Mathematical biosciences最新文献

Modelling the impact of organic molecules and phosphate ions on biosilica pattern formation in diatoms. 模拟有机分子和磷酸盐离子对硅藻中生物二氧化硅图案形成的影响。

Mathematical biosciences Pub Date : 2025-07-11 DOI: 10.1016/j.mbs.2025.109484

Svetlana Petrenko, Karen M Page

{"title":"Modelling the impact of organic molecules and phosphate ions on biosilica pattern formation in diatoms.","authors":"Svetlana Petrenko, Karen M Page","doi":"10.1016/j.mbs.2025.109484","DOIUrl":"https://doi.org/10.1016/j.mbs.2025.109484","url":null,"abstract":"The rapid and complex patterning of biosilica in diatom frustules is of great interest in nanotechnology, although it remains incompletely understood. Specific organic molecules, including long-chain polyamines, silaffins and silacidins are essential in this process. The molecular structure of synthesized polyamines significantly affects the quantity, size, and shape of silica precipitates. Experimental findings show that silica precipitation occurs at specific phosphate ion concentrations. We focus on the hypothesis that pattern formation in diatom valve structures is driven by phase separation of species-specific organic molecules. The resulting organic structures serve as templates for silica precipitation. We investigate the role of phosphate ions in the self-assembly of organic molecules and analyze how the reaction between them affects the morphology of the organic template. Using mathematical and computational techniques, we gain an understanding of the range of patterns that can arise in a phase-separating system. By varying the rate of dissociation and the initial concentrations of reacting components we demonstrate that the resulting geometric features are highly dependent on these factors. This approach provides insights into the parameters controlling patterning. Additionally, we consider the effects of prepatterns, mimicking silica ribs that preexist the pores, on the final patterns.","PeriodicalId":94129,"journal":{"name":"Mathematical biosciences","volume":" ","pages":"109484"},"PeriodicalIF":0.0,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144628368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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。

Mathematical biosciences Pub Date : 2025-07-04 DOI: 10.1016/j.mbs.2025.109501

Zhitao Zhao, Jing Yang, Russell Milne, Yawen Yan

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。

Mathematical biosciences Pub Date : 2025-06-27 DOI: 10.1016/j.mbs.2025.109485

Paolo Climaco, Noelle M Mitchell, Matthew 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 Tyler, Kyungae Yang, Anne M Andrews, Andrea L Bertozzi","doi":"10.1016/j.mbs.2025.109485","DOIUrl":"https://doi.org/10.1016/j.mbs.2025.109485","url":null,"abstract":"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.","PeriodicalId":94129,"journal":{"name":"Mathematical biosciences","volume":" ","pages":"109485"},"PeriodicalIF":0.0,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144532101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effects of fish-human transmission and different life stages of fish on Clonorchiasis: A novel mathematical model. 鱼-人传播和鱼的不同生命阶段对克隆氏病的影响：新型数学模型

Mathematical biosciences Pub Date : 2024-05-15 DOI: 10.1016/j.mbs.2024.109209

Wei Wang, Xiaohui Huang, Hao Wang

{"title":"Effects of fish-human transmission and different life stages of fish on Clonorchiasis: A novel mathematical model.","authors":"Wei Wang, Xiaohui Huang, Hao Wang","doi":"10.1016/j.mbs.2024.109209","DOIUrl":"10.1016/j.mbs.2024.109209","url":null,"abstract":"Clonorchiasis is a zoonotic disease mainly caused by eating raw fish and shrimp, and there is no vaccine to prevent it. More than 30 million people are infected worldwide, of which China alone accounts for about half, and is one of the countries most seriously affected by Clonorchiasis. In this work, we formulate a novel Ordinary Differential Equation (ODE) model to discuss the biological attributes of fish within authentic ecosystems and the complex lifecycle of Clonorchis sinensis. This model includes larval fish, adult fish, infected fish, humans, and cercariae. We derive the basic reproduction number and perform a rigorous stability analysis of the proposed model. Numerically, we use data from 2016 to 2021 in Guangxi, China, to discuss outbreaks of Clonorchiasis and obtain the basic reproduction number R0=1.4764. The fitted curve appropriately reflects the overall trend and replicates a low peak in the case number of Clonorchiasis. By reducing the release rate of cercariae in 2018, the fitted values of Clonorchiasis cases dropped rapidly and almost disappeared. If we decrease the transmission rate from infected fish to humans, Clonorchiasis can be controlled. Our studies also suggest that strengthening publicity education and cleaning water quality can effectively control the transmission of Clonorchiasis in Guangxi, China.","PeriodicalId":94129,"journal":{"name":"Mathematical biosciences","volume":" ","pages":"109209"},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140961248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mathematical modeling of brain metastases growth and response to therapies: A review. 脑转移瘤生长和对疗法反应的数学建模：综述。

Mathematical biosciences Pub Date : 2024-05-15 DOI: 10.1016/j.mbs.2024.109207

B. Ocaña-Tienda, Víctor M. Pérez-García

引用次数: 0