Mathematical Biosciences最新文献_第9页

An ant territory formation model with chemotaxis and alarm pheromones 具有趋化性和报警信息素的蚂蚁领地形成模型

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2025-10-01 Epub Date: 2025-07-30 DOI: 10.1016/j.mbs.2025.109498

Paulo Amorim , Rodrigo de Lima , Bruno Telch

{"title":"An ant territory formation model with chemotaxis and alarm pheromones","authors":"Paulo Amorim , Rodrigo de Lima , Bruno Telch","doi":"10.1016/j.mbs.2025.109498","DOIUrl":"10.1016/j.mbs.2025.109498","url":null,"abstract":"<div><div>We present and analyze a PDE model of ant territory formation, consisting of a system of reaction–advection–diffusion PDEs of chemotaxis type in two space dimensions. Following existing literature on rival ant nest interactions, two ant populations are divided into peaceful and aggressive compartments. When encountering members of the other colony, peaceful ants can turn into aggressive ants, which produce an alarm pheromone. This pheromone attracts other aggressive ants, and also turns peaceful ants into aggressive ants. It is belived that these dynamics can help explain the formation of well segregated territories, which are observed in the field. We include these dynamics into a chemotaxis-type model, which we analyze and simulate. We prove that, under a small initial mass condition, weak solutions are globally bounded, and obtain a global well-posedness result (without any mass conditions) under a mild sublinear growth assumption on the pheromone deposition term. Besides the mathematical results, we show through simulations that well-defined, non-overlapping territories emerge from the dynamics, especially in the beginning of territory formation. Our analysis therefore supports the hypothesis that these interaction dynamics are an important part of the observed territorial patterns in ants.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"388 ","pages":"Article 109498"},"PeriodicalIF":1.8,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144757907","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

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability GMFOLD：用于高通量dna适体二级结构分类和机器学习可解释性的子图匹配。

IF 1.9 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-06-27 DOI: 10.1016/j.mbs.2025.109485

Paolo Climaco , Noelle M. Mitchell , Matthew J. Tyler , Kyungae Yang , Anne M. Andrews , Andrea L. Bertozzi

{"title":"GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability","authors":"Paolo Climaco , Noelle M. Mitchell , Matthew J. Tyler , Kyungae Yang , Anne M. Andrews , Andrea L. Bertozzi","doi":"10.1016/j.mbs.2025.109485","DOIUrl":"10.1016/j.mbs.2025.109485","url":null,"abstract":"<div><div>Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary structures. Given a specific aptamer primary sequence, there are well-established computational tools (notably mfold) to predict the secondary structure via free energy minimization algorithms. While mfold generates secondary structures for individual sequences, there is a need for a high-throughput process whereby thousands of DNA structures can be predicted in real-time for use in an interactive setting, when combined with aptamer selections that generate candidate pools that are too large to be experimentally interrogated. We developed a new Python code for high-throughput aptamer secondary structure determination (GMfold). GMfold uses subgraph matching methods to group aptamer candidates by secondary structure similarities. We also improve an open-source code, SeqFold, to incorporate subgraph matching concepts. We represent each secondary structure as a lowest-energy bipartite subgraph matching of the DNA graph to itself. These new tools enable thousands of DNA sequences to be compared based on their secondary structures, using machine-learning algorithms. This process is advantageous when analyzing sequences that arise from aptamer selections via systematic evolution of ligands by exponential enrichment (SELEX). This work is a building block for future machine-learning-informed DNA-aptamer selection processes to identify aptamers with improved target affinity and selectivity and advance aptamer biosensors and therapeutics.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"387 ","pages":"Article 109485"},"PeriodicalIF":1.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144532101","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

Modeling mixotroph-bacterium dynamics: Spatial homogeneity vs heterogeneity 混合营养细菌动力学建模：空间同质性vs异质性。

IF 1.9 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-07-05 DOI: 10.1016/j.mbs.2025.109501

Zhitao Zhao , Jing Yang , Russell Milne , Yawen Yan

引用次数: 0

Flow-driven dynamics in a mussel-algae system with nonlinear boundary interactions 具有非线性边界相互作用的贻贝-藻类系统的流动驱动动力学

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-07-26 DOI: 10.1016/j.mbs.2025.109507

Chaochao Li , Hao Wang , Shangjiang Guo

引用次数: 0

Recurrent patterns of disease spread post the acute phase of a pandemic: Insights from a coupled system of a differential equation for disease transmission and a delayed algebraic equation for behavioral adaptation 大流行急性期后疾病传播的复发模式：来自疾病传播微分方程和行为适应延迟代数方程耦合系统的见解

IF 1.9 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-06-21 DOI: 10.1016/j.mbs.2025.109480

Tianyu Cheng, Jianhong Wu

{"title":"Recurrent patterns of disease spread post the acute phase of a pandemic: Insights from a coupled system of a differential equation for disease transmission and a delayed algebraic equation for behavioral adaptation","authors":"Tianyu Cheng, Jianhong Wu","doi":"10.1016/j.mbs.2025.109480","DOIUrl":"10.1016/j.mbs.2025.109480","url":null,"abstract":"<div><div>We introduce a coupled system of a disease transmission differential equation and a behavioral adaptation algebraic renewal equation to understand the mechanisms of nonlinear oscillations post-acute phase of a pandemic. This extends the Zhang–Scarabel–Murty–Wu model, which was formulated and analyzed to describe multi-wave patterns observed at the early stage during the acute phase of the COVID-19 pandemic. Our extension involves the depletion of susceptible population due to infection and contains a nonlinear disease transmission term to reflect the recovery and temporal immunity in the infected population past the acute phase of the pandemic. Examining whether and how incorporating this depletion of susceptible population impacts interwoven disease transmission dynamics and behavioral adaptation is the objective of our current research. We introduce some prototypical risk aversion functions to characterize behavioral responses to perceived risks and show how the risk aversion behaviors and the logistic delay in implementation of behavioral adaptation combined contribute to a dynamic equilibrium state described by a periodic oscillatory wave. We also link the period between two consecutive peaks to basic epidemic parameters, the community flexibility to behavioral change, and the population’s tolerance to perceived risks.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"387 ","pages":"Article 109480"},"PeriodicalIF":1.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478349","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

Threshold dynamics of a Wolbachia-driven mosquito suppression model on two patches 沃尔巴克氏体驱动的两个斑块上蚊虫抑制模型的阈值动态。

IF 1.9 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-06-29 DOI: 10.1016/j.mbs.2025.109495

Xiaoke Ma, Ying Su

{"title":"Threshold dynamics of a Wolbachia-driven mosquito suppression model on two patches","authors":"Xiaoke Ma, Ying Su","doi":"10.1016/j.mbs.2025.109495","DOIUrl":"10.1016/j.mbs.2025.109495","url":null,"abstract":"<div><div>The release of <em>Wolbachia</em>-infected mosquitoes is a promising and biologically safe measure for controlling wild mosquitoes. Numerous studies have been devoted to finding optimal control strategies using mathematical tools. However, the effects of dispersal of uninfected and infected mosquitoes remain poorly understood. To characterize the spatial discretization of release sites, we investigate a two-patch mosquito suppression model with time delay and impulsive release. Specifically, we assume that the waiting period between two consecutive releases is equal to the sexual lifespan of infected males. We confirm the well-posedness and monotonicity of the solution and explore the existence and stability of equilibria. By some technical skills, sufficient conditions for the bistable dynamics are provided. Then, the existence of the unstable separatrix is established by some sharp estimates when choosing constant functions as initial values. More interestingly, the monotonicity of this separatrix in the release number is proved, implying the existence of an optimal release strategy. We further find that uniform release on two patches is more effective than single-patch release. Additionally, the higher the cytoplasmic incompatibility intensity, the more likely wild mosquitoes are to be suppressed.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"387 ","pages":"Article 109495"},"PeriodicalIF":1.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144532102","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

Persistence index for harvested populations 收获种群的持久性指数。

IF 1.8 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-07-18 DOI: 10.1016/j.mbs.2025.109497

Jerzy A. Filar , Matthew H. Holden , Manuela Mendiolar , Sabrina H. Streipert

引用次数: 0

Stochastic model of siRNA endosomal escape mediated by fusogenic peptides 融合肽介导siRNA内体逃逸的随机模型。

IF 1.9 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-06-05 DOI: 10.1016/j.mbs.2025.109476

Nisha Yadav , Jessica Boulos , Angela Alexander-Bryant , Keisha Cook

{"title":"Stochastic model of siRNA endosomal escape mediated by fusogenic peptides","authors":"Nisha Yadav , Jessica Boulos , Angela Alexander-Bryant , Keisha Cook","doi":"10.1016/j.mbs.2025.109476","DOIUrl":"10.1016/j.mbs.2025.109476","url":null,"abstract":"<div><div>Gene silencing via small interfering RNA (siRNA) represents a transformative tool in cancer therapy, offering specificity and reduced off-target effects compared to conventional treatments. A crucial step in siRNA-based therapies is endosomal escape, the release of siRNA from endosomes into the cytoplasm. Quantifying endosomal escape is challenging due to the dynamic nature of the process and limitations in imaging and analytical techniques. Traditional methods often rely on fluorescence intensity measurements or manual image processing, which are time-intensive and fail to capture continuous dynamics. This paper presents a novel computational framework that integrates automated image processing to analyze time-lapse fluorescent microscopy data of endosomal escape, hierarchical Bayesian inference, and stochastic simulations. Our method employs image segmentation techniques such as binary masks, Gaussian filters, and multichannel color quantification to extract precise spatial and temporal data from microscopy images. Using a hierarchical Bayesian approach, we estimate the parameters of a compartmental model that describes endosomal escape dynamics, accounting for variability over time. These parameters inform a Gillespie stochastic simulation algorithm, ensuring realistic simulations of siRNA release events over time. By combining these techniques, our framework provides a scalable and reproducible method for quantifying endosomal escape. The model captures uncertainty and variability in parameter estimation, and endosomal escape dynamics. Additionally, synthetic data generation allows researchers to validate experimental findings and explore alternative conditions without extensive laboratory work. This integrated approach not only improves the accuracy of endosomal escape quantification but also provides predictive insights for optimizing siRNA delivery systems and advancing gene therapy research.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"387 ","pages":"Article 109476"},"PeriodicalIF":1.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251660","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 stochastic model of prion dynamics with conversion and fragmentation 具有转换和碎裂的朊病毒动力学随机模型

IF 1.9 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-07-24 DOI: 10.1016/j.mbs.2025.109505

Arpan Ghosh , Peter Olofsson , Suzanne S. Sindi

引用次数: 0

Bistability between acute and chronic states in a Model of Hepatitis B Virus Dynamics 乙型肝炎病毒动力学模型中急性和慢性状态的双稳定性。

IF 1.9 4区数学

Mathematical Biosciences Pub Date : 2025-09-01 Epub Date: 2025-05-31 DOI: 10.1016/j.mbs.2025.109467

Nazia Afrin , Stanca M. Ciupe , Jessica M. Conway , Hayriye Gulbudak

{"title":"Bistability between acute and chronic states in a Model of Hepatitis B Virus Dynamics","authors":"Nazia Afrin , Stanca M. Ciupe , Jessica M. Conway , Hayriye Gulbudak","doi":"10.1016/j.mbs.2025.109467","DOIUrl":"10.1016/j.mbs.2025.109467","url":null,"abstract":"<div><div>Understanding the mechanisms responsible for different clinical outcomes following hepatitis B infection requires a systems investigation of dynamical interactions between the virus and the immune system. To help elucidate mechanisms of protection and those responsible from transition from acute to chronic disease, we developed a deterministic mathematical model of hepatitis B infection that accounts for cytotoxic immune responses resulting in infected cell death, non-cytotoxic immune responses resulting in infected cell cure and protective immunity from reinfection, and cell proliferation. We analyzed the model and presented outcomes based on three important disease markers: the basic reproduction number <span><math><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span>, the infected cells death rate <span><math><mi>δ</mi></math></span> (describing the effect of cytotoxic immune responses), and the liver carrying capacity <span><math><mi>K</mi></math></span> (describing the liver susceptibility to infection). Using asymptotic and bifurcation analysis techniques, we determined regions where virus is cleared, virus persists, and where clearance-persistence is determined by the size of viral inoculum. These results can guide the development of personalized intervention.</div></div>","PeriodicalId":51119,"journal":{"name":"Mathematical Biosciences","volume":"387 ","pages":"Article 109467"},"PeriodicalIF":1.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144210592","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