Biosystems最新文献_第6页

A Unified Holographic Framework for neural computation and consciousness: From lipid membranes to the Schumann resonance 神经计算和意识的统一全息框架：从脂质膜到舒曼共振。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-15 DOI: 10.1016/j.biosystems.2025.105669

Marco Cavaglià, Jack A. Tuszynski

引用次数: 0

Time-delayed intermittent oscillations and chaos in a transcriptional and post-transcriptional gene regulatory network for long-term memory 长期记忆的转录和转录后基因调控网络中的延时间歇性振荡和混沌

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-12 DOI: 10.1016/j.biosystems.2025.105655

Lijie Hao , Liao Yu , Zhuoqin Yang

{"title":"Time-delayed intermittent oscillations and chaos in a transcriptional and post-transcriptional gene regulatory network for long-term memory","authors":"Lijie Hao , Liao Yu , Zhuoqin Yang","doi":"10.1016/j.biosystems.2025.105655","DOIUrl":"10.1016/j.biosystems.2025.105655","url":null,"abstract":"<div><div>Noncoding RNAs play a crucial role in many biological processes ranging from gene expression regulation, genome defence to epigenetic inheritance. In this paper, a mathematical model with time delay is proposed to characterize gene regulation mediated by two small noncoding RNAs acting at transcriptional level and post-transcriptional level. Through bifurcation analysis of the model without time delay, complex dynamics such as monostability, bistability, excitability and oscillation are exhibited with changing parameters. Then, introducing the time delay in the monostable, bistable, excitable and oscillatory regions generates a variety of bifurcations, accompanied with intermittent oscillations, oscillations with discontinuously changing amplitudes and periods, and chaotic dynamics by quasi-periodic route or period-doubling cascade route. The abundant dynamical mechanism on bistable switches or oscillators accounts for many functional features of sncRNAs. As an application, the presented model can be used to qualitatively simulate experimental findings of long-term memory formation. The existence of bistability depending on appropriate time delay is critical for the sustained high state in the system, and the time delay may affect the number of repeated pulses of stimulation required for the establishment of long-term memory.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105655"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145521311","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

Natural born intelligence manifesto: Illustrating the dynamic perspective for consciousness 天生智慧宣言：阐释意识的动态视角。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-16 DOI: 10.1016/j.biosystems.2025.105677

Yukio-Pegio Gunji

引用次数: 0

Reframing neural decussation: A vision-based theory for contralateral control 重构神经对话：一个基于视觉的对侧控制理论。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-20 DOI: 10.1016/j.biosystems.2025.105683

Ghassan Ahmed Mubasher Mohamedsalih

{"title":"Reframing neural decussation: A vision-based theory for contralateral control","authors":"Ghassan Ahmed Mubasher Mohamedsalih","doi":"10.1016/j.biosystems.2025.105683","DOIUrl":"10.1016/j.biosystems.2025.105683","url":null,"abstract":"<div><div>Neural decussation, the systematic crossing of sensory and motor pathways at the midline, is one of the most prominent features of the vertebrate nervous system, yet its functional rationale has remained unresolved. This work proposes the Visual-Origin Theory of Neuronal Decussation, which argues that contralateral organization arises as a direct consequence of visual field optical geometry. Light rays from the right visual hemifield physically cross the midsagittal plane before reaching the temporal retina, and so do rays from the left hemifield in the opposite direction. The decussation of nasal retinal fibers in the optic chiasm does not create this crossing; it preserves a pre-existing physical pattern, thereby aligning each cerebral hemisphere with the contralateral half of external space, the only configuration that places a processing center directly “behind” the region of the world it must monitor and act upon. Once hemispheric ownership of visual space is established, motor pathways must follow the same spatial logic. The sensorimotor decussations are therefore the downstream continuation of the same spatial imperative: the shortest, fastest, and most coherent route from a field-specific sensory representation to the effectors acting in that same field is a single midline crossing in the brainstem. A proof-by-exclusion analysis shows that alternative wiring schemes, including fully ipsilateral or reversed crossing patterns, disrupt binocular vision, slow rapid left–right motor responses, and generate visuomotor instabilities observed in clinical disorders of wiring. Comparative evidence across vertebrates, and contrasts with arthropods support the conclusion that neural decussation is an inevitable consequence of vision.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105683"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145812147","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

Viral thresholds and semiotic resonance: Rethinking the continuum between life and non-life 病毒阈值与符号共振：重新思考生命与非生命之间的连续性。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-28 DOI: 10.1016/j.biosystems.2025.105664

Nicola Zengiaro

{"title":"Viral thresholds and semiotic resonance: Rethinking the continuum between life and non-life","authors":"Nicola Zengiaro","doi":"10.1016/j.biosystems.2025.105664","DOIUrl":"10.1016/j.biosystems.2025.105664","url":null,"abstract":"<div><div>This article interrogates the ontological status of the virus, an entity that lacks cellular autonomy yet exhibits core evolutionary dynamics, to expose the limitations of classical definitions of life. The analysis moves beyond this classificatory impasse by integrating the paradigm of reticulate evolution, which repositions viruses as central agents in life's network history, with a materialist biosemiotics. This synthesis supports the paper's central thesis: that life is not an intrinsic property but an emergent condition defined by semiotic processes. To formalize this, we introduce the concept of semiotic resonance, a theoretical model defining life as the emergence of recursive interpretive coupling between material systems. This mechanism provides a physical and semiotic basis for biological organization, bridging the arbitrariness of codes with their material enactment. Ultimately, by reframing the virus as a paradigmatic case of resonance-dependent existence, this work proposes a shift in the study of life itself: away from classifying entities and toward an analysis of the relational thresholds where matter, meaning, and evolution converge.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105664"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650044","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

Turing instability on multiplex simplicial epidemic networks with cross-diffusion and behavioral delay 具有交叉扩散和行为延迟的多重简单流行病网络的图灵不稳定性。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-16 DOI: 10.1016/j.biosystems.2025.105679

Yue Liu, Jianwei Shen

{"title":"Turing instability on multiplex simplicial epidemic networks with cross-diffusion and behavioral delay","authors":"Yue Liu, Jianwei Shen","doi":"10.1016/j.biosystems.2025.105679","DOIUrl":"10.1016/j.biosystems.2025.105679","url":null,"abstract":"<div><div>Modern epidemics are characterized by the emergence of spatial hotspots and periodic outbreaks. This paper reveals that such complex spatiotemporal patterns are driven by a combination of many-body transmission pathways and delayed behavioral responses. We propose a reaction–diffusion epidemic model defined on a multiplex simplicial complex and introduce the behavioral response delay. Through linear stability analysis, we derive the conditions for Turing instability and delay-induced Hopf bifurcation. The analysis reveals that higher-order topological structures and cross-diffusion expand the instability domain and promote the formation of spatial patterns. The higher-order aggregation of susceptible individuals is a key factor in triggering Turing instability, while the higher-order structure of the infected layer primarily modulates its extent. Furthermore, the behavioral response delay acts as a bifurcation parameter, inducing temporal oscillations when it exceeds a critical threshold. Numerical simulations corroborate our theoretical findings, reproducing clustered and periodic oscillation phenomena analogous to those observed during the COVID-19 pandemic. Our results provide the policy implication that dispersing higher-order susceptible clusters and reducing response delays can mitigate spatial heterogeneity and recurrent outbreaks. This work deepens the understanding of epidemic dynamics by elucidating how network topology and human behavior jointly shape complex contagion patterns.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105679"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145783377","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

Evolutionary computation for reconstructing threshold networks of the tryptophan operon in Escherichia coli 大肠杆菌色氨酸操纵子阈值网络重构的进化计算。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-18 DOI: 10.1016/j.biosystems.2025.105682

Gonzalo A. Ruz , Thomas Ledger , Matthew Macauley

{"title":"Evolutionary computation for reconstructing threshold networks of the tryptophan operon in Escherichia coli","authors":"Gonzalo A. Ruz , Thomas Ledger , Matthew Macauley","doi":"10.1016/j.biosystems.2025.105682","DOIUrl":"10.1016/j.biosystems.2025.105682","url":null,"abstract":"<div><div>A recent Boolean model of the tryptophan operon in <em>Escherichia coli</em> has been developed, aiming to capture the operon’s on/off states through a set of fixed points. However, when updated synchronously, the model also reveals the presence of unwanted spurious limit cycles, that have a larger basin of attraction. This study introduces an evolutionary computation framework to search for threshold network models that accurately portray the desired fixed points while eliminating occurrences of limit cycles. Employing both differential evolution and particle swarm optimization within the proposed framework, the latter emerges as the most efficient and effective method based on simulation results. Notably, networks were successfully identified for both continuous weight matrix values within the real interval <span><math><mrow><mo>[</mo><mo>−</mo><mn>1</mn><mo>,</mo><mn>1</mn><mo>]</mo></mrow></math></span> and discrete values limited to <span><math><mrow><mo>{</mo><mo>−</mo><mn>1</mn><mo>,</mo><mn>0</mn><mo>,</mo><mn>1</mn><mo>}</mo></mrow></math></span>. The results confirm that the proposed evolutionary computation framework is capable of identifying threshold networks that accurately model the asymptotic behavior of the tryptophan operon in <em>Escherichia coli</em>.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105682"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800925","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

Chemiosmotic vs conformational models of oxidative phosphorylation: Theory and mechanistic insights 氧化磷酸化的化学渗透与构象模型：理论和机制见解。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-21 DOI: 10.1016/j.biosystems.2025.105637

Sungchul Ji

引用次数: 0

Transformation of the inherent energy in food to ATP and transformations of our knowledge about the mechanism 食物中固有能量转化为三磷酸腺苷以及我们对这一机制的认识的转变。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-10 DOI: 10.1016/j.biosystems.2025.105681

Ole H. Petersen CBE FRS

引用次数: 0

On the transitional character and regularity of planetary abiogenesis 论行星自然发生的过渡性和规律性。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-21 DOI: 10.1016/j.biosystems.2025.105660

Serge Dolgikh

{"title":"On the transitional character and regularity of planetary abiogenesis","authors":"Serge Dolgikh","doi":"10.1016/j.biosystems.2025.105660","DOIUrl":"10.1016/j.biosystems.2025.105660","url":null,"abstract":"<div><div>The emergence of biology from planetary chemistry remains one of the central open questions in planetary physics, chemistry and biochemistry. In this study, we address an important aspect of this problem: whether abiogenesis is a statistically regular process under broadly defined planetary conditions, or a unique, highly contingent event. To examine it, we introduce a conceptual framework of regularity-relevant classes of adaptive planetary physico-chemical systems: the adaptability ladder model, that formalizes the progression from chemically rich but unorganized environments to stable biochemical systems. The model provides a structured approach to the regularity question, examining potential constrains and bottlenecks in specific adaptive classes and formulate formal statements of the regularity hypothesis: specialized for individual classes and strong (or general) across the full adaptive spectrum. We then assess their differential detectability across observation channels: laboratory simulation, in situ exploration, and remote sensing. Our analysis reveals a strong complementarity between detection channels and the regularity classes, with fragile proto-biotic states accessible primarily through laboratory studies. We observe that under the regularity hypothesis, such early adaptive states should emerge reproducibly under appropriate simulated planetary conditions. This result establishes a direct and testable link between laboratory experimentation and the general question of the regularity of biological emergence, positioning lab-based studies as central to future progress. The framework extends conventional definitions of planetary habitability, traditionally focused on terrestrial-class physical and chemical conditions by incorporating informational aspects, specifically compositional and interactive diversity. This broader perspective informs the strategic prioritization of empirical search efforts, bridging theoretical insights with observable planetary conditions.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105660"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589795","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