Blair Lyons, Saurabh S Mogre, Karthik Vegesna, Jessica S Yu, Mark Hansen, Aadarsh Raghunathan, Graham T Johnson, Eran Agmon, Matthew Akamatsu
{"title":"对比模拟肌动蛋白丝压缩揭示了计算成本和捕获超捻之间的权衡。","authors":"Blair Lyons, Saurabh S Mogre, Karthik Vegesna, Jessica S Yu, Mark Hansen, Aadarsh Raghunathan, Graham T Johnson, Eran Agmon, Matthew Akamatsu","doi":"10.17912/micropub.biology.001347","DOIUrl":null,"url":null,"abstract":"<p><p>The dynamic bending and twisting of actin drives numerous cellular processes. To compare how different spatial scales in actin models capture these dynamics, we developed two models of actin filaments: one at monomer-scale using ReaDDy and one at fiber-scale using Cytosim. Simulating filament compression across a range of velocities, we found a divergence between the monomer- and fiber-scale simulations; notably, the monomer-scale simulations more effectively captured filament supertwist, characteristic of helical structure, but at a higher computational cost. Such comparisons can aid in designing more efficient and accurate multi-scale biological models. Interactive visualizations at https://simularium.github.io/subcell-website.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11795302/pdf/","citationCount":"0","resultStr":"{\"title\":\"Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist.\",\"authors\":\"Blair Lyons, Saurabh S Mogre, Karthik Vegesna, Jessica S Yu, Mark Hansen, Aadarsh Raghunathan, Graham T Johnson, Eran Agmon, Matthew Akamatsu\",\"doi\":\"10.17912/micropub.biology.001347\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The dynamic bending and twisting of actin drives numerous cellular processes. To compare how different spatial scales in actin models capture these dynamics, we developed two models of actin filaments: one at monomer-scale using ReaDDy and one at fiber-scale using Cytosim. Simulating filament compression across a range of velocities, we found a divergence between the monomer- and fiber-scale simulations; notably, the monomer-scale simulations more effectively captured filament supertwist, characteristic of helical structure, but at a higher computational cost. Such comparisons can aid in designing more efficient and accurate multi-scale biological models. Interactive visualizations at https://simularium.github.io/subcell-website.</p>\",\"PeriodicalId\":74192,\"journal\":{\"name\":\"microPublication biology\",\"volume\":\"2025 \",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2025-01-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11795302/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"microPublication biology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.17912/micropub.biology.001347\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"microPublication biology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.17912/micropub.biology.001347","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"","JCRName":"","Score":null,"Total":0}
Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist.
The dynamic bending and twisting of actin drives numerous cellular processes. To compare how different spatial scales in actin models capture these dynamics, we developed two models of actin filaments: one at monomer-scale using ReaDDy and one at fiber-scale using Cytosim. Simulating filament compression across a range of velocities, we found a divergence between the monomer- and fiber-scale simulations; notably, the monomer-scale simulations more effectively captured filament supertwist, characteristic of helical structure, but at a higher computational cost. Such comparisons can aid in designing more efficient and accurate multi-scale biological models. Interactive visualizations at https://simularium.github.io/subcell-website.