Pub Date : 2025-12-09DOI: 10.1016/j.jtbi.2025.112330
Anca Rǎdulescu , Richard Halpern , Drew Kozlowski
The study of intra-guild interactions in an ecosystem is an active and impactful direction of inquiry. This is true in particular for fragile systems in which even small perturbations of their functional parameters can produce dramatic effects like species endangerment or extinction, leading the system to enter an unsustainable regime and eventually collapse. In this context, it is important to understand which factors can lead to such effects and for which systems, so that one can act proactively and timely to prevent them. We built and studied a mathematical model that captures the natural interactions in an intra-guild, three species system (i.e., in which two species are predators of the third, but such that one of the predators also consumes the other). The nonlinear components of the model were documented on existing literature and assembled as a system of Lotka-Volterra ordinary differential equations. Our analytical computations and numerical explorations revealed sequences of transcritical and Hopf bifurcations underlying counterintuitive transitions of the system into regions of vulnerability to external noise. We conclude that, in order to avoid extinction, one needs to rigorously prescribe a well-documented, prediction-based approach to population control.
{"title":"A model of predation and survival in a system of three interacting species","authors":"Anca Rǎdulescu , Richard Halpern , Drew Kozlowski","doi":"10.1016/j.jtbi.2025.112330","DOIUrl":"10.1016/j.jtbi.2025.112330","url":null,"abstract":"<div><div>The study of intra-guild interactions in an ecosystem is an active and impactful direction of inquiry. This is true in particular for fragile systems in which even small perturbations of their functional parameters can produce dramatic effects like species endangerment or extinction, leading the system to enter an unsustainable regime and eventually collapse. In this context, it is important to understand which factors can lead to such effects and for which systems, so that one can act proactively and timely to prevent them. We built and studied a mathematical model that captures the natural interactions in an intra-guild, three species system (i.e., in which two species are predators of the third, but such that one of the predators also consumes the other). The nonlinear components of the model were documented on existing literature and assembled as a system of Lotka-Volterra ordinary differential equations. Our analytical computations and numerical explorations revealed sequences of transcritical and Hopf bifurcations underlying counterintuitive transitions of the system into regions of vulnerability to external noise. We conclude that, in order to avoid extinction, one needs to rigorously prescribe a well-documented, prediction-based approach to population control.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"620 ","pages":"Article 112330"},"PeriodicalIF":2.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745840","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}
The receptor-binding domain (RBD) of the spike protein is a critical functional component responsible for binding between the SARS-CoV-2 and the ACE2 receptor, as well as monoclonal antibodies. This research focuses on evaluating the ability of SARS-CoV-2 variants to reduce or evade neutralizing antibody responses. The RBD structures of wild type, Delta, and Omicron structures along with nine RBD-directed antibodies downloaded from the Protein Data Bank were subjected to docking simulations via the HADDOCK 2.4 server to calculate Haddock score, binding affinity (ΔG) and dissociation constant (Kd). The resulting complexes underwent molecular dynamics simulations for 100 ns using GROMACS, and the binding free energy was calculated using gmx_MMPBSA. The findings indicated that the L452R and T478K mutations in Delta, as well as the K417N, E484A, S477N, and Q493R mutations in Omicron, were predicted to be pivotal factors in the interaction with antibodies. Omicron exhibited a greater potential for immune evasion compared to Delta. Notably, the Sotrovimab antibody demonstrated robust interactions with both variants. Etesevimab exhibited strong binding with Delta but displayed a weaker connection with Omicron. Therefore, Sotrovimab and Etesevimab remain promising candidates for in vitro and in vivo testing against SARS-CoV-2 variants.
{"title":"Antibody escape of SARS-CoV-2 variants of concern on receptor-binding domain: A computational approach","authors":"Dac-Nhan Nguyen , Quoc-Thai Nguyen , Thoai-My Dang , Phuong-Uyen Tran-Thi , Viet-Hung Tran , Minh-Tri Le , Lam-Truong Tuong , Van-Thanh Tran , Phuong Nguyen Hoai Huynh , Khac-Minh Thai","doi":"10.1016/j.jtbi.2025.112345","DOIUrl":"10.1016/j.jtbi.2025.112345","url":null,"abstract":"<div><div>The receptor-binding domain (RBD) of the spike protein is a critical functional component responsible for binding between the SARS-CoV-2 and the ACE2 receptor, as well as monoclonal antibodies. This research focuses on evaluating the ability of SARS-CoV-2 variants to reduce or evade neutralizing antibody responses. The RBD structures of wild type, Delta, and Omicron structures along with nine RBD-directed antibodies downloaded from the Protein Data Bank were subjected to docking simulations via the HADDOCK 2.4 server to calculate Haddock score, binding affinity (<em>ΔG</em>) and dissociation constant (<em>K<sub>d</sub></em>). The resulting complexes underwent molecular dynamics simulations for 100 ns using GROMACS, and the binding free energy was calculated using gmx_MMPBSA. The findings indicated that the L452R and T478K mutations in Delta, as well as the K417N, E484A, S477N, and Q493R mutations in Omicron, were predicted to be pivotal factors in the interaction with antibodies. Omicron exhibited a greater potential for immune evasion compared to Delta. Notably, the Sotrovimab antibody demonstrated robust interactions with both variants. Etesevimab exhibited strong binding with Delta but displayed a weaker connection with Omicron. Therefore, Sotrovimab and Etesevimab remain promising candidates for <em>in vitro</em> and <em>in vivo</em> testing against SARS-CoV-2 variants.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"619 ","pages":"Article 112345"},"PeriodicalIF":2.0,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145710607","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}
Pub Date : 2025-12-02DOI: 10.1016/j.jtbi.2025.112331
Juan Segura , Marcos Marvá , Daniel Franco
Habitat fragmentation is a leading cause of biodiversity loss, and efforts to enhance connectivity through, for example, biological corridors are a common conservation strategy to mitigate it. However, understanding the effects of dispersal variation on the total biomass of spatially structured populations is still far from being well understood. For the simplest situation, i.e., a population occupying a habitat divided into two patches, recent studies have shown that there are only four possible response scenarios to increased connectivity in discrete- and continuous-time models under Beverton-Holt and logistic local dynamics, respectively. This paper explores whether the number of patches in a metapopulation influences the number of response scenarios to increased dispersal. We will show that for given local dynamics the number of possible response scenarios significantly increases when the number of patches increases from two to three. Moreover, the paper revisits the problem of how network topology affects total biomass dynamics for low dispersal rates. We will show that the previous claim that bidirectional connectivity always increases biomass at low dispersal rates when connecting sources is false. Indeed, we will prove that transiting from a chain topology to a ring topology can either increase or decrease the total biomass for low dispersal rates if one considers more realistic production functions or if the probability of using a concrete path is not the same in the whole metapopulation.
{"title":"Dispersal in multi-patch metapopulations: The impact of patch number and network topology","authors":"Juan Segura , Marcos Marvá , Daniel Franco","doi":"10.1016/j.jtbi.2025.112331","DOIUrl":"10.1016/j.jtbi.2025.112331","url":null,"abstract":"<div><div>Habitat fragmentation is a leading cause of biodiversity loss, and efforts to enhance connectivity through, for example, biological corridors are a common conservation strategy to mitigate it. However, understanding the effects of dispersal variation on the total biomass of spatially structured populations is still far from being well understood. For the simplest situation, i.e., a population occupying a habitat divided into two patches, recent studies have shown that there are only four possible response scenarios to increased connectivity in discrete- and continuous-time models under Beverton-Holt and logistic local dynamics, respectively. This paper explores whether the number of patches in a metapopulation influences the number of response scenarios to increased dispersal. We will show that for given local dynamics the number of possible response scenarios significantly increases when the number of patches increases from two to three. Moreover, the paper revisits the problem of how network topology affects total biomass dynamics for low dispersal rates. We will show that the previous claim that bidirectional connectivity always increases biomass at low dispersal rates when connecting sources is false. Indeed, we will prove that transiting from a chain topology to a ring topology can either increase or decrease the total biomass for low dispersal rates if one considers more realistic production functions or if the probability of using a concrete path is not the same in the whole metapopulation.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"619 ","pages":"Article 112331"},"PeriodicalIF":2.0,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145679323","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}
Pub Date : 2025-11-29DOI: 10.1016/j.jtbi.2025.112332
Yusuke Ikegawa , Chihiro Himuro , Atsushi Honma
Reproductive interference (RI) includes any negative effect on reproductive success of females that is induced by interspecific sexual interactions. Although previous population dynamic models of RI have focused on population-level processes (e.g., changes in population size), individual-level processes (e.g., search and courtship by males and subsequent choice by females) have been largely overlooked. In this study, we constructed a discrete-time population dynamic model comprising two species, assuming iterative courtship and mating within each reproductive time period (i.e., individual-level process) and subsequent population dynamics (i.e., population-level process). We assumed that if males (or females) have wide acceptance range to their counterparts, correct courtship (or mating) to conspecifics and incorrect courtship to heterospecifics would increase simultaneously. We also assumed that two species have different demographics (species 1 with higher reproduction and mortality, species 2 with lower reproduction and mortality). We showed that intermediate acceptance range of females mitigated the negative effect of courtship from heterospecific males on mating success. However, the initially more abundant species 1 can be outcompeted by the initially less abundant species 2. This is because the net negative effect of losing mating opportunities due to RI was greater for species 1 with higher mortality than for species 2 with lower mortality. Overall, the results of reproductive success, which are derived only from individual-level processes, are not always consistent with the demographic consequences, which are derived from both individual- and population-level processes. We propose that analyzing the RI system by considering both individual- and population-level processes is necessary.
{"title":"Demographic consequences of the loss of mating opportunities in a two-species reproductive interference system","authors":"Yusuke Ikegawa , Chihiro Himuro , Atsushi Honma","doi":"10.1016/j.jtbi.2025.112332","DOIUrl":"10.1016/j.jtbi.2025.112332","url":null,"abstract":"<div><div>Reproductive interference (RI) includes any negative effect on reproductive success of females that is induced by interspecific sexual interactions. Although previous population dynamic models of RI have focused on population-level processes (e.g., changes in population size), individual-level processes (e.g., search and courtship by males and subsequent choice by females) have been largely overlooked. In this study, we constructed a discrete-time population dynamic model comprising two species, assuming iterative courtship and mating within each reproductive time period (i.e., individual-level process) and subsequent population dynamics (i.e., population-level process). We assumed that if males (or females) have wide acceptance range to their counterparts, correct courtship (or mating) to conspecifics and incorrect courtship to heterospecifics would increase simultaneously. We also assumed that two species have different demographics (species 1 with higher reproduction and mortality, species 2 with lower reproduction and mortality). We showed that intermediate acceptance range of females mitigated the negative effect of courtship from heterospecific males on mating success. However, the initially more abundant species 1 can be outcompeted by the initially less abundant species 2. This is because the net negative effect of losing mating opportunities due to RI was greater for species 1 with higher mortality than for species 2 with lower mortality. Overall, the results of reproductive success, which are derived only from individual-level processes, are not always consistent with the demographic consequences, which are derived from both individual- and population-level processes. We propose that analyzing the RI system by considering both individual- and population-level processes is necessary.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"619 ","pages":"Article 112332"},"PeriodicalIF":2.0,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650219","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}
Pub Date : 2025-11-29DOI: 10.1016/j.jtbi.2025.112317
Griffin Kutler Dodd, Rob J. de Boer
The current standard treatment for HIV-1 infection is antiretroviral therapy, which effectively suppresses viral replication but requires a lifelong drug regimen. An alternative treatment approach is a single injection of a modified version of the HIV-1 virus, termed a therapeutic interfering particle (TIP), that lacks replication machinery and suppresses the wild-type virus by competing for viral proteins. Here, we derive a novel ordinary differential equation model of TIP dynamics. We confirm results from previous models that TIPs can reduce viral load when doubly infected cells produce at least as many virus particles as singly infected cells. By deriving the basic reproduction number of a TIP, we predict that concurrent antiretroviral therapy should make it more difficult for a TIP to persist in a host. Adding an immune response to our model reveals that even a moderate immune response against virally infected cells drastically decreases the range of parameter values for which therapy is effective. Together, these results show that the success of TIPs depend on the properties of the wild-type virus and even more strongly on the immune response, which makes it hard to predict therapeutic success.
{"title":"Immune responses may make HIV-1 therapeutic interfering particles less effective","authors":"Griffin Kutler Dodd, Rob J. de Boer","doi":"10.1016/j.jtbi.2025.112317","DOIUrl":"10.1016/j.jtbi.2025.112317","url":null,"abstract":"<div><div>The current standard treatment for HIV-1 infection is antiretroviral therapy, which effectively suppresses viral replication but requires a lifelong drug regimen. An alternative treatment approach is a single injection of a modified version of the HIV-1 virus, termed a therapeutic interfering particle (TIP), that lacks replication machinery and suppresses the wild-type virus by competing for viral proteins. Here, we derive a novel ordinary differential equation model of TIP dynamics. We confirm results from previous models that TIPs can reduce viral load when doubly infected cells produce at least as many virus particles as singly infected cells. By deriving the basic reproduction number <span><math><msubsup><mi>R</mi><mn>0</mn><mi>T</mi></msubsup></math></span> of a TIP, we predict that concurrent antiretroviral therapy should make it more difficult for a TIP to persist in a host. Adding an immune response to our model reveals that even a moderate immune response against virally infected cells drastically decreases the range of parameter values for which therapy is effective. Together, these results show that the success of TIPs depend on the properties of the wild-type virus and even more strongly on the immune response, which makes it hard to predict therapeutic success.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"619 ","pages":"Article 112317"},"PeriodicalIF":2.0,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145649812","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}
Pub Date : 2025-11-18DOI: 10.1016/j.jtbi.2025.112308
Ning Wei , Joyce Lin
Cardiac cells communicate electrically to coordinate heart contractions and pump blood. Gap junctions in the intercalated discs (ID) between myocytes form low-resistance pathways that facilitate electrical propagation. Traditionally, gap junctional coupling is considered the primary mechanism for cell communication, but experimental studies show that conduction can persist even with impaired gap junctions. For example, in gap junction-deficient rats, the heart still shows slow, discontinuous signal propagation, suggesting the existence of other communication mechanisms. One such mechanism is ephaptic coupling (EpC), an electrical field effect in the ID that maintains conduction even in the absence of gap junctions. EpC has been explored experimentally and numerically, especially in altered ID under normal and diseased conditions. However, a lack of direct evidence emphasizes the need to study its physiological role in the heart. Some research indicates that EpC can increase conduction velocity (CV) and reduce conduction failure, but its effects on cardiac arrhythmias are not well understood. Our study focuses on reentry arrhythmia, where rapid, irregular heartbeats can lead to cardiac arrest. Previous modeling work suggests that strong EpC can terminate reentry in ischemic hearts, though the mechanism remains unclear. We aim to investigate the mechanisms underlying reentry termination across different levels of EpC and gap junctional coupling using a two-dimensional discrete bidomain model with EpC. Our results identify two mechanisms: (1) Strong EpC terminates reentry through self-attenuation, driven by inactivation of fast sodium currents and (2) moderate EpC terminates reentry through self-collision, influenced by increased CV and anisotropy. A boundary where termination does not occur is also observed.
{"title":"Mechanisms of reentry arrhythmia termination with ephaptic coupling and gap junctional coupling","authors":"Ning Wei , Joyce Lin","doi":"10.1016/j.jtbi.2025.112308","DOIUrl":"10.1016/j.jtbi.2025.112308","url":null,"abstract":"<div><div>Cardiac cells communicate electrically to coordinate heart contractions and pump blood. Gap junctions in the intercalated discs (ID) between myocytes form low-resistance pathways that facilitate electrical propagation. Traditionally, gap junctional coupling is considered the primary mechanism for cell communication, but experimental studies show that conduction can persist even with impaired gap junctions. For example, in gap junction-deficient rats, the heart still shows slow, discontinuous signal propagation, suggesting the existence of other communication mechanisms. One such mechanism is ephaptic coupling (EpC), an electrical field effect in the ID that maintains conduction even in the absence of gap junctions. EpC has been explored experimentally and numerically, especially in altered ID under normal and diseased conditions. However, a lack of direct evidence emphasizes the need to study its physiological role in the heart. Some research indicates that EpC can increase conduction velocity (CV) and reduce conduction failure, but its effects on cardiac arrhythmias are not well understood. Our study focuses on reentry arrhythmia, where rapid, irregular heartbeats can lead to cardiac arrest. Previous modeling work suggests that strong EpC can terminate reentry in ischemic hearts, though the mechanism remains unclear. We aim to investigate the mechanisms underlying reentry termination across different levels of EpC and gap junctional coupling using a two-dimensional discrete bidomain model with EpC. Our results identify two mechanisms: (1) Strong EpC terminates reentry through self-attenuation, driven by inactivation of fast sodium currents and (2) moderate EpC terminates reentry through self-collision, influenced by increased CV and anisotropy. A boundary where termination does not occur is also observed.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112308"},"PeriodicalIF":2.0,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145566408","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}
Pub Date : 2025-11-17DOI: 10.1016/j.jtbi.2025.112307
Zita Borbála Fülöp, Raimondo Penta
Electroporation-based therapies such as electrochemotherapy (ECT) hold a great promise for improving cancer treatments. While highly effective for superficial tumours, its application for deep-seated malignancies is challenged by complex microstructural properties, and current models often lack a multiscale theoretical framework to capture those phenomena. Here we develop and solve a novel system of coupled partial differential equations of Darcy-Laplace type obtained by applying the asymptotic homogenisation technique. We study the tumour response stimulated by an electric field. We derive effective macroscale equations for the pressure, velocity, and electric potential, whilst incorporating both hydraulic and electric microscale tissue heterogeneities. Our coupled multiscale approach bridges the gap between the tumour microstructure and macroscale dynamics, offering a more comprehensive understanding of how tumour size, morphology, and hydraulic-electrical interactions influence interstitial flow. We present a parametric analysis of the hydraulic conductivity tensor and macroscale numerical simulation results for pressure and velocity fields, highlighting the role of the electric field in modulating fluid flow. Our findings provide meaningful insights towards advancing ECT protocols.
{"title":"Multiscale analysis of electrically stimulated vascularised tumours","authors":"Zita Borbála Fülöp, Raimondo Penta","doi":"10.1016/j.jtbi.2025.112307","DOIUrl":"10.1016/j.jtbi.2025.112307","url":null,"abstract":"<div><div>Electroporation-based therapies such as electrochemotherapy (ECT) hold a great promise for improving cancer treatments. While highly effective for superficial tumours, its application for deep-seated malignancies is challenged by complex microstructural properties, and current models often lack a multiscale theoretical framework to capture those phenomena. Here we develop and solve a novel system of coupled partial differential equations of Darcy-Laplace type obtained by applying the asymptotic homogenisation technique. We study the tumour response stimulated by an electric field. We derive effective macroscale equations for the pressure, velocity, and electric potential, whilst incorporating both hydraulic and electric microscale tissue heterogeneities. Our coupled multiscale approach bridges the gap between the tumour microstructure and macroscale dynamics, offering a more comprehensive understanding of how tumour size, morphology, and hydraulic-electrical interactions influence interstitial flow. We present a parametric analysis of the hydraulic conductivity tensor and macroscale numerical simulation results for pressure and velocity fields, highlighting the role of the electric field in modulating fluid flow. Our findings provide meaningful insights towards advancing ECT protocols.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"619 ","pages":"Article 112307"},"PeriodicalIF":2.0,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145558390","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}
Pub Date : 2025-11-15DOI: 10.1016/j.jtbi.2025.112319
Arni S.R. Srinivasa Rao , Steven G. Krantz , John P. Barile
Despite the widespread use of deterministic models in understanding and controlling epidemics, they are often criticized for their inability to provide timely practical solutions during rapid spread. Similarly, conventional stochastic and statistical models also have limitations in providing time-sensitive solutions. These models are useful for implementing policy measures when there is enough time to make changes. In this article, we propose a novel approach to address these limitations by introducing a graphical network model with time-sensitive data blending to enhance deterministic epidemic models like the SIR model. This innovative approach could be valuable for rapidly spreading epidemics, providing timely model-based solutions to control their spread. For the first time, this article introduces higher-dimensional transmission rate functions in the literature and methods to obtain such functions.
{"title":"Integrating community level transmission geographical networks into a dynamical system for better epidemic control","authors":"Arni S.R. Srinivasa Rao , Steven G. Krantz , John P. Barile","doi":"10.1016/j.jtbi.2025.112319","DOIUrl":"10.1016/j.jtbi.2025.112319","url":null,"abstract":"<div><div>Despite the widespread use of deterministic models in understanding and controlling epidemics, they are often criticized for their inability to provide timely practical solutions during rapid spread. Similarly, conventional stochastic and statistical models also have limitations in providing time-sensitive solutions. These models are useful for implementing policy measures when there is enough time to make changes. In this article, we propose a novel approach to address these limitations by introducing a graphical network model with time-sensitive data blending to enhance deterministic epidemic models like the SIR model. This innovative approach could be valuable for rapidly spreading epidemics, providing timely model-based solutions to control their spread. For the first time, this article introduces higher-dimensional transmission rate functions in the literature and methods to obtain such functions.</div><div>AMS MSC 2020 classifications: 92D30; 62P10; 65T60.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112319"},"PeriodicalIF":2.0,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145544131","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}
Pub Date : 2025-11-15DOI: 10.1016/j.jtbi.2025.112314
Neha Bansal, Katerina Kaouri, Thomas E. Woolley
Epidemiological models can inform policymaking on disease control strategies, and these models often rely on sampled contact networks. The Random Walk (RW) sampling algorithm, commonly used for network sampling, produces size-biased samples that over-represent highly connected individuals, leading to biased estimates of disease spread. The Metropolis-Hastings Random Walk (MHRW) addresses this by providing samples representative of the underlying network’s connectivity distribution. We compare MHRW and RW in reducing size bias across four network types: Erdös-Rényi (ER), Small-world (SW), Negative-binomial (NB), and Scale-free (SF). We simulate disease spread using a stochastic Susceptible-Infected-Recovered (SIR) framework. RW tends to overestimate infections (by 25 % in ER, SW, NB) and secondary infections (by 25 % in ER, SW and 80 % in NB), and underestimate time-to-infection in NB networks. MHRW reduces the size bias, except on SF networks, where both algorithms provide non-representative samples and highly variable estimates. We find that RW is appropriate for fast-spreading, high-mortality epidemics in homogeneous or moderately random networks (ER, SW). In contrast, MHRW is better suited for slower and low-severity epidemics and can be effective in both homogeneous and heterogeneous networks (ER, SW, NB). However, MHRW is computationally expensive and less accurate when duplicate nodes are removed. We also analyse real-world data from cattle movement and human contact networks; MHRW generates disease spread estimates closer to the underlying network than RW. Our findings guide the selection of sampling algorithms based on network structure and epidemic characteristics, enhancing the reliability of disease modelling for policymaking.
流行病学模型可以为疾病控制战略的决策提供信息,而这些模型往往依赖于抽样接触网络。随机漫步(RW)抽样算法通常用于网络抽样,它产生的样本有大小偏差,过度代表高度联系的个体,导致对疾病传播的估计有偏差。Metropolis-Hastings Random Walk (MHRW)通过提供代表底层网络连接分布的样本来解决这个问题。我们比较了MHRW和RW在四种网络类型(Erdös-Rényi (ER)、小世界(SW)、负二项(NB)和无标度(SF))中减少尺寸偏差的效果。我们使用随机易感-感染-恢复(SIR)框架模拟疾病传播。RW倾向于高估感染(在ER、SW、NB中为25%)和继发性感染(在ER、SW中为25%,在NB中为80%),并低估NB网络中的感染时间。除了SF网络,MHRW减少了大小偏差,其中两种算法都提供了非代表性样本和高度可变的估计。我们发现RW适用于同质或中等随机网络中快速传播、高死亡率的流行病(ER, SW)。相比之下,MHRW更适合于较慢和低严重程度的流行病,并且可以在同质和异质网络中有效(ER、SW、NB)。然而,MHRW的计算成本很高,并且在删除重复节点时准确性较低。我们还分析了来自牛的运动和人类接触网络的真实数据;MHRW产生的疾病传播估计值比RW更接近基础网络。我们的研究结果指导了基于网络结构和流行病特征的抽样算法的选择,提高了疾病建模为政策制定提供的可靠性。
{"title":"Reducing size bias in epidemic network modelling","authors":"Neha Bansal, Katerina Kaouri, Thomas E. Woolley","doi":"10.1016/j.jtbi.2025.112314","DOIUrl":"10.1016/j.jtbi.2025.112314","url":null,"abstract":"<div><div>Epidemiological models can inform policymaking on disease control strategies, and these models often rely on sampled contact networks. The Random Walk (RW) sampling algorithm, commonly used for network sampling, produces size-biased samples that over-represent highly connected individuals, leading to biased estimates of disease spread. The Metropolis-Hastings Random Walk (MHRW) addresses this by providing samples representative of the underlying network’s connectivity distribution. We compare MHRW and RW in reducing size bias across four network types: Erdös-Rényi (ER), Small-world (SW), Negative-binomial (NB), and Scale-free (SF). We simulate disease spread using a stochastic Susceptible-Infected-Recovered (SIR) framework. RW tends to overestimate infections (by 25 % in ER, SW, NB) and secondary infections (by 25 % in ER, SW and 80 % in NB), and underestimate time-to-infection in NB networks. MHRW reduces the size bias, except on SF networks, where both algorithms provide non-representative samples and highly variable estimates. We find that RW is appropriate for fast-spreading, high-mortality epidemics in homogeneous or moderately random networks (ER, SW). In contrast, MHRW is better suited for slower and low-severity epidemics and can be effective in both homogeneous and heterogeneous networks (ER, SW, NB). However, MHRW is computationally expensive and less accurate when duplicate nodes are removed. We also analyse real-world data from cattle movement and human contact networks; MHRW generates disease spread estimates closer to the underlying network than RW. Our findings guide the selection of sampling algorithms based on network structure and epidemic characteristics, enhancing the reliability of disease modelling for policymaking.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112314"},"PeriodicalIF":2.0,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145544122","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}
Pub Date : 2025-11-14DOI: 10.1016/j.jtbi.2025.112316
Oscar Delaney, Christopher~R.~P. Brown, Andrew~D. Letten, Jan Engelstäder
An increasingly important goal in the design of antimicrobial treatment regimens is to minimise the probability of resistance evolving, without harming individual patients’ outcomes. A key characteristic to consider when choosing an antibiotic for treatment is its mode of action: bacteriostatic (growth-inhibiting) or bactericidal (mortality-inducing). We present a theoretical model comparing the efficacy of bacteriostatic, bactericidal, and intermediate drugs at preventing the evolutionary rescue of an initially susceptible bacterial population. We find that, all else equal, in resource-abundant environments, bacteriostatic drugs are best, as they constrain cell divisions and thus allow fewer resistance mutations to occur. This contrasts with the prevailing assumption that bactericidal drugs are best as they actively kill cells. When multiple drugs are employed, using one bacteriostatic and one bactericidal drug is usually optimal, because the cell division rate cannot fall below zero, so there are diminishing returns to bacteriostatic activity from two drugs. Severe resource constraints mean that growth rates are already low, and thus there is less benefit to bacteriostatic drugs further limiting growth, so bactericidal drugs are favoured. If these findings are empirically verified in the laboratory and in vivo, they could significantly guide clinical practice.
{"title":"Drug mode of action and resource constraints modulate antimicrobial resistance evolution","authors":"Oscar Delaney, Christopher~R.~P. Brown, Andrew~D. Letten, Jan Engelstäder","doi":"10.1016/j.jtbi.2025.112316","DOIUrl":"10.1016/j.jtbi.2025.112316","url":null,"abstract":"<div><div>An increasingly important goal in the design of antimicrobial treatment regimens is to minimise the probability of resistance evolving, without harming individual patients’ outcomes. A key characteristic to consider when choosing an antibiotic for treatment is its mode of action: bacteriostatic (growth-inhibiting) or bactericidal (mortality-inducing). We present a theoretical model comparing the efficacy of bacteriostatic, bactericidal, and intermediate drugs at preventing the evolutionary rescue of an initially susceptible bacterial population. We find that, all else equal, in resource-abundant environments, bacteriostatic drugs are best, as they constrain cell divisions and thus allow fewer resistance mutations to occur. This contrasts with the prevailing assumption that bactericidal drugs are best as they actively kill cells. When multiple drugs are employed, using one bacteriostatic and one bactericidal drug is usually optimal, because the cell division rate cannot fall below zero, so there are diminishing returns to bacteriostatic activity from two drugs. Severe resource constraints mean that growth rates are already low, and thus there is less benefit to bacteriostatic drugs further limiting growth, so bactericidal drugs are favoured. If these findings are empirically verified in the laboratory and in vivo, they could significantly guide clinical practice.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112316"},"PeriodicalIF":2.0,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535110","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}