Bowei Ouyang , Aaron C. True , John P. Crimaldi , Bard Ermentrout
{"title":"Simple olfactory navigation in air and water","authors":"Bowei Ouyang , Aaron C. True , John P. Crimaldi , Bard Ermentrout","doi":"10.1016/j.jtbi.2024.111941","DOIUrl":"10.1016/j.jtbi.2024.111941","url":null,"abstract":"<div><p>Two simple algorithms based on combining odor concentration differences across time and space along with information on the flow direction are tested for their ability to locate an odor source in four different odor landscapes. Image data taken from air plumes in three different regimes and a water plume are used as test environments for a bilateral (“stereo sampling”) algorithm using concentration differences across two sensors and a “casting” algorithm that uses successive samples to decide orientation. Agents are started at random locations and orientations in the landscape and allowed to move until they reach the source of the odor (success) or leave the imaged area (failure). Parameters for the algorithm are chosen to optimize success and to minimize path length to the source. Success rates over 90% are consistently obtained with path lengths that can be as low as twice the starting distance from the source in air and four times the distance in the highly turbulent water plumes. We find that parameters that optimize success often lead to more exploratory pathways to the source. Information about the direction from which the odor is coming is necessary for successful navigation in the water plume and reduces the path length in the three tested air plumes.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111941"},"PeriodicalIF":1.9,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022519324002261/pdfft?md5=4baa947541fb13fb4cd0d1e55ea650d5&pid=1-s2.0-S0022519324002261-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180330","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}
Hyejeong Lee Cheon , Nataliya Kizilova , Eirik G. Flekkøy , Matthew J. Mason , Lars P. Folkow , Signe Kjelstrup
{"title":"The nasal cavity of the bearded seal: An effective and robust organ for retaining body heat and water","authors":"Hyejeong Lee Cheon , Nataliya Kizilova , Eirik G. Flekkøy , Matthew J. Mason , Lars P. Folkow , Signe Kjelstrup","doi":"10.1016/j.jtbi.2024.111933","DOIUrl":"10.1016/j.jtbi.2024.111933","url":null,"abstract":"<div><p>We report the effects of varying physiological and other properties on the heat and water exchange in the maxilloturbinate structure (MT) of the bearded seal (<em>Erignathus barbatus</em> or Eb) in realistic environments, using a computational fluid dynamics (CFD) model. We find that the water retention in percent is very high (about 90 %) and relatively unaffected by either cold (−30 °C) or warm (10 °C) conditions. The retention of heat is also high, around 80 % . Based on a consideration of entropy production by the maxilloturbinate system, we show that anatomical and physiological properties of the seal provide good conditions for heat and water exchange at the mucus lining in the seal’s nasal cavity. At normal values of tidal volume and maxilloturbinate (MT) length, the air temperature in the MT reaches the body temperature before the air has left the MT channels. This confers a safety factor which is expected to be helpful in exercise, when ventilation increases.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111933"},"PeriodicalIF":1.9,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022519324002182/pdfft?md5=8ad7be5d090c3b97f8f54edfd0f34a9f&pid=1-s2.0-S0022519324002182-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180331","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":"Connectivity between two fishing sites can lead to an emergence phenomenon related to Maximum Sustainable Yield","authors":"Doanh Nguyen-Ngoc , Tri Nguyen-Huu , Pierre Auger","doi":"10.1016/j.jtbi.2024.111913","DOIUrl":"10.1016/j.jtbi.2024.111913","url":null,"abstract":"<div><p>In this study, we examine the effects of connectivity on the total catch of a fishery consisting of two fishing sites when the fish population is a predator of a larger prey–predator system. To this end, we analyze a prey–predator fish community model in a two-site environment and compute catch at Maximum Sustainable Yield (MSY). We exhibit some emergence phenomenon: the total catch can be greater than the sum of the catch at two isolated sites due to connectivity. This result is obtained when the two sites are heterogeneous. We show that the increase in capture at MSY is maximal for a certain value of the carrying capacity of the second site, all other parameters remaining constant, including the carrying capacity of the first site. A stronger phenomenon can also be observed: even if none of the sites is viable for fishing, the entire system can be viable. We then study the effects of the heterogeneity of the sites and illustrate our results through simulations. It is shown that the excess yield at MSY can become very significant when the characteristics of the prey and predator in terms of potential growth are opposite at each site.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111913"},"PeriodicalIF":1.9,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146819","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}
L. Roques , N. Boutillon , P. Zamberletti , J. Papaïx
{"title":"Polymorphic population expansion velocity in a heterogeneous environment","authors":"L. Roques , N. Boutillon , P. Zamberletti , J. Papaïx","doi":"10.1016/j.jtbi.2024.111932","DOIUrl":"10.1016/j.jtbi.2024.111932","url":null,"abstract":"<div><p>How does the spatial heterogeneity of landscapes interact with the adaptive evolution of populations to influence their spreading speed? This question arises in agricultural contexts where a pathogen population spreads in a landscape composed of several types of crops, as well as in epidemiological settings where a virus spreads among individuals with distinct immune profiles. To address it, we introduce an analytical method based on reaction–diffusion models. We focus on spatially periodic environments with two distinct patches, where the dispersing population consists of two specialized morphs, each potentially mutating to the other. We present new formulas for the speed together with criteria for persistence, accounting for both rapidly and slowly varying environments, as well as small and large mutation rates. Altogether, our analytical and numerical results yield a comprehensive understanding of persistence and spreading dynamics. In particular, compared to a situation without mutations or to a single morph spreading in a heterogeneous landscape, the introduction of mutations to a second morph with reverse specialization, while consistently impeding persistence, can significantly increase speed, even if the mutation rate between the two morphs is very small. Additionally, we find that the amplitude of the spatial fragmentation effect is significantly increased in this case. This has implications for agroecology, emphasizing the higher importance of landscape structure in influencing adaptation-driven population dynamics.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111932"},"PeriodicalIF":1.9,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146820","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}
Alessandro Maria Selvitella , Kathleen Lois Foster
{"title":"An approximate solution of the SLIP model under the regime of linear angular dynamics during stance and the stability of symmetric periodic running gaits","authors":"Alessandro Maria Selvitella , Kathleen Lois Foster","doi":"10.1016/j.jtbi.2024.111934","DOIUrl":"10.1016/j.jtbi.2024.111934","url":null,"abstract":"<div><p>Terrestrial locomotion is a complex phenomenon that is often linked to the survival of an individual and of an animal species. Mathematical models seek to express in quantitative terms how animals move, but this is challenging because the ways in which the nervous and musculoskeletal systems interact to produce body movement is not completely understood. Models with many variables tend to lack biological interpretability and describe the motion of an animal with too many independent degrees of freedom. Instead, reductionist models aim to describe the essential features of a gait with the smallest number of variables, often concentrating on the center of mass dynamics. In particular, spring–mass models have been successful in extracting and describing important characteristics of running. In this paper, we consider the spring loaded inverted pendulum model under the regime of constant angular velocity, small compression, and small angle swept during stance. We provide conditions for the asymptotic stability of periodic trajectories for the full range of parameters. The hypothesis of linear angular dynamics during stance is successfully tested on publicly available human data of individuals running on a treadmill at different velocities. Our analysis highlights a novel bifurcation phenomenon for varying <em>Froude number</em>: there are periodic trajectories of the spring loaded inverted pendulum model that are stable only in a restricted range of <em>Froude numbers</em>, while they become unstable for smaller or larger <em>Froude numbers</em>.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111934"},"PeriodicalIF":1.9,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022519324002194/pdfft?md5=0493b950fcf6e94cd914fad010fbf3ec&pid=1-s2.0-S0022519324002194-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146818","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":"Identifiability of speciation times under the multispecies coalescent","authors":"Laura Kubatko , Alexander Leonard , Julia Chifman","doi":"10.1016/j.jtbi.2024.111927","DOIUrl":"10.1016/j.jtbi.2024.111927","url":null,"abstract":"<div><p>The advent of rapid and inexpensive sequencing technologies has necessitated the development of computationally efficient methods for analyzing sequence data for many genes simultaneously in a phylogenetic framework. The coalescent process is the most commonly used model for linking the underlying genealogies of individual genes with the global species-level phylogeny, but inference under the coalescent model is computationally daunting in the typical inference frameworks (e.g., the likelihood and Bayesian frameworks) due to the dimensionality of the space of both gene trees and species trees. Here we consider estimation of the branch lengths in fixed species trees with three or four taxa, and show that these branch lengths are identifiable. We also show that for three and four taxa simple estimators for the branch lengths can be derived based on observed site pattern frequencies. Properties of these estimators, such as their asymptotic variances and large-sample distributions, are examined, and performance of the estimators is assessed using simulation. Finally, we use these estimators to develop a hypothesis test that can be used to delimit species under the coalescent model for three or four putative taxa.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111927"},"PeriodicalIF":1.9,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114874","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}
Jian Wang , Zhenmin Fan , Jiashuai Liu , Kailei Liu , ChaoJun Yan , Xia Ye , Xiaoyan Deng
{"title":"Influence of stent strut and its associated injury on thrombus formation: A dissipative particle dynamics study","authors":"Jian Wang , Zhenmin Fan , Jiashuai Liu , Kailei Liu , ChaoJun Yan , Xia Ye , Xiaoyan Deng","doi":"10.1016/j.jtbi.2024.111929","DOIUrl":"10.1016/j.jtbi.2024.111929","url":null,"abstract":"<div><p>Vascular stent intervention is a pivotal treatment for coronary atherosclerosis, though in-stent thrombosis remains a significant postoperative complication with an unclear underlying mechanism. This study utilized dissipated particle dynamics analysis to investigate the impact of stent and its injury on platelet behavior. The findings suggest that thrombus formation upstream of the stent is mainly initiated by upstream arterial injury, which leads to increased platelet accumulation and activation in that area. While thrombosis downstream of the stent is more directly influenced by the stent itself. The morphology and size of in-stent thrombosis can vary significantly due to the different contributions of the stent and underlying injuries. Additionally, the volume of in-stent thrombosis is affected by the extent of the injury and the viscosity of platelets, showing a notable increase in volume with the lengthening of the injury area and rise in platelet viscosity. This study provides a novel theoretical framework for optimizing stent placement strategies and structural designs by examining the effects of stent struts and associated injuries on thrombus formation.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111929"},"PeriodicalIF":1.9,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142094224","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":"Effects of delay and error in the feedback structure of ecological management","authors":"Nao Takashina","doi":"10.1016/j.jtbi.2024.111926","DOIUrl":"10.1016/j.jtbi.2024.111926","url":null,"abstract":"<div><p>Ecosystems face various emergent uncertainties owing to factors such as climate change and accelerating anthropogenic impacts. Uncertainty is a major challenge and a barrier that ecosystem management faces, because it is difficult to precisely predict a priori risks that can have significant impacts on ecosystems. Hence, management with adaptive capacity is recommended to deal with such uncertainties, and feedback structures are central mechanisms for such flexible management. This study used mathematical models to clarify the specific impacts of feedback structures on ecosystem management, such as resource and wildlife management. In particular, the impact of errors in estimating ecosystem status when providing feedback and the impact of the time lag before feedback effects were implemented into management were examined. Overestimation of ecosystem status or a large time lag led to undesirable temporal oscillations in ecosystem status. However, these scenarios can be avoided when combined with management practices that limit the impact of management on the ecosystem, such as input control. Ecosystem management tends to have a large spatiotemporal scale, and implementing highly accurate monitoring and sophisticated feedback structures is difficult. However, the results suggest that effective ecosystem management with a simple feedback structure can be achieved through such complementary institutional design.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111926"},"PeriodicalIF":1.9,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S002251932400211X/pdfft?md5=8661dc96f9ca0bad20aaf599745ac828&pid=1-s2.0-S002251932400211X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074565","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}
Shyni Unni Kumaran , Lavanya Rajagopal , Manavaalan Gunasekaran
{"title":"Sensitivity assessment of optimal control strategies and cost-effectiveness analysis of a novel Candida Auris environmental transmission model in intensive care facilities","authors":"Shyni Unni Kumaran , Lavanya Rajagopal , Manavaalan Gunasekaran","doi":"10.1016/j.jtbi.2024.111931","DOIUrl":"10.1016/j.jtbi.2024.111931","url":null,"abstract":"<div><p>Candida Auris is an emerging fungal pathogen flagged by CDC as a serious global health threat among nosocomial infections in the recent times. As an evolving pathogen that often goes misidentified or unidentified under standard laboratory tests, it has the ability to cause fatal infections among the target population involving patients with serious medical conditions admitted to intensive care facilities, due to its capacity to resist anti-fungal treatment and the ability to persist in the hospital environment for long periods. The subject of this paper is to develop a deterministic model to study the transmission nature of <em>Candida Auris</em> wherein measures like apt admission screening methods with weekly screening follow-ups, transmission prevention, proper treatment protocols and environmental disinfection procedures are introduced as constant mitigating controls into the model initially which are later redefined as variable control functions during the optimal control analysis. The theory of optimal control implemented into the model helps us to understand the sensitivity of each control strategy upon the behaviour of each state variable. Further, cost-effectiveness analysis is rigorously conducted using incremental cost-effectiveness ratio (ICER) to identify and rank the control strategies involved based on their economic efficiency. Numerical simulation for the optimal control analysis is performed in MATLAB using the Forward–Backward Sweep Method and the findings are illustrated graphically.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111931"},"PeriodicalIF":1.9,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074566","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":"Simulation analyses of the evolution of intra-inflorescence flowering patterns assuming selection on anthesis interval among individual flowers","authors":"Yu Watanabe, Satoki Sakai","doi":"10.1016/j.jtbi.2024.111930","DOIUrl":"10.1016/j.jtbi.2024.111930","url":null,"abstract":"<div><p>What conditions select flowering patterns within inflorescences, or variation in the anthesis interval within inflorescences among plants? Under what conditions are gradual blooming and simultaneous blooming, both traits related to floral display size, advantageous? We constructed a simulation model in which the opening times and longevities of individual flowers within inflorescences, the sizes of attractive structures of individual flowers, and the numbers of ovules and pollen grains produced by individual flowers evolve. Individual plants in the population compete for pollinators, and plants are selected by pollinators according to their floral display sizes and amounts of resources allocated to attractive structures. We found that, if the proportion of pollen on a pollinator deposited on a stigma was low, gradual blooming did not evolve even if inbreeding depression was greater than 0.5. This is because the amount of outcross-pollen on pollinators decreased at a low rate during flower visits within a single inflorescence, and the selfing rate was suppressed to a low level even if the floral display size was large. On the other hand, if the proportion of pollen deposition was high, gradual blooming evolved even if inbreeding depression was smaller than 0.5. This may be because gradual blooming can enhance pollen delivery to other plants by reducing the loss of self-pollen by geitonogamy. On the other hand, allocation ratios among floral organs (female and male organs and attractive structures) were independent of the degree of simultaneous and gradual blooming within inflorescences. We concluded that the evolution of gradual blooming is more strongly affected by the proportion of pollen on a pollinator deposited on a stigma than by inbreeding depression.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"594 ","pages":"Article 111930"},"PeriodicalIF":1.9,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022519324002157/pdfft?md5=bc2b7b415516b3d64d5cbf27a764ed55&pid=1-s2.0-S0022519324002157-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057257","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}