首页 > 最新文献

Biosystems最新文献

英文 中文
Light-induced ATP production and proton translocation, two independent phenomena in Halobacterium salinarum archaea cells 光诱导三磷酸腺苷产生和质子易位,两个独立的现象在盐盐菌古细菌细胞
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-25 DOI: 10.1016/j.biosystems.2025.105633
Gabi Drochioiu
Bacteriorhodopsin (BR) is involved in the process of light-induced release of ATP molecules from F1F0-ATP synthase in the simplest bacterial cells. We have identified the M412 intermediate of BR to be a key for understanding the phenomena related to ATP production in Halobacterium salinarum cells. In addition, the release of protons and, consequently, the increase in BR acidity upon illumination can be explained by its fluorescence, and the Förster cycle allows the calculation of pKa changes. The light-induced excitation of electrons in unprotonated M412 intermediate can serve as an energy source and not protons. To reinforce our conclusions, we reexamined data from recent literature as well as older findings.
在最简单的细菌细胞中,细菌视紫红质(BR)参与光诱导ATP分子从F1F0-ATP合成酶释放的过程。我们已经确定BR的M412中间体是理解盐盐杆菌细胞中ATP产生相关现象的关键。此外,质子的释放以及BR在光照下酸度的增加可以用其荧光来解释,并且Förster循环允许计算pKa的变化。在未质子化的M412中间体中,光诱导激发的电子可以作为能量源,而不是质子。为了加强我们的结论,我们重新检查了最近文献中的数据以及以前的发现。
{"title":"Light-induced ATP production and proton translocation, two independent phenomena in Halobacterium salinarum archaea cells","authors":"Gabi Drochioiu","doi":"10.1016/j.biosystems.2025.105633","DOIUrl":"10.1016/j.biosystems.2025.105633","url":null,"abstract":"<div><div>Bacteriorhodopsin (BR) is involved in the process of light-induced release of ATP molecules from F<sub>1</sub>F<sub>0</sub>-ATP synthase in the simplest bacterial cells. We have identified the M<sub>412</sub> intermediate of BR to be a key for understanding the phenomena related to ATP production in <em>Halobacterium salinarum</em> cells. In addition, the release of protons and, consequently, the increase in BR acidity upon illumination can be explained by its fluorescence, and the Förster cycle allows the calculation of pKa changes. The light-induced excitation of electrons in unprotonated M<sub>412</sub> intermediate can serve as an energy source and not protons. To reinforce our conclusions, we reexamined data from recent literature as well as older findings.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105633"},"PeriodicalIF":1.9,"publicationDate":"2025-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An energy landscape-based theoretical framework for understanding the self-organization of functions in a living system under the dynamical component interaction 一个基于能量景观的理论框架,用于理解动态成分相互作用下生命系统中功能的自组织。
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-24 DOI: 10.1016/j.biosystems.2025.105631
Ryunosuke Suzuki , Taiji Adachi
In a living system composed of interacting components such as molecules, cells, and tissues, each component often changes its internal states in response to interactions with its surrounding components. For example, individual tissues exhibit component-level responsive behavior, such as growth and remodeling, in response to their mechanical interactions, resulting in the self-organization of functions of a multi-tissue system. Along with the responsive behavior of the components, their interactions exhibit dynamical changes, which strongly influence the self-organization of system functions. To understand how the self-organization of system functions occurs from such dynamical interactions due to component-level responsive behavior, this study proposes a theoretical framework that formulates the dynamics of interactions among components due to the component-level responsive behavior. For modeling the responsive internal state changes, we assign an energy landscape and its associated energy rate landscape for each component, leading to the generalized gradient flow model of responsive behavior. Then, we represent interaction dynamics based on temporal changes in these energy and energy rate landscapes by formulating temporal changes in the environmental states of each component due to the responsive behavior of individual components. Through case studies using simplified models of mechanically interacting tissues under morphological changes, our theoretical framework demonstrates that temporal changes in applied forces due to morphological changes of individual tissues determine the self-organization of system functions. These findings highlight that expressing interaction dynamics based on temporal changes in energy and energy rate landscapes offers a powerful theoretical framework for understanding how component-level responsive behavior organizes system functions.
在由分子、细胞和组织等相互作用的成分组成的生命系统中,每个成分经常改变其内部状态,以响应其周围成分的相互作用。例如,个体组织表现出组件级的响应行为,如生长和重塑,以响应它们的机械相互作用,导致多组织系统功能的自组织。随着组件的响应行为,它们之间的相互作用表现出动态变化,这强烈影响系统功能的自组织。为了理解系统功能的自组织是如何从组件级响应行为的动态交互中发生的,本研究提出了一个理论框架,该框架阐述了组件级响应行为导致的组件之间交互的动力学。为了对响应性内部状态变化进行建模,我们为每个组件分配了一个能量景观及其相关的能量率景观,从而得到响应行为的广义梯度流模型。然后,我们根据这些能量和能量率景观的时间变化,通过表述由于单个组件的响应行为而导致的每个组件的环境状态的时间变化来表示相互作用动态。通过使用形态变化下机械相互作用组织的简化模型进行案例研究,我们的理论框架表明,单个组织形态变化引起的施加力的时间变化决定了系统功能的自组织。这些发现强调,基于能量和能量率景观的时间变化来表达交互动力学,为理解组件级响应行为如何组织系统功能提供了一个强大的理论框架。
{"title":"An energy landscape-based theoretical framework for understanding the self-organization of functions in a living system under the dynamical component interaction","authors":"Ryunosuke Suzuki ,&nbsp;Taiji Adachi","doi":"10.1016/j.biosystems.2025.105631","DOIUrl":"10.1016/j.biosystems.2025.105631","url":null,"abstract":"<div><div>In a living system composed of interacting components such as molecules, cells, and tissues, each component often changes its internal states in response to interactions with its surrounding components. For example, individual tissues exhibit component-level responsive behavior, such as growth and remodeling, in response to their mechanical interactions, resulting in the self-organization of functions of a multi-tissue system. Along with the responsive behavior of the components, their interactions exhibit dynamical changes, which strongly influence the self-organization of system functions. To understand how the self-organization of system functions occurs from such dynamical interactions due to component-level responsive behavior, this study proposes a theoretical framework that formulates the dynamics of interactions among components due to the component-level responsive behavior. For modeling the responsive internal state changes, we assign an energy landscape and its associated energy rate landscape for each component, leading to the generalized gradient flow model of responsive behavior. Then, we represent interaction dynamics based on temporal changes in these energy and energy rate landscapes by formulating temporal changes in the environmental states of each component due to the responsive behavior of individual components. Through case studies using simplified models of mechanically interacting tissues under morphological changes, our theoretical framework demonstrates that temporal changes in applied forces due to morphological changes of individual tissues determine the self-organization of system functions. These findings highlight that expressing interaction dynamics based on temporal changes in energy and energy rate landscapes offers a powerful theoretical framework for understanding how component-level responsive behavior organizes system functions.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105631"},"PeriodicalIF":1.9,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145370392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cooperation in structured populations via coupled reputation and learning: A spatial evolutionary game approach 基于声誉和学习的结构化群体合作:空间进化博弈方法
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-22 DOI: 10.1016/j.biosystems.2025.105630
Shouwei Li , Bo Peng , Baochen Li , Yan Shi
This study presents an agent-based model to investigate cooperation dynamics in spatial evolutionary games by integrating memory-based reputation tracking with heterogeneous adaptive learning. Agents interact on a lattice network and update their strategies based on both neighbors’ historical cooperation rates and payoff differences, governed by a modified Fermi rule with individual sensitivity parameters. Simulation results demonstrate that this dual-layered mechanism sustains cooperation even under strong defection incentives and limited interaction ranges. The model also reveals how memory length and learning heterogeneity jointly influence spatial cooperation patterns and strategy diversity. These findings offer new insights into decentralized mechanisms that promote cooperation in structured populations, with implications for evolutionary biology, distributed systems, and behavioral economics.
本研究将基于记忆的声誉跟踪与异质自适应学习相结合,提出了一种基于智能体的空间进化博弈合作动力学模型。智能体在晶格网络上相互作用,并根据邻居的历史合作率和收益差异更新策略,由具有个体敏感性参数的修改费米规则控制。仿真结果表明,即使在强背叛激励和有限互动范围下,该双层机制仍能维持合作。该模型还揭示了记忆长度和学习异质性如何共同影响空间合作模式和策略多样性。这些发现为促进结构化群体合作的分散机制提供了新的见解,并对进化生物学、分布式系统和行为经济学产生了影响。
{"title":"Cooperation in structured populations via coupled reputation and learning: A spatial evolutionary game approach","authors":"Shouwei Li ,&nbsp;Bo Peng ,&nbsp;Baochen Li ,&nbsp;Yan Shi","doi":"10.1016/j.biosystems.2025.105630","DOIUrl":"10.1016/j.biosystems.2025.105630","url":null,"abstract":"<div><div>This study presents an agent-based model to investigate cooperation dynamics in spatial evolutionary games by integrating memory-based reputation tracking with heterogeneous adaptive learning. Agents interact on a lattice network and update their strategies based on both neighbors’ historical cooperation rates and payoff differences, governed by a modified Fermi rule with individual sensitivity parameters. Simulation results demonstrate that this dual-layered mechanism sustains cooperation even under strong defection incentives and limited interaction ranges. The model also reveals how memory length and learning heterogeneity jointly influence spatial cooperation patterns and strategy diversity. These findings offer new insights into decentralized mechanisms that promote cooperation in structured populations, with implications for evolutionary biology, distributed systems, and behavioral economics.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105630"},"PeriodicalIF":1.9,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145365332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spectral bounds for Sombor and Sombor energy indices: A graph-theoretic study of neurotransmitter molecular networks Sombor和Sombor能量指数的谱界:神经递质分子网络的图论研究。
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-16 DOI: 10.1016/j.biosystems.2025.105620
Nalini Devi K. , Srinivasa G.
This paper applies the recently introduced Sombor index and its spectral extension, the Sombor energy, to model and analyze the structural complexity of neurotransmitter molecular graphs. Let G denote a molecular graph whose vertices and edges correspond to atoms and covalent bonds, respectively. For each G, we compute SO(G) and SOE(G), and derive degree-based, spectral-radius, and Frobenius-norm bounds to quantify molecular irregularity. Unlike traditional indices such as Zagreb or Wiener, Sombor descriptors incorporate both degree heterogeneity and geometric weighting, offering refined sensitivity to branching and aromaticity. Comparative analysis across inhibitory (glycine, GABA) and excitatory or modulatory (dopamine, serotonin, norepinephrine) neurotransmitters reveals that higher Sombor measures correspond to greater structural and functional complexity. These results confirm that Sombor-based descriptors capture biologically interpretable differences in molecular organization. The study thereby extends spectral graph theory to neurochemical systems, providing a quantitative framework for cheminformatics, drug design, and functional classification of neurotransmitters.
本文应用近年来引入的Sombor指数及其谱扩展Sombor能量来模拟和分析神经递质分子图的结构复杂性。设G表示一个分子图,其顶点和边分别对应于原子和共价键。对于每个G,我们计算SO(G)和SOE(G),并推导基于度的、光谱半径和frobenius -范数界限,以量化分子的不规则性。与传统的指数如Zagreb或Wiener不同,Sombor描述符结合了程度异质性和几何加权,提供了对分支和芳香性的精细敏感性。抑制性神经递质(甘氨酸、GABA)和兴奋性或调节性神经递质(多巴胺、血清素、去甲肾上腺素)的对比分析表明,Sombor水平越高,结构和功能的复杂性越高。这些结果证实,基于sombor的描述符捕获了分子组织中生物学上可解释的差异。因此,该研究将谱图理论扩展到神经化学系统,为化学信息学、药物设计和神经递质功能分类提供了定量框架。
{"title":"Spectral bounds for Sombor and Sombor energy indices: A graph-theoretic study of neurotransmitter molecular networks","authors":"Nalini Devi K. ,&nbsp;Srinivasa G.","doi":"10.1016/j.biosystems.2025.105620","DOIUrl":"10.1016/j.biosystems.2025.105620","url":null,"abstract":"<div><div>This paper applies the recently introduced Sombor index and its spectral extension, the Sombor energy, to model and analyze the structural complexity of neurotransmitter molecular graphs. Let <span><math><mi>G</mi></math></span> denote a molecular graph whose vertices and edges correspond to atoms and covalent bonds, respectively. For each <span><math><mi>G</mi></math></span>, we compute <span><math><mrow><mi>S</mi><mi>O</mi><mrow><mo>(</mo><mi>G</mi><mo>)</mo></mrow></mrow></math></span> and <span><math><mrow><mi>S</mi><mi>O</mi><mi>E</mi><mrow><mo>(</mo><mi>G</mi><mo>)</mo></mrow></mrow></math></span>, and derive degree-based, spectral-radius, and Frobenius-norm bounds to quantify molecular irregularity. Unlike traditional indices such as Zagreb or Wiener, Sombor descriptors incorporate both degree heterogeneity and geometric weighting, offering refined sensitivity to branching and aromaticity. Comparative analysis across inhibitory (glycine, GABA) and excitatory or modulatory (dopamine, serotonin, norepinephrine) neurotransmitters reveals that higher Sombor measures correspond to greater structural and functional complexity. These results confirm that Sombor-based descriptors capture biologically interpretable differences in molecular organization. The study thereby extends spectral graph theory to neurochemical systems, providing a quantitative framework for cheminformatics, drug design, and functional classification of neurotransmitters.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105620"},"PeriodicalIF":1.9,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
When Maxwell’s Demon leaves the room 麦克斯韦的恶魔离开房间的时候。
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-14 DOI: 10.1016/j.biosystems.2025.105618
P.G. Tello , S. Kauffman
This work revisits the Maxwell Demon paradigm to explore its implications for evolutionary dynamics from an information-theoretic perspective. By removing the Demon as an intentional agent, we reinterpret the emergence of order as a natural outcome of physical laws combined with stochastic processes. Using models inspired by information theory, such as binary and Z-channels, we show how random fluctuations (e.g., stochastic resonance) can decrease entropy, generate mutual information, and induce non-ergodicity. These dynamics highlight the role of memory and correlation as emergent features of purely physical interactions without recourse to purposeful agency. In this framework, evolutionary exaptations, rather than sole adaptations, emerge as key drivers of biological evolution. Finally, we connect our analysis with recent contributions on agency and memory, underscoring the relevance of informational concepts for understanding the purposeless yet structured dynamics of evolutionary processes.
这项工作重新审视了麦克斯韦妖范式,从信息论的角度探索其对进化动力学的影响。通过移除恶魔作为一个有意的代理人,我们将秩序的出现重新解释为物理定律与随机过程相结合的自然结果。使用受信息论启发的模型,如二进制和z通道,我们展示了随机波动(例如随机共振)如何减少熵,产生互信息,并诱导非遍历性。这些动态强调了记忆和关联作为纯粹物理交互的紧急特征的作用,而不依赖于有目的的代理。在这个框架中,进化的期望,而不是单一的适应,成为生物进化的关键驱动力。最后,我们将我们的分析与最近对代理和记忆的贡献联系起来,强调信息概念与理解进化过程中无目的但结构化的动态的相关性。
{"title":"When Maxwell’s Demon leaves the room","authors":"P.G. Tello ,&nbsp;S. Kauffman","doi":"10.1016/j.biosystems.2025.105618","DOIUrl":"10.1016/j.biosystems.2025.105618","url":null,"abstract":"<div><div>This work revisits the Maxwell Demon paradigm to explore its implications for evolutionary dynamics from an information-theoretic perspective. By removing the Demon as an intentional agent, we reinterpret the emergence of order as a natural outcome of physical laws combined with stochastic processes. Using models inspired by information theory, such as binary and Z-channels, we show how random fluctuations (e.g., stochastic resonance) can decrease entropy, generate mutual information, and induce non-ergodicity. These dynamics highlight the role of memory and correlation as emergent features of purely physical interactions without recourse to purposeful agency. In this framework, evolutionary exaptations, rather than sole adaptations, emerge as key drivers of biological evolution. Finally, we connect our analysis with recent contributions on agency and memory, underscoring the relevance of informational concepts for understanding the purposeless yet structured dynamics of evolutionary processes.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105618"},"PeriodicalIF":1.9,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145309894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The threat of asymptomatic carriers and the benefits of testing 无症状感染者的威胁和检测的好处。
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-13 DOI: 10.1016/j.biosystems.2025.105615
Luca Zamboni
I present a model of infectious disease transmission with asymptomatic carriers, social distancing, and diagnostic testing. First, I study the impact of asymptomatic carriers on the spread of an infectious disease in the absence of testing, to determine when their presence increases the overall prevalence of symptomatic infection and hence unhealthy agents. Then, I consider mass testing and isolation policies to identify and isolate asymptomatic carriers, and incorporate them into my model. I establish that diagnostic testing successfully reduces steady state disease prevalence. I then explore the implications of testing accuracy, explicitly studying the impact of false positive and false negative test results. I find that reducing the rate of false negatives is unambiguously beneficial, since it improves the identification and isolation of asymptomatic carriers. In contrast, reducing the rate of false positives can be detrimental: by limiting the unintended isolation of susceptible individuals, lower rates of false positives reduce the overall level of social distancing in the population and increase disease spread. Hence, I demonstrate how, under certain conditions, false positive results can improve social welfare.
我提出了一个无症状携带者、社会距离和诊断测试的传染病传播模型。首先,我研究了在没有检测的情况下,无症状携带者对传染病传播的影响,以确定他们的存在何时会增加有症状感染的总体患病率,从而增加不健康病原体。然后,我考虑大规模检测和隔离策略,以识别和隔离无症状携带者,并将其纳入我的模型。我确定诊断测试成功地降低了稳态疾病的患病率。然后探讨测试准确性的含义,明确研究假阳性和假阴性测试结果的影响。我发现,降低假阴性率无疑是有益的,因为它提高了对无症状携带者的识别和隔离。相比之下,降低假阳性率可能是有害的:通过限制对易感个体的意外隔离,较低的假阳性率降低了人群中社会距离的总体水平,并增加了疾病传播。因此,我证明了在某些条件下,假阳性结果如何能改善社会福利。
{"title":"The threat of asymptomatic carriers and the benefits of testing","authors":"Luca Zamboni","doi":"10.1016/j.biosystems.2025.105615","DOIUrl":"10.1016/j.biosystems.2025.105615","url":null,"abstract":"<div><div>I present a model of infectious disease transmission with asymptomatic carriers, social distancing, and diagnostic testing. First, I study the impact of asymptomatic carriers on the spread of an infectious disease in the absence of testing, to determine when their presence increases the overall prevalence of symptomatic infection and hence unhealthy agents. Then, I consider mass testing and isolation policies to identify and isolate asymptomatic carriers, and incorporate them into my model. I establish that diagnostic testing successfully reduces steady state disease prevalence. I then explore the implications of testing accuracy, explicitly studying the impact of false positive and false negative test results. I find that reducing the rate of false negatives is unambiguously beneficial, since it improves the identification and isolation of asymptomatic carriers. In contrast, reducing the rate of false positives can be detrimental: by limiting the unintended isolation of susceptible individuals, lower rates of false positives reduce the overall level of social distancing in the population and increase disease spread. Hence, I demonstrate how, under certain conditions, false positive results can improve social welfare.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105615"},"PeriodicalIF":1.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145304079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Information and the living tree of life: A theory of measurement grounded in biology 信息与生命之树一种以生物学为基础的测量理论。
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-11 DOI: 10.1016/j.biosystems.2025.105610
Kevin Hudnall
We extend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall and D’Souza, 2025). That work showed that time itself is multifractal – not a universal background dimension, but an observer-dependent geometry. Here we develop the corresponding theory of measurement: showing that a multifractal conception of time not only permend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall and D’Souza, 2025). That work showed that time itself is multifractal – not a universal background dimension, but an observer-dependent geometry. Here we develop the corresponding theory of measurement: showing that a multifractal conception of time not only permits measurement, but grounds it more rigorously in the structure of biology. The tree of life is modeled as the outcome of stochastic, convex branching, and we show how information-theoretic and fractal measures render its multifractal geometry into measurable, observer-relative time intervals. At the core is a dilation equation that expresses relative time elapse between entities as dimensionless ratios. Operational standards such as the SI second remain valid, but our framework makes explicit their lineage-dependence. This framework unifies measurement theory with biological form, preserves full compatibility with established science, and provides a biologically grounded theory of observation. It enables comparative analyses of duration and kinematics across lineages, with predictions that are directly open to experimental validation.
我们扩展了以前从生物谱系的多重分形结构中导出时间的正式框架(Hudnall & D'Souza, 2025)。这项工作表明,时间本身是多重分形的——不是一个普遍的背景维度,而是一个依赖于观察者的几何形状。在这里,我们发展了相应的测量理论:表明时间的多重分形概念不仅允许测量,而且更严格地以生物学结构为基础。生命之树被建模为随机凸分支的结果,我们展示了信息理论和分形测量如何将其多重分形几何呈现为可测量的,观察者相对的时间间隔。其核心是一个膨胀方程,它将实体之间的相对时间间隔表示为无因次比率。像SI second这样的操作标准仍然有效,但是我们的框架明确了它们的谱系依赖性。这一框架将测量理论与生物形式统一起来,保持了与已建立的科学的完全兼容性,并提供了一种基于生物学的观察理论。它可以对不同谱系的持续时间和运动学进行比较分析,并直接对实验验证进行预测。
{"title":"Information and the living tree of life: A theory of measurement grounded in biology","authors":"Kevin Hudnall","doi":"10.1016/j.biosystems.2025.105610","DOIUrl":"10.1016/j.biosystems.2025.105610","url":null,"abstract":"<div><div>We extend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall and D’Souza, 2025). That work showed that time itself is multifractal – not a universal background dimension, but an observer-dependent geometry. Here we develop the corresponding theory of measurement: showing that a multifractal conception of time not only permend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall and D’Souza, 2025). That work showed that time itself is multifractal – not a universal background dimension, but an observer-dependent geometry. Here we develop the corresponding theory of measurement: showing that a multifractal conception of time not only permits measurement, but grounds it more rigorously in the structure of biology. The tree of life is modeled as the outcome of stochastic, convex branching, and we show how information-theoretic and fractal measures render its multifractal geometry into measurable, observer-relative time intervals. At the core is a dilation equation that expresses relative time elapse between entities as dimensionless ratios. Operational standards such as the SI second remain valid, but our framework makes explicit their lineage-dependence. This framework unifies measurement theory with biological form, preserves full compatibility with established science, and provides a biologically grounded theory of observation. It enables comparative analyses of duration and kinematics across lineages, with predictions that are directly open to experimental validation.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105610"},"PeriodicalIF":1.9,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The limits of falsifiability: Dimensionality, measurement thresholds, and the sub-Landauer domain in biological systems 可证伪性的极限:维度、测量阈值和生物系统中的亚朗道尔域。
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-11 DOI: 10.1016/j.biosystems.2025.105608
Ian Todd
Karl Popper’s falsifiability criterion assumes that scientific hypotheses can be reduced to binary tests. We show this assumption is scale-dependent and can saturate in high-dimensional biological systems operating near physical measurement limits, especially near criticality. In neural networks, much relevant information exists as patterns below the Landauer threshold for irreversible bit recording—signals too weak for individual neurons to detect but detectable when pooled across populations. These sub-threshold patterns cannot be projected into binary outcomes without destroying their causal structure. We develop a framework connecting dimensionality, thermodynamic measurement limits, and biological epistemology, showing that Popperian logic represents a special case applicable only to low-dimensional systems with strong signals. Our analysis has implications for neuroscience, where aspects of conscious processing may in part depend on sub-threshold coherence patterns that resist binary measurement, motivating a shift from single-case hypothesis tests to multi-scale, ensemble-based inference. The framework extends to other complex biological systems including ecological networks, protein folding dynamics, and evolutionary processes where causal relationships exist as irreducible multi-dimensional structures operating below classical measurement thresholds.
卡尔·波普尔的可证伪性准则假定科学假设可以简化为二元检验。我们表明这种假设是尺度相关的,并且可以在接近物理测量极限的高维生物系统中饱和,特别是接近临界。在神经网络中,许多相关信息以低于不可逆比特记录的兰道尔阈值的模式存在,这些信号对于单个神经元来说太弱而无法检测到,但当它们汇集在一起时却可以检测到。这些亚阈值模式不能在不破坏其因果结构的情况下投射到二元结果中。我们开发了一个连接维度、热力学测量极限和生物认识论的框架,表明波普尔逻辑代表一种特殊情况,仅适用于具有强信号的低维系统。我们的分析对神经科学具有启示意义,在神经科学中,意识处理的各个方面可能部分依赖于抵制二元测量的亚阈值相干模式,从而促使从单例假设检验转向多尺度、基于集合的推理。该框架扩展到其他复杂的生物系统,包括生态网络、蛋白质折叠动力学和进化过程,其中因果关系作为不可约的多维结构存在,运行在经典的测量阈值以下。
{"title":"The limits of falsifiability: Dimensionality, measurement thresholds, and the sub-Landauer domain in biological systems","authors":"Ian Todd","doi":"10.1016/j.biosystems.2025.105608","DOIUrl":"10.1016/j.biosystems.2025.105608","url":null,"abstract":"<div><div>Karl Popper’s falsifiability criterion assumes that scientific hypotheses can be reduced to binary tests. We show this assumption is <em>scale-dependent</em> and can <em>saturate</em> in high-dimensional biological systems operating near physical measurement limits, especially near criticality. In neural networks, much relevant information exists as patterns below the Landauer threshold for irreversible bit recording—signals too weak for individual neurons to detect but detectable when pooled across populations. These sub-threshold patterns cannot be projected into binary outcomes without destroying their causal structure. We develop a framework connecting dimensionality, thermodynamic measurement limits, and biological epistemology, showing that Popperian logic represents a special case applicable only to low-dimensional systems with strong signals. Our analysis has implications for neuroscience, where aspects of conscious processing may in part depend on sub-threshold coherence patterns that resist binary measurement, motivating a shift from single-case hypothesis tests to multi-scale, ensemble-based inference. The framework extends to other complex biological systems including ecological networks, protein folding dynamics, and evolutionary processes where causal relationships exist as irreducible multi-dimensional structures operating below classical measurement thresholds.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105608"},"PeriodicalIF":1.9,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Antagonistic coinfection in rock–paper–scissors models during concurrent epidemics 同时流行期间石头剪刀布模型的拮抗共感染
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-11 DOI: 10.1016/j.biosystems.2025.105616
J. Menezes , R. Menezes , S. Batista , E. Rangel
We investigate the dynamics of dual disease epidemics within the spatial rock–paper–scissors model. In this framework, individuals from all species are equally susceptible to infection by two distinct pathogens transmitted via person-to-person contact. We assume antagonistic mortality, where the simultaneous occurrence of coinfection reduces the probability of host mortality due to complications arising from either coexisting disease. Specifically, we explore two scenarios: global antagonism, where the presence of one pathogen inhibits the progression of the other in coinfected hosts, and uneven antagonism, where only one pathogen affects the development of the other. Using stochastic simulations, we show that the characteristic length scale of the spatial patterns emerging from random initial conditions diminishes as antagonism becomes more significant. We find that antagonism enhances species population growth and reduces the average probability of healthy organisms becoming infected. Additionally, introducing individuals’ mobility restrictions significantly decreases both organisms’ infection risk and selection pressures. Our results demonstrate that combining mobility restrictions with antagonistic coinfection can increase organisms’ life expectancy by up to 54%. Our findings show that integrating antagonistic coinfection and mobility restriction strategies into ecological models may provide insights into designing interventions for managing concurrent epidemics in complex systems.
我们在空间石头剪刀布模型中研究了双重疾病流行的动力学。在这一框架下,所有物种的个体都同样容易受到通过人与人接触传播的两种不同病原体的感染。我们假设拮抗性死亡,其中同时发生的共感染降低了因共存疾病引起的并发症而导致宿主死亡的可能性。具体来说,我们探讨了两种情况:全球拮抗,其中一种病原体的存在抑制了共同感染宿主中另一种病原体的进展,以及不均匀拮抗,其中只有一种病原体影响另一种病原体的发展。通过随机模拟,我们发现从随机初始条件中出现的空间模式的特征长度尺度随着拮抗变得更加显著而减小。我们发现拮抗作用促进了物种种群的增长,降低了健康生物体被感染的平均概率。此外,引入个体的流动性限制显著降低了生物的感染风险和选择压力。我们的研究结果表明,将移动性限制与拮抗共感染相结合可以使生物体的预期寿命延长高达54%。我们的研究结果表明,将拮抗共感染和流动性限制策略整合到生态模型中,可能为设计干预措施以管理复杂系统中的并发流行病提供见解。
{"title":"Antagonistic coinfection in rock–paper–scissors models during concurrent epidemics","authors":"J. Menezes ,&nbsp;R. Menezes ,&nbsp;S. Batista ,&nbsp;E. Rangel","doi":"10.1016/j.biosystems.2025.105616","DOIUrl":"10.1016/j.biosystems.2025.105616","url":null,"abstract":"<div><div>We investigate the dynamics of dual disease epidemics within the spatial rock–paper–scissors model. In this framework, individuals from all species are equally susceptible to infection by two distinct pathogens transmitted via person-to-person contact. We assume antagonistic mortality, where the simultaneous occurrence of coinfection reduces the probability of host mortality due to complications arising from either coexisting disease. Specifically, we explore two scenarios: global antagonism, where the presence of one pathogen inhibits the progression of the other in coinfected hosts, and uneven antagonism, where only one pathogen affects the development of the other. Using stochastic simulations, we show that the characteristic length scale of the spatial patterns emerging from random initial conditions diminishes as antagonism becomes more significant. We find that antagonism enhances species population growth and reduces the average probability of healthy organisms becoming infected. Additionally, introducing individuals’ mobility restrictions significantly decreases both organisms’ infection risk and selection pressures. Our results demonstrate that combining mobility restrictions with antagonistic coinfection can increase organisms’ life expectancy by up to 54%. Our findings show that integrating antagonistic coinfection and mobility restriction strategies into ecological models may provide insights into designing interventions for managing concurrent epidemics in complex systems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105616"},"PeriodicalIF":1.9,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A hybrid phase-synchronization framework for rotary motors: Discrete dynamics in ATP synthase and continuous dynamics in the bacterial flagellar motor 旋转马达的混合相位同步框架:ATP合酶的离散动力学和细菌鞭毛马达的连续动力学。
IF 1.9 4区 生物学 Q2 BIOLOGY Pub Date : 2025-10-11 DOI: 10.1016/j.biosystems.2025.105617
Carey Witkov
ATP synthase functions as a dual-rotor molecular motor, with the F0 and F1 units stepping in mismatched increments, yet achieving near 100% chemomechanical efficiency of the F1 motor under near-reversible conditions. This raises the question of how stable phase synchronization is maintained despite such symmetry mismatch. We address this problem by modeling ATP synthase as a driven oscillator system in which the central elastic stalk acts as a torsional filter, transmitting and modulating torque. We propose a hybrid synchronization model that integrates continuous and discrete dynamics, governed by a torsional energy-dependent mixing parameter that determines interpolation between limits. The resulting single hybrid phase synchronization equation captures both gradual continuous phase drift and discrete pulsed entrainment. This framework reproduces key experimental features, including stable synchronization, intermittent slip events in ATP synthase, and recovery dynamics under varying loads, and offers testable predictions. In the discrete limit, the model specializes to a van Slooten-type pulse map that accords with the well-established 120° stepping of F1-ATPase; in the continuous limit, it reduces to an Adler-type equation appropriate for the near-constant-torque behavior of the bacterial flagellar motor. This framing unifies two historically separate descriptions without requiring a literal mode change within a single molecule and clarifies how elastic energy can interpolate between limits via the mixing parameter σ(E). The hybrid model proposes that ATP synthase and the bacterial flagellar motor exploit elastic filtering and energy-regulated regime interpolation between limits to achieve robust rotational coordination, providing new insights into the dynamics of biological rotary motors.
ATP合酶的功能就像一个双转子分子马达,F0和F1亚基以不匹配的增量步进,但却能达到接近100%的效率。这就提出了一个问题,即在这种对称性不匹配的情况下,如何保持稳定的相位同步。我们通过将ATP合酶建模为驱动振荡器系统来解决这个问题,其中中心弹性杆充当扭转过滤器,传输和调制扭矩。我们提出了一个混合同步模型,它集成了连续和离散动力学,由一个依赖于扭转能量的混合参数控制,该参数决定了极限之间的插值。由此产生的单一混合相位同步方程既捕获渐进的连续相位漂移,又捕获离散脉冲夹带。该框架再现了关键的实验特征,包括稳定的同步、相滑移和不同负载下的恢复动态,并提供了可测试的预测。结果表明,ATP合酶利用弹性过滤和极限之间的能量调节状态插值来实现鲁棒旋转协调,为生物旋转马达的动力学提供了新的见解。在混合的离散极限下,该模型专为Van sloten型脉冲图,该脉冲图符合已建立的f1 - atp酶的120°步进;在连续极限下,它简化为适合于细菌鞭毛马达的近恒定扭矩行为的阿德勒型方程。这种框架统一了两种历史上分开的描述,而不需要在单个分子内进行字面模式变化,并阐明了弹性能如何通过混合参数σ(E)在极限之间插入。
{"title":"A hybrid phase-synchronization framework for rotary motors: Discrete dynamics in ATP synthase and continuous dynamics in the bacterial flagellar motor","authors":"Carey Witkov","doi":"10.1016/j.biosystems.2025.105617","DOIUrl":"10.1016/j.biosystems.2025.105617","url":null,"abstract":"<div><div>ATP synthase functions as a dual-rotor molecular motor, with the F<span><math><msub><mrow></mrow><mrow><mn>0</mn></mrow></msub></math></span> and F<span><math><msub><mrow></mrow><mrow><mn>1</mn></mrow></msub></math></span> units stepping in mismatched increments, yet achieving near 100% chemomechanical efficiency of the F<span><math><msub><mrow></mrow><mrow><mn>1</mn></mrow></msub></math></span> motor under near-reversible conditions. This raises the question of how stable phase synchronization is maintained despite such symmetry mismatch. We address this problem by modeling ATP synthase as a driven oscillator system in which the central elastic stalk acts as a torsional filter, transmitting and modulating torque. We propose a hybrid synchronization model that integrates continuous and discrete dynamics, governed by a torsional energy-dependent mixing parameter that determines interpolation between limits. The resulting single hybrid phase synchronization equation captures both gradual continuous phase drift and discrete pulsed entrainment. This framework reproduces key experimental features, including stable synchronization, intermittent slip events in ATP synthase, and recovery dynamics under varying loads, and offers testable predictions. In the discrete limit, the model specializes to a van Slooten-type pulse map that accords with the well-established 120° stepping of F<span><math><msub><mrow></mrow><mrow><mn>1</mn></mrow></msub></math></span>-ATPase; in the continuous limit, it reduces to an Adler-type equation appropriate for the near-constant-torque behavior of the bacterial flagellar motor. This framing unifies two historically separate descriptions without requiring a literal mode change within a single molecule and clarifies how elastic energy can interpolate between limits via the mixing parameter <span><math><mrow><mi>σ</mi><mrow><mo>(</mo><mi>E</mi><mo>)</mo></mrow></mrow></math></span>. The hybrid model proposes that ATP synthase and the bacterial flagellar motor exploit elastic filtering and energy-regulated regime interpolation between limits to achieve robust rotational coordination, providing new insights into the dynamics of biological rotary motors.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105617"},"PeriodicalIF":1.9,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
Biosystems
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1