Journal of Mathematical Biology最新文献

Network transformation-based analysis of biochemical systems. 基于网络转换的生化系统分析。

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-11-08 DOI: 10.1007/s00285-024-02152-2

Dylan Antonio Talabis, Eduardo Mendoza

{"title":"Network transformation-based analysis of biochemical systems.","authors":"Dylan Antonio Talabis, Eduardo Mendoza","doi":"10.1007/s00285-024-02152-2","DOIUrl":"https://doi.org/10.1007/s00285-024-02152-2","url":null,"abstract":"A dynamical system obtains a wide variety of kinetic realizations, which is advantageous for the analysis of biochemical systems. A reaction network, derived from a dynamical system, may or may not possess some properties needed for a thorough analysis. We improve and extend the work of Johnston and Hong et al. on network translations to network transformations, where the network is modified while preserving the dynamical system. These transformations can shrink, extend, or retain the stoichiometric subspace. Here, we show that a positive dependent network can be translated to a weakly reversible network. Using the kinetic realizations of (1) calcium signaling in the olfactory system and (2) metabolic insulin signaling, we demonstrate the benefits of transformed systems with positive deficiency for analyzing biochemical systems. Furthermore, we present an algorithm for a network transformation of a weakly reversible non-complex factorizable kinetic (NFK) system to a weakly reversible complex factorizable kinetic (CFK) system, thereby enhancing the Subspace Coincidence Theorem for NFK systems of Nazareno et al. Finally, using the transformed kinetic realization of monolignol biosynthesis in Populus xylem, we study the structural and kinetic properties of transformed systems, including the invariance of concordance and variation of injectivity and mono-/multi-stationarity under network transformation.","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606880","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

Directional flow in perivascular networks: mixed finite elements for reduced-dimensional models on graphs. 血管周围网络中的定向流动：图上降维模型的混合有限元。

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-11-07 DOI: 10.1007/s00285-024-02154-0

Ingeborg G Gjerde, Miroslav Kuchta, Marie E Rognes, Barbara Wohlmuth

{"title":"Directional flow in perivascular networks: mixed finite elements for reduced-dimensional models on graphs.","authors":"Ingeborg G Gjerde, Miroslav Kuchta, Marie E Rognes, Barbara Wohlmuth","doi":"10.1007/s00285-024-02154-0","DOIUrl":"https://doi.org/10.1007/s00285-024-02154-0","url":null,"abstract":"Flow of cerebrospinal fluid through perivascular pathways in and around the brain may play a crucial role in brain metabolite clearance. While the driving forces of such flows remain enigmatic, experiments have shown that pulsatility is central. In this work, we present a novel network model for simulating pulsatile fluid flow in perivascular networks, taking the form of a system of Stokes-Brinkman equations posed over a perivascular graph. We apply this model to study physiological questions concerning the mechanisms governing perivascular fluid flow in branching vascular networks. Notably, our findings reveal that even long wavelength arterial pulsations can induce directional flow in asymmetric, branching perivascular networks. In addition, we establish fundamental mathematical and numerical properties of these Stokes-Brinkman network models, with particular attention to increasing graph order and complexity. By introducing weighted norms, we show the well-posedness and stability of primal and dual variational formulations of these equations, and that of mixed finite element discretizations.","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606867","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

Equilibria of large random Lotka-Volterra systems with vanishing species: a mathematical approach. 具有消失物种的大型随机 Lotka-Volterra 系统的均衡：一种数学方法。

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-11-07 DOI: 10.1007/s00285-024-02155-z

Imane Akjouj, Walid Hachem, Mylène Maïda, Jamal Najim

引用次数: 0

Application of the first exit time stochastic model with self-repair mechanism to human mortality rates. 将具有自我修复机制的第一出口时间随机模型应用于人类死亡率。

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-11-06 DOI: 10.1007/s00285-024-02150-4

Noriyuki Shimoyama, Masayasu Hosonuma

引用次数: 0

Cellular diffusion processes in singularly perturbed domains. 奇异扰动域中的细胞扩散过程

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-11-04 DOI: 10.1007/s00285-024-02160-2

Paul C Bressloff

{"title":"Cellular diffusion processes in singularly perturbed domains.","authors":"Paul C Bressloff","doi":"10.1007/s00285-024-02160-2","DOIUrl":"10.1007/s00285-024-02160-2","url":null,"abstract":"There are many processes in cell biology that can be modeled in terms of particles diffusing in a two-dimensional (2D) or three-dimensional (3D) bounded domain <math><mrow><mi>Ω</mi> <mo>⊂</mo> <msup><mrow><mi>R</mi></mrow> <mi>d</mi></msup> </mrow> </math> containing a set of small subdomains or interior compartments <math><msub><mi>U</mi> <mi>j</mi></msub> </math> , <math><mrow><mi>j</mi> <mo>=</mo> <mn>1</mn> <mo>,</mo> <mo>…</mo> <mo>,</mo> <mi>N</mi></mrow> </math> (singularly-perturbed diffusion problems). The domain <math><mi>Ω</mi></math> could represent the cell membrane, the cell cytoplasm, the cell nucleus or the extracellular volume, while an individual compartment could represent a synapse, a membrane protein cluster, a biological condensate, or a quorum sensing bacterial cell. In this review we use a combination of matched asymptotic analysis and Green's function methods to solve a general type of singular boundary value problems (BVP) in 2D and 3D, in which an inhomogeneous Robin condition is imposed on each interior boundary <math><mrow><mi>∂</mi> <msub><mi>U</mi> <mi>j</mi></msub> </mrow> </math> . This allows us to incorporate a variety of previous studies of singularly perturbed diffusion problems into a single mathematical modeling framework. We mainly focus on steady-state solutions and the approach to steady-state, but also highlight some of the current challenges in dealing with time-dependent solutions and randomly switching processes.","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576652","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

Stoichiometric theory in optimal foraging strategy. 最佳觅食策略中的定量理论

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-11-02 DOI: 10.1007/s00285-024-02158-w

Shohel Ahmed, Juping Ji, Hao Wang

引用次数: 0

Steady state distributions of moving particles in one dimension: with an eye towards axonal transport. 一维运动粒子的稳态分布：着眼于轴突运输。

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-10-30 DOI: 10.1007/s00285-024-02157-x

J C Dallon, Emily Evans, Christopher P Grant, Stephanie Portet

{"title":"Steady state distributions of moving particles in one dimension: with an eye towards axonal transport.","authors":"J C Dallon, Emily Evans, Christopher P Grant, Stephanie Portet","doi":"10.1007/s00285-024-02157-x","DOIUrl":"10.1007/s00285-024-02157-x","url":null,"abstract":"Axonal transport, propelled by motor proteins, plays a crucial role in maintaining the homeostasis of functional and structural components over time. To establish a steady-state distribution of moving particles, what conditions are necessary for axonal transport? This question is pertinent, for instance, to both neurofilaments and mitochondria, which are structural and functional cargoes of axonal transport. In this paper we prove four theorems regarding steady state distributions of moving particles in one dimension on a finite domain. Three of the theorems consider cases where particles approach a uniform distribution at large time. Two consider periodic boundary conditions and one considers reflecting boundary conditions. The other theorem considers reflecting boundary conditions where the velocity is space dependent. If the theoretical results hold in the complex setting of the cell, they would imply that the uniform distribution of neurofilaments observed under healthy conditions appears to require a continuous distribution of neurofilament velocities. Similarly, the spatial distribution of axonal mitochondria may be linked to spatially dependent transport velocities that remain invariant over time.","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142548659","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

Stochastic optimal control of pre-exposure prophylaxis for HIV infection for a jump model. 针对跳跃模型的艾滋病毒感染暴露前预防的随机优化控制。

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-10-29 DOI: 10.1007/s00285-024-02151-3

Jasmina Ɖorđević, Kristina Rognlien Dahl

引用次数: 0

Spatiotemporal dynamics in a fractional diffusive SIS epidemic model with mass action infection mechanism. 具有大规模行动感染机制的分数扩散 SIS 流行病模型的时空动力学。

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-10-24 DOI: 10.1007/s00285-024-02153-1

Peng Shi, Wan-Tong Li, Fei-Ying Yang

引用次数: 0

Correction: The effect of viscoelasticity of the tissue on the magneto-responsive drug delivery system. 更正：组织的粘弹性对磁响应给药系统的影响。

IF 2.2 4区数学

Journal of Mathematical Biology Pub Date : 2024-10-17 DOI: 10.1007/s00285-024-02128-2

Ebrahim Azhdari, Jahed Naghipoor

引用次数: 0