{"title":"量化圆内和圆外粒子之间的随机碰撞","authors":"Xi Chen , Hui Wang , Jinqiao Duan","doi":"10.1016/j.physd.2024.134361","DOIUrl":null,"url":null,"abstract":"<div><p>Random collisions of particles occur in various biophysical and physical systems. Inspired by the binding of receptor and ligand on the cell membrane, we devised a method based on stochastic dynamical modeling to quantify the likelihood of two random particles colliding on a circle. We consider the dynamics of a receptor binding to a ligand on the cell membrane, where the receptor and ligand perform different motions and are thus modeled by stochastic differential equations with non-Gaussian noise. We use neural networks based on the Onsager–Machlup function to compute the probability <span><math><msub><mrow><mi>P</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> of an unbounded receptor diffusing to the cell membrane. Meanwhile, we compute the probability <span><math><msub><mrow><mi>P</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> of the extracellular ligand arriving at the cell membrane by solving the associated nonlocal Fokker–Planck equation. We can then calculate the most probable binding probability by combining <span><math><msub><mrow><mi>P</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> and <span><math><msub><mrow><mi>P</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span>. In this way, we conclude with some indication of how the receptors could distribute on the membrane, as well as where the ligand will most probably encounter the receptor, contributing to a better understanding of the cell’s response to external stimuli and communication with other cells.</p></div>","PeriodicalId":20050,"journal":{"name":"Physica D: Nonlinear Phenomena","volume":"470 ","pages":"Article 134361"},"PeriodicalIF":2.7000,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Quantifying random collisions between particles inside and outside a circle\",\"authors\":\"Xi Chen , Hui Wang , Jinqiao Duan\",\"doi\":\"10.1016/j.physd.2024.134361\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Random collisions of particles occur in various biophysical and physical systems. Inspired by the binding of receptor and ligand on the cell membrane, we devised a method based on stochastic dynamical modeling to quantify the likelihood of two random particles colliding on a circle. We consider the dynamics of a receptor binding to a ligand on the cell membrane, where the receptor and ligand perform different motions and are thus modeled by stochastic differential equations with non-Gaussian noise. We use neural networks based on the Onsager–Machlup function to compute the probability <span><math><msub><mrow><mi>P</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> of an unbounded receptor diffusing to the cell membrane. Meanwhile, we compute the probability <span><math><msub><mrow><mi>P</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> of the extracellular ligand arriving at the cell membrane by solving the associated nonlocal Fokker–Planck equation. We can then calculate the most probable binding probability by combining <span><math><msub><mrow><mi>P</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> and <span><math><msub><mrow><mi>P</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span>. In this way, we conclude with some indication of how the receptors could distribute on the membrane, as well as where the ligand will most probably encounter the receptor, contributing to a better understanding of the cell’s response to external stimuli and communication with other cells.</p></div>\",\"PeriodicalId\":20050,\"journal\":{\"name\":\"Physica D: Nonlinear Phenomena\",\"volume\":\"470 \",\"pages\":\"Article 134361\"},\"PeriodicalIF\":2.7000,\"publicationDate\":\"2024-09-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Physica D: Nonlinear Phenomena\",\"FirstCategoryId\":\"100\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0167278924003117\",\"RegionNum\":3,\"RegionCategory\":\"数学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MATHEMATICS, APPLIED\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Physica D: Nonlinear Phenomena","FirstCategoryId":"100","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0167278924003117","RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MATHEMATICS, APPLIED","Score":null,"Total":0}
Quantifying random collisions between particles inside and outside a circle
Random collisions of particles occur in various biophysical and physical systems. Inspired by the binding of receptor and ligand on the cell membrane, we devised a method based on stochastic dynamical modeling to quantify the likelihood of two random particles colliding on a circle. We consider the dynamics of a receptor binding to a ligand on the cell membrane, where the receptor and ligand perform different motions and are thus modeled by stochastic differential equations with non-Gaussian noise. We use neural networks based on the Onsager–Machlup function to compute the probability of an unbounded receptor diffusing to the cell membrane. Meanwhile, we compute the probability of the extracellular ligand arriving at the cell membrane by solving the associated nonlocal Fokker–Planck equation. We can then calculate the most probable binding probability by combining and . In this way, we conclude with some indication of how the receptors could distribute on the membrane, as well as where the ligand will most probably encounter the receptor, contributing to a better understanding of the cell’s response to external stimuli and communication with other cells.
期刊介绍:
Physica D (Nonlinear Phenomena) publishes research and review articles reporting on experimental and theoretical works, techniques and ideas that advance the understanding of nonlinear phenomena. Topics encompass wave motion in physical, chemical and biological systems; physical or biological phenomena governed by nonlinear field equations, including hydrodynamics and turbulence; pattern formation and cooperative phenomena; instability, bifurcations, chaos, and space-time disorder; integrable/Hamiltonian systems; asymptotic analysis and, more generally, mathematical methods for nonlinear systems.