of sterile insects released to ensure population elimination, under the constraint that the releases occur only in a prescribed subset of patches. For illustrative purposes, we explore through numerical simulations different dispersal network configurations. We also consider additional control by mass trapping (MT), which can affect the sterile insects entering trapped areas. The main contribution of this work is to enable the identification of the best spatial strategies for releasing sterile insects under practical constraints, in order to achieve population elimination.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13601138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Backward bifurcations in discrete-time epidemic models with vaccination.","authors":"Azmy S Ackleh, Jenita Jahangir, Amy Veprauskas","doi":"10.1007/s11538-026-01752-x","DOIUrl":"10.1007/s11538-026-01752-x","url":null,"abstract":"<p><p>We develop a discrete-time Susceptible-Infectious-Susceptible model with Vaccination (SISV) in which vaccination reduces but does not necessarily eliminate the risk of infection. After establishing the stability of the disease-free equilibrium (DFE), we apply an extension of the Fundamental Bifurcation Theorem to study the endemic dynamics arising when the DFE loses stability at the threshold quantity <math> <mrow><msub><mi>R</mi> <mn>0</mn></msub> <mo>=</mo> <mn>1</mn></mrow> </math> , where <math><msub><mi>R</mi> <mn>0</mn></msub> </math> denotes the basic reproduction number. We find that, as with its continuous-time counterpart, a backward bifurcation may occur in this model leading to bistable dynamics provided that the vaccine does not provide complete protection from infection and infected individuals are able to recover from the disease. For comparison purposes, we also present a second model formulation based on a different ordering of events, an issue that does not appear in continuous-time models. Specifically, we swap the order that vaccination and disease transmission occur within a unit of time. In contrast to the first model, we show that this alternative formulation may produce a backward bifurcation even when vaccination is completely effective.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isabella V Gimón, Conner Sandefur, Santiago Schnell
{"title":"Reproducible Agent-Based Simulations of Protein Aggregation: A FAIR Implementation.","authors":"Isabella V Gimón, Conner Sandefur, Santiago Schnell","doi":"10.1007/s11538-026-01739-8","DOIUrl":"10.1007/s11538-026-01739-8","url":null,"abstract":"<p><p>Aberrant protein aggregation is implicated in many neurodegenerative diseases and is strongly modulated by intracellular spatial constraints such as macromolecular crowding and clearance. Computational studies of aggregation, however, frequently lack the documentation and provenance required for independent reproduction. We present a spatial, lattice-based agent‑based model of intracellular protein aggregation implemented in Julia and packaged as a research software object aligned with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. Individual monomers undergo reversible activation, oligomer nucleation, aggregate growth, and optional oligomer clearance; stochastic movement and local encounters on a 3D face-centered cubic lattice capture spatial heterogeneity and crowding. The accompanying repository includes centralized parameters, machine-readable metadata, version-pinned dependencies, example runs, and automated post-simulation analysis. Ensemble simulations reproduce canonical aggregation phases (lag, nucleation, growth, saturation) and illustrate that oligomer removal reduces the final aggregate burden. The model also supports configurable macromolecular crowding via spherical obstacles, enabling systematic exploration of crowding effects on aggregation kinetics. Runtime benchmarking shows that 300 independent simulations (1,000 monomers; 5,000 timesteps), executed as 15 concurrent single-threaded jobs on institutional high-performance computing resources, completed in approximately 25 h of wall-clock time, enabling parameter sweeps and ensemble averaging. Together, the model and its FAIR packaging provide a reproducible template for transparent, extensible agent-based computational biology.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149007759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Ancestral Sequences Cannot be Accurately Reconstructed via Interpolation in a Variational Autoencoder's Latent Space.","authors":"Evan Gorstein, Mengze Tang, Hailey Bruzzone, Claudia Solís-Lemus","doi":"10.1007/s11538-026-01749-6","DOIUrl":"10.1007/s11538-026-01749-6","url":null,"abstract":"<p><p>Standard methods for ancestral sequence reconstruction (ASR) rely on substitution models for the residues in a biological sequence and assume independent evolution across these sites, ignoring the epistatic interactions that shape molecular evolution. In contrast, deep learning models like variational autoencoders (VAEs) can learn low-dimensional representations (\"embeddings\") of sequences in a protein family that may implicitly handle these dependencies, raising the possibility of performing more accurate ASR by interpolating between extant sequence embeddings within the VAE's latent space. In this study, we test this hypothesis by developing and evaluating a VAE-based ASR pipeline. Benchmarking this approach against established likelihood-based and parsimony methods using various simulations of protein evolution, including scenarios with and without epistasis, we find that the VAE-based approach is consistently and significantly outperformed by standard methods, even in epistatic regimes where it was hypothesized to have an advantage. We further show that this failure is not due to a lack of phylogenetic structure in the latent space, which does contain evolutionary signal. Rather, the primary limitation is the information loss inherent to the autoencoding process: the VAE's decoder cannot generate sequences with sufficient fidelity for the precise demands of ASR.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13589712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149007696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
James W G Doran, Dennis Mujuni, Kit Gallagher, Christian A Yates, Ruth Bowness
{"title":"An Agent-Based Modelling Approach to Investigate the Impact of Sex and Gender on Tuberculosis Transmission: A Case Study of Kampala, Uganda.","authors":"James W G Doran, Dennis Mujuni, Kit Gallagher, Christian A Yates, Ruth Bowness","doi":"10.1007/s11538-026-01734-z","DOIUrl":"10.1007/s11538-026-01734-z","url":null,"abstract":"<p><p>Tuberculosis (TB) is an airborne disease caused by the pathogen Mycobacterium tuberculosis. In 2023, it returned to being the leading cause of death from an infectious agent globally, replacing COVID-19. More than 10 million people are diagnosed with TB every year. The majority of cases in adults occur in males (62.5% of all global adult cases in 2023, compared to 37.5% in females). The main reasons for males suffering from a higher burden of global TB cases, compared to females, may be in large part due to population-scale factors, such as employment type, the quantity and type of social contacts they make, and their health-seeking behaviours. To investigate which population-scale factors are most important in determining this higher TB burden in males, we have developed an age- and sex/gender-stratified, spatially heterogeneous epidemiological agent-based model. We have focused specifically on Kampala, the capital of Uganda, which is a high-burden TB country. We considered counterfactual scenarios to elucidate the impact of sex and gender on the epidemiology of TB, in order to deduce which factors have greater explanatory power in producing the observed differences between sexes/genders. Within-host parameters had the largest effect on overall case numbers among the scenarios considered. On the other hand, behavioural factors (particularly assortative mixing and gender-specific contact patterns) appear important in explaining the elevated male-to-female case ratio. We also found that super-spreaders appear to cause a majority of infections, with males and individuals with cavitary TB causing more infections on average. Our model provides a proof-of-concept framework that could help support public health policy after further validation.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13562183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148928734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Polynomial-Time Completion of Phylogenetic Tree Sets.","authors":"Aleksandr Koshkarov, Nadia Tahiri","doi":"10.1007/s11538-026-01711-6","DOIUrl":"10.1007/s11538-026-01711-6","url":null,"abstract":"<p><p>Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can preserve both taxa and branch-length information. This work introduces a polynomial-time algorithm for set-wide completion of phylogenetic trees with partial taxon overlap. The proposed method identifies and extracts maximal completion subtrees that frequently appear across the source trees and constructs a weighted majority-rule consensus. Branch lengths are scaled using rates derived from common leaves. Each consensus subtree is inserted at the position that minimizes the quadratic distance error measured against information from the source trees, with candidate positions restricted to the original branches of the target tree. We demonstrate that the algorithm runs in polynomial time and preserves distances among the original taxa, yielding a unique completion that is order-independent with respect to the processing order of target trees. An experimental evaluation on amphibians, mammals, sharks, and squamates shows that the proposed method consistently achieves the lowest distance to the subset reference trees across subsets among all methods, in both topology and branch lengths. An open-source Python implementation of the proposed algorithm and the biological datasets utilized in this study are publicly available at: https://github.com/tahiri-lab/overlap-treeset-completion/ .</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148928747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evolution of Cooperation in Spatially Structured Group-Selection Models of the Continuous Prisoner's Dilemma.","authors":"Yaroslav Ispolatov, Burton Simon, Michael Doebeli","doi":"10.1007/s11538-026-01750-z","DOIUrl":"10.1007/s11538-026-01750-z","url":null,"abstract":"<p><p>We consider continuous Prisoner's Dilemma games played in a spatial setting by group-structured populations. The evolutionary dynamics is driven by within-group individual-level birth and death events, and by group-level fission and extinction events. Within groups, individuals play well-mixed games, while groups play games on a 1-dimensional spatial grid against their nearest neighbours. Payoffs from individual-level games affect birth rates of individuals, and payoffs from group-level games affect group extinction and fission probabilities. It is well known that the within-group evolution by itself always results in a complete loss of cooperation, and that in the group-level games, defection is also favoured if these games are played in well-mixed populations of groups. Here we show that despite this double disadvantage, cooperation can be maintained due to spatially structured group-level dynamics. Mirroring results from one-level selection models, the spatial nature of games between groups and the resulting fissioning and extinction events is essential for the evolution of cooperation in these models, but needs to manifest itself in specific ways in order to be effective: we find that higher levels of cooperation evolve when the selection generated by games between groups acts locally rather than globally.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"88 10","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148918553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}