Physics of collective transport and traffic phenomena in biology: progress in 20 years
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arXiv
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866916463060713472 |
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| author | Chowdhury, Debashish Schadschneider, Andreas Nishinari, Katsuhiro |
| author_facet | Chowdhury, Debashish Schadschneider, Andreas Nishinari, Katsuhiro |
| contents | Enormous progress have been made in the last 20 years since the publication of our review \cite{csk05polrev} 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 {\it Leptogenys processionalis} 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2410_23735 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Physics of collective transport and traffic phenomena in biology: progress in 20 years Chowdhury, Debashish Schadschneider, Andreas Nishinari, Katsuhiro Biological Physics Statistical Mechanics Cellular Automata and Lattice Gases Quantitative Methods Enormous progress have been made in the last 20 years since the publication of our review \cite{csk05polrev} 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 {\it Leptogenys processionalis} 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. |
| title | Physics of collective transport and traffic phenomena in biology: progress in 20 years |
| topic | Biological Physics Statistical Mechanics Cellular Automata and Lattice Gases Quantitative Methods |
| url | https://arxiv.org/abs/2410.23735 |