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对肌动蛋白丝压缩的模拟进行比较,揭示了计算成本与捕捉超螺旋之间的权衡。

Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist.

作者信息

Lyons Blair, Mogre Saurabh S, Vegesna Karthik, Yu Jessica S, Hansen Mark, Raghunathan Aadarsh, Johnson Graham T, Agmon Eran, Akamatsu Matthew

机构信息

Allen Institute for Cell Science, Seattle, WA, USA.

Department of Biology, University of Washington, Seattle, WA, USA.

出版信息

MicroPubl Biol. 2025 Jan 21;2025. doi: 10.17912/micropub.biology.001347. eCollection 2025.

Abstract

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.

摘要

肌动蛋白的动态弯曲和扭转驱动着众多细胞过程。为了比较肌动蛋白模型中不同空间尺度如何捕捉这些动态,我们开发了两种肌动蛋白丝模型:一种是使用ReaDDy的单体尺度模型,另一种是使用Cytosim的纤维尺度模型。通过在一系列速度下模拟细丝压缩,我们发现单体尺度和纤维尺度模拟之间存在差异;值得注意的是,单体尺度模拟更有效地捕捉了螺旋结构特有的细丝超扭曲,但计算成本更高。这样的比较有助于设计更高效、准确的多尺度生物学模型。交互式可视化请访问https://simularium.github.io/subcell-website。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d5e3/11795302/c156294724cf/25789430-2025-micropub.biology.001347.jpg

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