Bulletin of Mathematical Biology最新文献_第5页

Computations in living organisms modeled by marked graphs. 用标记图形模拟生物体的计算。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-25 DOI: 10.1007/s11538-025-01499-x

John M Myers, Hadi Madjid

{"title":"Computations in living organisms modeled by marked graphs.","authors":"John M Myers, Hadi Madjid","doi":"10.1007/s11538-025-01499-x","DOIUrl":"10.1007/s11538-025-01499-x","url":null,"abstract":"The accurate copying of nucleotides in DNA replication is arguably a digital computation. So are some cognitive capacities found in all organisms. In 2005 we proved that linking quantum calculations to evidence requires guesswork subject to revision (Madjid and Myers 2005). Based on this proof, we assume computations by living organisms undergo incessant unpredictable changes in their structure. This raises a question: how can changes in computations be made while preserving the integrity of the organism? We offer an answer expressed in the mathematics of marked graphs. Computations as networks of logical operations can be represented by marked graphs with live and safe markings. We represent a sequence of changes by a sequence of marked graphs. Then \"Preserving the integrity of the organism\" is expressed by preserving liveness and safety throughout the sequence of marked graphs. For example, we show how a single slime-mold amoeba inserts itself into a slime-mold filament without interrupting computation spread along the filament. Because interpretations of mathematics are mathematically undetermined, a quite different interpretation of the same sequence of marked graphs is possible. An alternative interpretation of the sequence of marked graphs is to see them as a cartoon of the insertion of a fragment of thought into a chain of human thoughts.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"118"},"PeriodicalIF":2.2,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12296834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144706397","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}

引用次数: 0

Wave Propagation Phenomena in Nonlinear Hierarchical Neural Networks with Predictive Coding Feedback Dynamics. 具有预测编码反馈动力学的非线性层次神经网络中的波传播现象。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-24 DOI: 10.1007/s11538-025-01492-4

Andrea Alamia, Léa Dalliès, Grégory Faye, Rufin VanRullen

{"title":"Wave Propagation Phenomena in Nonlinear Hierarchical Neural Networks with Predictive Coding Feedback Dynamics.","authors":"Andrea Alamia, Léa Dalliès, Grégory Faye, Rufin VanRullen","doi":"10.1007/s11538-025-01492-4","DOIUrl":"10.1007/s11538-025-01492-4","url":null,"abstract":"We propose a mathematical framework to systematically explore the propagation properties of a class of continuous in time nonlinear neural network models comprising a hierarchy of processing areas, mutually connected according to the principles of predictive coding. We precisely determine the conditions under which upward propagation, downward propagation or even propagation failure can occur in both bi-infinite and semi-infinite idealizations of the model. We also study the long-time behavior of the system when either a fixed external input is constantly presented at the first layer of the network or when this external input consists in the presentation of constant input with large amplitude for a fixed time window followed by a reset to a down state of the network for all later times. In both cases, we numerically demonstrate the existence of threshold behavior for the amplitude of the external input characterizing whether or not a full propagation within the network can occur. Our theoretical results are consistent with predictive coding theories and allow us to identify regions of parameters that could be associated with dysfunctional perceptions.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"115"},"PeriodicalIF":2.2,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12289805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144706400","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}

引用次数: 0

Estimation and Analysis of Time-dependent Transmission Rates Based on a Multi-population Reinfection Model. 基于多种群再感染模型的时变传播率估计与分析。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-23 DOI: 10.1007/s11538-025-01495-1

Zihan Wang, Zhihua Liu

引用次数: 0

Modeling the Impact of Dedifferentiation on Colorectal Cancer Growth and Chemo-Immunotherapy Response. 模拟去分化对结直肠癌生长和化学免疫治疗反应的影响。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-22 DOI: 10.1007/s11538-025-01496-0

Yuman Wang, Mengfan Tan, Da Zhou

{"title":"Modeling the Impact of Dedifferentiation on Colorectal Cancer Growth and Chemo-Immunotherapy Response.","authors":"Yuman Wang, Mengfan Tan, Da Zhou","doi":"10.1007/s11538-025-01496-0","DOIUrl":"10.1007/s11538-025-01496-0","url":null,"abstract":"Tumor cell heterogeneity poses a significant challenge in the treatment of colorectal cancer, with dedifferentiation being a key factor in the emergence and maintenance of such heterogeneity. Does dedifferentiation necessarily promote colorectal cancer growth? What are its regulatory mechanisms in treatment response? These critical questions remain insufficiently understood. To investigate this issue, we develop a cancer cell population dynamics model. Our findings reveal that dedifferentiation impacts cancer growth in complex and varied patterns. Specifically, dedifferentiation can either facilitate or hinder cancer growth, with the outcomes depending on the dedifferentiation probability and the growth rates of different types of tumor cells. Subsequently, we consider the implications of dedifferentiation for various treatment strategies. Chemotherapy, which simultaneously promotes cell death and induces dedifferentiation, shows variable efficacy, potentially leading to tumor shrinkage or growth. In contrast, the combination of chemotherapy and high-intensity immunotherapy significantly enhances therapeutic outcomes, achieving more stable tumor control. These findings underscore the importance of incorporating dedifferentiation dynamics into colorectal cancer growth models and treatment designs, highlighting the advantages of combination therapy in overcoming the limitations of monotherapy.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"113"},"PeriodicalIF":2.2,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688904","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

Understanding Immune Dynamics in Liver Transplant Through Mathematical Modeling. 通过数学建模了解肝移植中的免疫动力学。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-19 DOI: 10.1007/s11538-025-01480-8

Julia Bruner, Kyle Adams, Skylar Grey, Mahya Aghaee, Sergio Duarte, Ali Zarrinpar, Helen Moore

{"title":"Understanding Immune Dynamics in Liver Transplant Through Mathematical Modeling.","authors":"Julia Bruner, Kyle Adams, Skylar Grey, Mahya Aghaee, Sergio Duarte, Ali Zarrinpar, Helen Moore","doi":"10.1007/s11538-025-01480-8","DOIUrl":"10.1007/s11538-025-01480-8","url":null,"abstract":"Liver transplant can be a life-saving procedure for patients with end-stage liver disease. With the introduction of modern immunosuppressive therapies, short-term survival has significantly improved. However, long-term survival has not substantially improved in decades. Consequently, causes of death are now more likely to be due to the toxicities and side-effects of long-term immunosuppression rather than rejection. In order to study the balance of immunosuppression and rejection, we developed the first mechanistic mathematical model of liver transplant and immune system dynamics. We determined key cells and interactions in the model using literature information; we then used sensitivity analysis to determine key pathways driving the health status of the transplanted liver. We found that dynamics related to cytotoxic T cells and IL-2, in addition to the liver itself, are key determinants of liver graft injury. This has significant implications for the use of tests to monitor patients, and therapeutic strategies to prevent or treat liver transplantation rejection. Future work to collect appropriate data and parametrize the model would be valuable in improving our understanding of the dynamics of this system. We also note that our model could be tailored to model transplant of other organs.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 8","pages":"112"},"PeriodicalIF":2.2,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667165","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}

引用次数: 0

Extended Discrete-Time Population Model to Describe the Competition of Nutrient-Producing Protocells. 描述营养物产生原细胞竞争的扩展离散时间种群模型。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-18 DOI: 10.1007/s11538-025-01488-0

Richárd Kicsiny, Tamás Bódai, László Székely, Zoltán Varga

{"title":"Extended Discrete-Time Population Model to Describe the Competition of Nutrient-Producing Protocells.","authors":"Richárd Kicsiny, Tamás Bódai, László Székely, Zoltán Varga","doi":"10.1007/s11538-025-01488-0","DOIUrl":"10.1007/s11538-025-01488-0","url":null,"abstract":"Modeling the behavior of simple communities of protocells (as basic life-like organisms) is of vital importance since their better understanding may help to describe more complex (artificial and real) ecological systems. In this paper, we extend a recently developed discrete-time dynamic population model (called preliminary model) to a more general, completely reformulated version for describing the competition in a community of three protocell species (one generalist and two specialists). The advantage for the generalist is that it produces more kinds of nutrients than the specialists. In contrast to the preliminary model, the reproduction times and the times of (first) appearance of the three species can be all different in the extended model. The aim is to achieve the most basic/fundamental model that already displays complex population phenomena, like competitive exclusion, keystone species and an interesting \"anomaly\" regarding the connection between the survival of certain species and the decreasing rates of certain nutrients in the environment. Although, we could achieve this aim with a three-species model, at the simplest level, the model can be easily extended for more species in the future. The mentioned \"anomaly\" is a new discovery as it was not observed in the preliminary model. A particular equilibrium, when only the generalist survives, is exactly analyzed, where, interestingly, the golden ratio arises regarding the densities of the protocells of different ages. In future works, the extended model may serve as a useful tool for studying further phenomena in ecosystems, in their pure/abstract form.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 8","pages":"111"},"PeriodicalIF":2.2,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12274253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658471","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}

引用次数: 0

Accidental and Regulated Cell Death in Yeast Colony Biofilms. 酵母菌落生物膜中的意外和调控细胞死亡。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-17 DOI: 10.1007/s11538-025-01470-w

Daniel J Netherwood, Alexander K Y Tam, Campbell W Gourlay, Tea Knežević, Jennifer M Gardner, Vladimir Jiranek, Benjamin J Binder, J Edward F Green

{"title":"Accidental and Regulated Cell Death in Yeast Colony Biofilms.","authors":"Daniel J Netherwood, Alexander K Y Tam, Campbell W Gourlay, Tea Knežević, Jennifer M Gardner, Vladimir Jiranek, Benjamin J Binder, J Edward F Green","doi":"10.1007/s11538-025-01470-w","DOIUrl":"10.1007/s11538-025-01470-w","url":null,"abstract":"The yeast species Saccharomyces cerevisiae is one of the most intensively studied organisms on the planet due to it being an excellent eukaryotic model organism in molecular and cell biology. In this work, we investigate the growth and morphology of yeast colony biofilms, where proliferating yeast cells reside within a self-produced extracellular matrix. This research area has garnered significant scientific interest due to its applicability in the biological and biomedical sectors. A central feature of yeast colony biofilm expansion is cellular demise, which is onset by one of two independent mechanisms: either accidental cell death (ACD) or regulated cell death (RCD). In this article, we generalise a continuum model for the nutrient-limited growth of a yeast colony biofilm to include the effects of ACD and RCD. This new model involves a system of four coupled nonlinear reaction-diffusion equations for the yeast-cell density, the nutrient concentration, and two species of dead cells. Numerical solutions of the spatially one and two-dimensional governing equations reveal the impact that ACD and RCD have on expansion speed, morphology and cell distribution within the colony biofilm. Our results are in good qualitative agreement with our own experiments.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 8","pages":"110"},"PeriodicalIF":2.2,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648657","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}

引用次数: 0

Parameter Optimization for a Neurotransmission Recovery Model. 神经传递恢复模型的参数优化。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-07 DOI: 10.1007/s11538-025-01486-2

Ariane Ernst, Anastasia Bankowski, Meida Jusyte, Toluwani Okunola, Tino Petrov, Alexander M Walter, Stefanie Winkelmann

引用次数: 0

Pattern Formation as a Resilience Mechanism in Cancer Immunotherapy. 模式形成作为肿瘤免疫治疗的弹性机制。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-01 DOI: 10.1007/s11538-025-01485-3

Molly Brennan, Andrew L Krause, Edgardo Villar-Sepúlveda, Christopher B Prior

{"title":"Pattern Formation as a Resilience Mechanism in Cancer Immunotherapy.","authors":"Molly Brennan, Andrew L Krause, Edgardo Villar-Sepúlveda, Christopher B Prior","doi":"10.1007/s11538-025-01485-3","DOIUrl":"10.1007/s11538-025-01485-3","url":null,"abstract":"Mathematical and computational modelling in oncology has played an increasingly important role in not only understanding the impact of various approaches to treatment on tumour growth, but in optimizing dosing regimens and aiding the development of treatment strategies. However, as with all modelling, only an approximation is made in the description of the biological and physical system. Here we show that tissue-scale spatial structure can have a profound impact on the resilience of tumours to immunotherapy using a classical model incorporating IL-2 compounds and effector cells as treatment parameters. Using linear stability analysis, numerical continuation, and direct simulations, we show that diffusing cancer cell populations can undergo pattern-forming (Turing) instabilities, leading to spatially-structured states that persist far into treatment regimes where the corresponding spatially homogeneous systems would uniformly predict a cancer-free state. These spatially-patterned states persist in a wide range of parameters, as well as under time-dependent treatment regimes. Incorporating treatment via domain boundaries can increase this resistance to treatment in the interior of the domain, further highlighting the importance of spatial modelling when designing treatment protocols informed by mathematical models. Counter-intuitively, this mechanism shows that increased effector cell mobility can increase the resilience of tumours to treatment. We conclude by discussing practical and theoretical considerations for understanding this kind of spatial resilience in other models of cancer treatment, in particular those incorporating more realistic spatial transport. This paper belongs to the special collection: Problems, Progress and Perspectives in Mathematical and Computational Biology.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 8","pages":"106"},"PeriodicalIF":2.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12214011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539054","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}

引用次数: 0

The Detailed Balance Property and Chemical Systems out of Equilibrium. 详细的平衡性质和非平衡化学系统。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-07-01 DOI: 10.1007/s11538-025-01487-1

E Franco, J J L Velázquez

引用次数: 0