Mathematical Biosciences最新文献

A mathematical perspective on hypothesis-driven model construction: A case study in pea 假设驱动模型构建的数学视角：以Pea为例。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-02 DOI: 10.1016/j.mbs.2026.109635

Brodie A.J. Lawson , Elizabeth A. Dun , Christine A. Beveridge , Nicole Z. Fortuna , Kevin Burrage

{"title":"A mathematical perspective on hypothesis-driven model construction: A case study in pea","authors":"Brodie A.J. Lawson , Elizabeth A. Dun , Christine A. Beveridge , Nicole Z. Fortuna , Kevin Burrage","doi":"10.1016/j.mbs.2026.109635","DOIUrl":"10.1016/j.mbs.2026.109635","url":null,"abstract":"<div><div>Mechanistic models in systems biology enable biophysically-backed testing of hypothesised mechanisms. However, determination of their parameter values is highly challenging, and the data available for calibration is frequently qualitative in nature. Acknowledging this, many approaches abandon mechanistic description, avoiding parameterisation and simulating biological network behaviours in a qualitative fashion. Appealing are the methods that capture some of the best of both types of approach, maintaining a qualitative perspective while using mechanistic models that naturally generalise to quantitative data and carry biochemical implications. Here, using a pea branching network model as an exemplar, we demonstrate the conversion of biological hypotheses into simplified, parameter-free mathematical models, elucidating the biophysical assumptions implicitly made by this approach and analysing the exemplar model’s behaviour. Using likelihood-free Bayesian calibration, we compare the parameter-free model to the set of plausible calibrations of its parameterised analog, hence demonstrating that almost all of the qualitative conclusions given data — including both suitability of a hypothesised network structure, and sensitivity analysis — are obtained by the parameter-free paradigm. Altogether, our findings highlight the usefulness of parameter-free treatments of quantitative models, and also deepen understanding of branching network function across mutant and grafted plants.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"395 ","pages":"Article 109635"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146121479","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}

引用次数: 0

A partition method for bounding continuous-time Markov chain models of general reaction network 一般反应网络连续时间马尔可夫链边界模型的一种划分方法。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-04 DOI: 10.1016/j.mbs.2026.109639

Guillaume Ballif , Laurent Pfeiffer , Jakob Ruess

{"title":"A partition method for bounding continuous-time Markov chain models of general reaction network","authors":"Guillaume Ballif , Laurent Pfeiffer , Jakob Ruess","doi":"10.1016/j.mbs.2026.109639","DOIUrl":"10.1016/j.mbs.2026.109639","url":null,"abstract":"<div><div>In this work, we present a general method to establish properties of multi-dimensional continuous-time Markov chains representing stochastic reaction networks. This method consists of grouping states together (via a partition of the state space), then constructing two one-dimensional birth and death processes that lower and upper bound the initial process under simple assumptions on the infinitesimal generators of the processes. The construction of these bounding processes is based on coupling arguments and transport theory. The bounding processes are easy to analyse analytically and numerically and allow us to derive properties on the initial continuous-time Markov chain. We focus on two important properties: the behavior of the process at infinity through the existence of a stationary distribution and the error in truncating the state space to numerically solve the master equation describing the time evolution of the probability distribution of the process. We derive explicit formulas for constructing the optimal bounding processes for a given partition, making the method easy to use in practice. We finally discuss the importance of the choice of the partition to obtain relevant results and illustrate the method on two examples of chemical reaction networks.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"395 ","pages":"Article 109639"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146133738","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}

引用次数: 0

Traveling wave formation enables strain coexistence in a spatial model of bacterial cross-feeding 行波形成使菌株共存在细菌交叉喂养的空间模型。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-08 DOI: 10.1016/j.mbs.2026.109647

Parsa Pakzad, Donald DeAngelis

{"title":"Traveling wave formation enables strain coexistence in a spatial model of bacterial cross-feeding","authors":"Parsa Pakzad, Donald DeAngelis","doi":"10.1016/j.mbs.2026.109647","DOIUrl":"10.1016/j.mbs.2026.109647","url":null,"abstract":"<div><div>Cross-feeding is a form of metabolic cooperation in microbial populations where one species or strain produces a byproduct that serves as a nutrient for another. This interaction can promote division of labor, resource efficiency, and species coexistence. The extent to which spatial heterogeneity and metabolite diffusion shape cross-feeding interactions is not yet well resolved. In this study, we examine the spatial dynamics of cross-feeding between two bacterial strains using a two-dimensional chemostat lattice model. Both strains are capable of growing on glucose and acetate, but differ in resource preference. One, which we term glucose specialist, primarily consumes glucose, while the other, which we term acetate specialist, primarily consumes acetate. Moreover, elevated acetate amount inhibits the growth of both strains. Metabolite dynamics are governed by reaction-diffusion equations, and bacterial motility is implemented through partially random local dispersal rules.</div><div>Our simulations reveal that the emergence of traveling waves plays a critical role in enabling long-term coexistence of the two strains. Specifically, clusters of glucose specialists self-organize into wave-like structures that propagate toward regions of elevated acetate amount. These traveling waves suppress inhibitory acetate level ahead of the front, creating favorable conditions in their wake for the acetate specialists to grow. The resulting spatiotemporal patterns—characterized by merging wave fronts and sequential colonization—allow both strains to persist over the long term, despite competitive and inhibitory interactions. Mathematical analysis is used to support and interpret the simulation results. These findings demonstrate how spatial self-organization and reaction-diffusion dynamics can mediate coexistence in microbial cross-feeding systems, offering new insights into the ecological and evolutionary stability of microbial communities.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"395 ","pages":"Article 109647"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159832","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}

引用次数: 0

Bifurcation analysis and fear-induced reactions in non-refuged prey with cooperative hunting among predators: Deterministic and stochastic dynamics 非避难猎物与捕食者合作狩猎的分岔分析与恐惧诱导反应：确定性与随机动力学。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-05 DOI: 10.1016/j.mbs.2026.109641

Subarna Roy , Abhijit Sarkar , Nazmul Sk , Pankaj Kumar Tiwari , Ranjit Kumar Upadhyay

{"title":"Bifurcation analysis and fear-induced reactions in non-refuged prey with cooperative hunting among predators: Deterministic and stochastic dynamics","authors":"Subarna Roy , Abhijit Sarkar , Nazmul Sk , Pankaj Kumar Tiwari , Ranjit Kumar Upadhyay","doi":"10.1016/j.mbs.2026.109641","DOIUrl":"10.1016/j.mbs.2026.109641","url":null,"abstract":"<div><div>The impacts of fear, refuge-seeking behavior of prey, and modified cooperative hunting among predators are collectively included in a mathematical model to explore predator-prey dynamics. The stability of the system’s equilibrium points and the occurrence of different bifurcations are analyzed. The system exhibits bistability, characterized by the presence of two stable equilibrium points. Numerical investigation reveals that elevated fear levels simplify the species’ coexistence, even when considering increased refuge and prey birth rate. When hunting cooperation rate is extremely high, prey survival becomes unsustainable, particularly with lower birth rate, unless refuge is sought. Conversely, ample refuge capacity allows prey to persist despite lower birth rates. To create time-series solutions and examine stationary distributions, we run multiple simulations. Notably, species have a tendency to fluctuate around the mean values of the deterministic state when there are minimal external disruptions. Interestingly, an increased noise intensity on predators shifts the system’s dynamics to a predator-free equilibrium from coexistence of prey and predators.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"395 ","pages":"Article 109641"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138235","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}

引用次数: 0

Tumor growth and immune response: On the impact of the space-structuration of the tumor microenvironment 肿瘤生长与免疫反应：肿瘤微环境空间结构的影响

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-21 DOI: 10.1016/j.mbs.2026.109650

Christian Tayou Fotso , Fabienne Anjuère , Véronique M. Braud , Florence Hubert , Thierry Goudon

引用次数: 0

Modeling periodic transcriptions in tandem gene systems 串联基因系统周期性转录的建模。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-10 DOI: 10.1016/j.mbs.2026.109648

Wangyang Wu , Shumin Tan , Moxun Tang , Qiwen Sun

{"title":"Modeling periodic transcriptions in tandem gene systems","authors":"Wangyang Wu , Shumin Tan , Moxun Tang , Qiwen Sun","doi":"10.1016/j.mbs.2026.109648","DOIUrl":"10.1016/j.mbs.2026.109648","url":null,"abstract":"<div><div>We study periodic gene transcription in a tandem gene system, where an external periodic signal modulates the expression of an upstream gene, whose products subsequently regulate the expression of a downstream gene. For the external signal characterized by cosine-wave modulation of the transcription rate, we derive analytical formulas for the mean transcription levels, delays, amplitudes, and noise intensities. The results reveal that the mean transcription levels of both genes exhibit periodic behavior, where the transcription of the downstream gene shows a phase delay with the amplitude proportional to that of the upstream gene. Numerical simulations confirm these findings, demonstrating that the noise increases with the signal strength and is consistently higher for the downstream gene. The delays are determined by the signal’s angular frequency and mRNA degradation rates. This work provides insights into the propagation of periodic signals in gene networks, highlighting the coupling roles of stochastic fluctuations and gene regulations in transcriptional dynamics. The findings have important implications for understanding the regulation of circadian rhythms and for the rational design of synthetic gene circuits.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"395 ","pages":"Article 109648"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146184001","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}

引用次数: 0

Why does nature force the creation of proteobacteria community in the estuarine ecosystem? - A theoretical model 为什么大自然强迫在河口生态系统中创造变形菌群？-理论模型。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-06 DOI: 10.1016/j.mbs.2026.109642

Devdatta Adhikary , Sukdev Biswas , Arnab Banerjee , Sabyasachi Bhattacharya

{"title":"Why does nature force the creation of proteobacteria community in the estuarine ecosystem? - A theoretical model","authors":"Devdatta Adhikary , Sukdev Biswas , Arnab Banerjee , Sabyasachi Bhattacharya","doi":"10.1016/j.mbs.2026.109642","DOIUrl":"10.1016/j.mbs.2026.109642","url":null,"abstract":"<div><div>Estuarine ecosystems are among the most dynamic and ecologically significant environments, shaped by intricate interactions among microbial communities, such as proteobacteria and their predator. Proteobacteria, owing to their remarkable tolerance to salinity and unique mixotrophic capabilities, dominate this ecosystem. These traits raise a fundamental ecological question: do proteobacteria act as stabilising agents in estuarine health, and why has evolution favoured their multifunctionality over strict autotrophy or heterotrophy? This study presents a novel theoretical framework, comprising both deterministic and stochastic models, emphasizing key phenomenological traits of mixotrophic proteobacteria in estuarine ecosystems. The autotrophic component is captured using Secchi depth as a proxy for light availability and photosynthetic potential, while heterotrophic behaviour is linked to salinity-driven nutrient uptake. Through analytical exploration and numerical simulations, we find that salinity serves as a crucial control parameter, producing characteristic oscillatory dynamics and a ”bubbling effect” that delineates transitions between stability and instability. The photosynthetic capability of mixotrophic proteobacteria emerges as a critical stabilizing mechanism, particularly under fluctuating salinity and turbidity conditions. Our model identifies critical thresholds for Secchi depth, salinity-driven microzooplankton grazing and nutrient inflow-outflow that underpin estuarine stability. The stochastic extension, incorporating Gaussian white noise, demonstrates that under strong environmental noise, microzooplankton are more prone to extinction than proteobacteria. This work lays a theoretical foundation for future ecological modelling and adaptive estuarine management in the context of climate-driven change.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"395 ","pages":"Article 109642"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146145313","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}

引用次数: 0

Replicator-mutator dynamics for public goods games with institutional incentives 具有制度激励的公共物品博弈的复制-突变动力学。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-06 DOI: 10.1016/j.mbs.2026.109644

N. Balabanova , M.H. Duong , T.A. Han

引用次数: 0

Impact of human adherence level to control measures on cystic echinococcosis transmission 人类对囊性包虫病传播控制措施依从性的影响。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-07 DOI: 10.1016/j.mbs.2026.109643

Xinmiao Rong, Fengyun Zhu

{"title":"Impact of human adherence level to control measures on cystic echinococcosis transmission","authors":"Xinmiao Rong, Fengyun Zhu","doi":"10.1016/j.mbs.2026.109643","DOIUrl":"10.1016/j.mbs.2026.109643","url":null,"abstract":"<div><div>Cystic echinococcosis (CE) is a widespread zoonotic disease that poses a serious threat to both human health and livestock production. Its control effectiveness largely depends on human adherence. A game-theoretic epidemiological model is developed to couple disease transmission with human behavioral responses, aiming to investigate the effects of human adherence on CE transmission. The equilibria and threshold dynamics are derived, and numerical simulations are conducted to explore how key factors influence disease prevalence, behavioral strategy switching, and control effectiveness. The results indicate that human adherence affects both transmission risk and infection levels, while a higher cost-to-risk ratio suppresses adherence, thereby weakening control outcomes. Model application to Xinjiang Province in China suggests that although CE transmission is currently under control (<em>R</em><sub>0</sub> < 1), recurrence may occur when the initial adherence level falls below the threshold (<span><math><mrow><msubsup><mi>x</mi><mi>A</mi><mo>*</mo></msubsup><mo>=</mo><mn>0.5706</mn></mrow></math></span>), indicating that when human behavior is considered, relying solely on the basic reproduction number <em>R</em><sub>0</sub> is insufficient to predict long-term transmission dynamics.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"395 ","pages":"Article 109643"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146151629","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}

引用次数: 0

A model for a population of trees structured by phenological traits 一个由物候特征构成的树木种群的模型。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2026-05-01 Epub Date: 2026-02-06 DOI: 10.1016/j.mbs.2026.109640

Sirine Boucenna , Vasilis Dakos , Gaël Raoul

{"title":"A model for a population of trees structured by phenological traits","authors":"Sirine Boucenna , Vasilis Dakos , Gaël Raoul","doi":"10.1016/j.mbs.2026.109640","DOIUrl":"10.1016/j.mbs.2026.109640","url":null,"abstract":"<div><div>In the context of global warming, tree populations rely on two primary mechanisms of adaptation: phenotypic plasticity, which enables individuals to adjust their behavior in response to environmental stress, and genetic evolution, driven by natural selection and genetic diversity within the population. Understanding the interplay between these mechanisms is crucial for assessing the impacts of climate change on forest ecosystems and for informing sustainable management strategies. In this manuscript, we focus on a specific phenological adaptation: the ability of trees to enter summer dormancy once a critical temperature threshold is exceeded. Individuals are characterized by this threshold temperature and by their seed production capacity. We first establish a detailed mathematical model describing the population dynamics under these traits, and progressively reduce it to a system of two coupled ordinary differential equations. This simpler macroscopic model is then analyzed numerically, to investigate how the population reacts to a shift in its environment: an temperature increase, a drop in precipitation levels, or a combination of the two. Our results highlight contrasting effects of water stress and temperature stress on population dynamics, as well as the ambivalent effect of the plasticity.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"395 ","pages":"Article 109640"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146145282","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}

引用次数: 0