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Physics of collective transport and traffic phenomena in biology: Progress in 20 years 生物学中的集体运输和交通现象物理学：20 年来的进展
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-19 DOI: 10.1016/j.plrev.2024.11.008
Debashish Chowdhury , Andreas Schadschneider , Katsuhiro Nishinari
{"title":"Physics of collective transport and traffic phenomena in biology: Progress in 20 years","authors":"Debashish Chowdhury ,&nbsp;Andreas Schadschneider ,&nbsp;Katsuhiro Nishinari","doi":"10.1016/j.plrev.2024.11.008","DOIUrl":"10.1016/j.plrev.2024.11.008","url":null,"abstract":"<div><div>Enormous progress has been made in the last 20 years since the publication of our review <span><span>[1]</span></span> in this journal on transport and traffic phenomena in biology. In this brief article we present a glimpse of the major advances during this period. First, we present similarities and differences between collective intracellular transport of a single micron-size cargo by multiple molecular motors and that of a cargo particle by a team of ants on the basis of the common principle of load-sharing. Second, we sketch several models all of which are biologically motivated extensions of the Asymmetric Simple Exclusion Process (ASEP); some of these models represent the traffic of molecular machines, like RNA polymerase (RNAP) and ribosome, that catalyze template-directed polymerization of RNA and proteins, respectively, whereas few other models capture the key features of the traffic of ants on trails. More specifically, using the ASEP-based models we demonstrate the effects of traffic of RNAPs and ribosomes on random and ‘programmed’ errors in gene expression as well as on some other subcellular processes. We recall a puzzling empirical result on the single-lane traffic of predatory ants <em>Leptogenys processionalis</em> as well as recent attempts to account for this puzzle. We also mention some surprising effects of lane-changing rules observed in a ASEP-based model for 3-lane traffic of army ants. Finally, we explain the conceptual similarities between the pheromone-mediated indirect communication, called stigmergy, between ants on a trail and the floor-field-mediated interaction between humans in a pedestrian traffic. For the floor-field model of human pedestrian traffic we present a major theoretical result that is relevant from the perspective of all types of traffic phenomena.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 409-422"},"PeriodicalIF":13.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Reaction-diffusion waves in biology: new trends, recent developments 生物学中的反应-扩散波：新趋势、最新发展。
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-19 DOI: 10.1016/j.plrev.2024.11.007
V. Volpert , S. Petrovskii
{"title":"Reaction-diffusion waves in biology: new trends, recent developments","authors":"V. Volpert ,&nbsp;S. Petrovskii","doi":"10.1016/j.plrev.2024.11.007","DOIUrl":"10.1016/j.plrev.2024.11.007","url":null,"abstract":"<div><div>Reaction-diffusion systems are widely used in the description of propagation phenomena in biological systems, where chemical and biological processes combine to produce spatial and temporal patterns. This paper explores the recent trends and developments in the study of reaction-diffusion waves, highlighting their relevance to diverse biological contexts such as population dynamics, ecology or biomedical applications. Progress in mathematical techniques and computational methods advances our ability to model these systems, providing deeper insights into wave propagation, stability, and bifurcations. We also discuss novel models and their implications for understanding processes such as biological invasions or disease proliferation. Overall, the integration of modern theoretical frameworks with experimental data continues to push the boundaries of this interdisciplinary field, revealing new applications and mechanisms underlying biological wave dynamics.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 1-20"},"PeriodicalIF":13.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
COVID-19 epidemic: From data to mathematical models COVID-19 流行病：从数据到数学模型对 Jacques Demongeot 和 Pierre Magal 撰写的 "COVID-19 数据驱动数学建模方法：Jacques Demongeot 和 Pierre Magal 的评论。
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-19 DOI: 10.1016/j.plrev.2024.11.011
François Hamel
{"title":"COVID-19 epidemic: From data to mathematical models","authors":"François Hamel","doi":"10.1016/j.plrev.2024.11.011","DOIUrl":"10.1016/j.plrev.2024.11.011","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 404-406"},"PeriodicalIF":13.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Kinematic coding: Measuring information in naturalistic behaviour 运动编码：测量自然行为中的信息
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-15 DOI: 10.1016/j.plrev.2024.11.009
Cristina Becchio , Kiri Pullar , Eugenio Scaliti , Stefano Panzeri
{"title":"Kinematic coding: Measuring information in naturalistic behaviour","authors":"Cristina Becchio ,&nbsp;Kiri Pullar ,&nbsp;Eugenio Scaliti ,&nbsp;Stefano Panzeri","doi":"10.1016/j.plrev.2024.11.009","DOIUrl":"10.1016/j.plrev.2024.11.009","url":null,"abstract":"<div><div>Recent years have seen an explosion of interest in naturalistic behaviour and in machine learning tools for automatically tracking it. However, questions about what to measure, how to measure it, and how to relate naturalistic behaviour to neural activity and cognitive processes remain unresolved. In this Perspective, we propose a general experimental and computational framework – kinematic coding – for measuring how information about cognitive states is encoded in structured patterns of behaviour and how this information is read out by others during social interactions. This framework enables the design of new experiments and the generation of testable hypotheses that link behaviour, cognition, and neural activity at the single-trial level. Researchers can employ this framework to identify single-subject, single-trial encoding and readout computations and address meaningful questions about how information encoded in bodily motion is transmitted and communicated.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 442-458"},"PeriodicalIF":13.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142702597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Long-living transients in ecological models: Recent progress, new challenges, and open questions 生态模型中的长寿瞬态：最新进展、新挑战和未决问题
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-13 DOI: 10.1016/j.plrev.2024.11.004
Andrew Morozov , Ulrike Feudel , Alan Hastings , Karen C. Abbott , Kim Cuddington , Christopher M. Heggerud , Sergei Petrovskii
{"title":"Long-living transients in ecological models: Recent progress, new challenges, and open questions","authors":"Andrew Morozov ,&nbsp;Ulrike Feudel ,&nbsp;Alan Hastings ,&nbsp;Karen C. Abbott ,&nbsp;Kim Cuddington ,&nbsp;Christopher M. Heggerud ,&nbsp;Sergei Petrovskii","doi":"10.1016/j.plrev.2024.11.004","DOIUrl":"10.1016/j.plrev.2024.11.004","url":null,"abstract":"<div><div>Traditionally, mathematical models in ecology placed an emphasis on asymptotic, long-term dynamics. However, a large number of recent studies highlighted the importance of transient dynamics in ecological and eco-evolutionary systems, in particular ‘long transients’ that can last for hundreds of generations or even longer. Many models as well as empirical studies indicated that a system can function for a long time in a certain state or regime (a ‘metastable regime’) but later exhibits an abrupt transition to another regime not preceded by any parameter change (or following the change that occurred long before the transition). This scenario where tipping occurs without any apparent source of a regime shift is also referred to as ‘metastability’. Despite considerable evidence of the presence of long transients in real-world systems as well as models, until recently research into long-living transients in ecology has remained in its infancy, largely lacking systematisation. Within the past decade, however, substantial progress has been made in creating a unifying theory of long transients in deterministic as well as stochastic systems. This has considerably accelerated further studies on long transients, in particular on those characterised by more complicated patterns and/or underlying mechanisms. The main goal of this review is to provide an overview of recent research on long transients and related regime shifts in models of ecological dynamics. We pay special attention to the role of environmental stochasticity, the effect of multiple timescales (slow-fast systems), transient spatial patterns, and relation between transients and spatial synchronisation. We also discuss current challenges and open questions in understanding transients with applications to ecosystems dynamics.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 423-441"},"PeriodicalIF":13.7,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142702598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Persons and their affective experiences. Comment on “The affective grounds of the mind. The affective pertinentization (APER) model” by salvatore et al. 人及其情感体验。评论 "心灵的情感基础。情感相关化（APER）模型 "的评论。
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-09 DOI: 10.1016/j.plrev.2024.11.005
Tania Zittoun
{"title":"Persons and their affective experiences. Comment on “The affective grounds of the mind. The affective pertinentization (APER) model” by salvatore et al.","authors":"Tania Zittoun","doi":"10.1016/j.plrev.2024.11.005","DOIUrl":"10.1016/j.plrev.2024.11.005","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 399-401"},"PeriodicalIF":13.7,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Affect and human functioning: Comment on the affective grounds of the mind: The Affective Pertinientization (APER) model by S. Salvatore, A. Palmieri, R. De Luca Picione, V. Bochnicchio, M. Reho, M. Rita Serio, G. Salvatore 情感与人类功能：评论心灵的情感基础：S. Salvatore、A. Palmieri、R. De Luca Picione、V. Bochnicchio、M. Reho、M. Rita Serio、G. Salvatore 所著的《情感警觉化（APER）模型》。
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-09 DOI: 10.1016/j.plrev.2024.11.006
Stephen Soldz
{"title":"Affect and human functioning: Comment on the affective grounds of the mind: The Affective Pertinientization (APER) model by S. Salvatore, A. Palmieri, R. De Luca Picione, V. Bochnicchio, M. Reho, M. Rita Serio, G. Salvatore","authors":"Stephen Soldz","doi":"10.1016/j.plrev.2024.11.006","DOIUrl":"10.1016/j.plrev.2024.11.006","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 402-403"},"PeriodicalIF":13.7,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 circuit of cognition: Operational closure and the interpenetration of views. Comment on “The affective grounds of the mind. The affective pertinentization (APER) model” by Salvatore et al. 认知回路：操作封闭与观点的相互渗透。评论 "心灵的情感基础。情感相关化（APER）模型 "的评论。
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-08 DOI: 10.1016/j.plrev.2024.11.003
Gordon Sammut, Rebekah Mifsud, Noellie Brockdorff
{"title":"The circuit of cognition: Operational closure and the interpenetration of views. Comment on “The affective grounds of the mind. The affective pertinentization (APER) model” by Salvatore et al.","authors":"Gordon Sammut,&nbsp;Rebekah Mifsud,&nbsp;Noellie Brockdorff","doi":"10.1016/j.plrev.2024.11.003","DOIUrl":"10.1016/j.plrev.2024.11.003","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 397-398"},"PeriodicalIF":13.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
What are the psychic forces present within a psychopathological state? Comment on “Nature heals: An informational entropy account of self-organization and change in field psychotherapy” by Pietro Sarasso, Wolfgang Tschacher, Felix Schoeller, Gianni Francesetti, Jan Roubal, Michela Gecele, Katiuscia Sacco, Irene Ronga 精神病理状态中存在哪些精神力量？评论 "自然治愈：Pietro Sarasso、Wolfgang Tschacher、Felix Schoeller、Gianni Francesetti、Jan Roubal、Michela Gecele、Katiuscia Sacco、Irene Ronga 对 "自然治愈：场心理疗法中自我组织和变化的信息熵解释 "的评论。
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-08 DOI: 10.1016/j.plrev.2024.11.001
G. de Felice
{"title":"What are the psychic forces present within a psychopathological state? Comment on “Nature heals: An informational entropy account of self-organization and change in field psychotherapy” by Pietro Sarasso, Wolfgang Tschacher, Felix Schoeller, Gianni Francesetti, Jan Roubal, Michela Gecele, Katiuscia Sacco, Irene Ronga","authors":"G. de Felice","doi":"10.1016/j.plrev.2024.11.001","DOIUrl":"10.1016/j.plrev.2024.11.001","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 395-396"},"PeriodicalIF":13.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Affective dynamics in unionization and solidarity: Comment on “The affective grounds of the mind. The Affective Pertinentization (APER) model” by Salvatore et al. 工会和团结中的情感动力：对 Salvatore 等人所著 "心灵的情感基础。Salvatore 等人的 "情感化模式（APER）"一文的评论。
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2024-11-07 DOI: 10.1016/j.plrev.2024.11.002
Kevin R. Carriere , Michael Richardson
{"title":"Affective dynamics in unionization and solidarity: Comment on “The affective grounds of the mind. The Affective Pertinentization (APER) model” by Salvatore et al.","authors":"Kevin R. Carriere ,&nbsp;Michael Richardson","doi":"10.1016/j.plrev.2024.11.002","DOIUrl":"10.1016/j.plrev.2024.11.002","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 392-394"},"PeriodicalIF":13.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
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