ArticleThe European physical journal. E, Soft matter2021
Modeling spatiotemporally varying protein-protein interactions in CyLaKS, the Cytoskeleton Lattice-based Kinetic Simulator.
Article in The European physical journal. E, Soft matter, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 10 citations in OpenAlex.
- Feedback between filament spacing, crosslinker binding, and self-organization in cytoskeletal bundles.bioRxiv : the preprint server for biology · 2026Article
- PRC1 resists microtubule sliding in two distinct resistive modes due to variations in the separation between overlapping microtubules.Molecular biology of the cell · 2025Article
- Form and function in biological filaments: a physicist's review.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2025Review
- Micron-scale protein transport along microtubules by kinesin-driven shepherding.bioRxiv : the preprint server for biology · 2025Article
- PRC1 resists microtubule sliding in two distinct resistive modes due to variations in the separation between overlapping microtubules.bioRxiv : the preprint server for biology · 2025Article
- Motor guidance by long-range communication on the microtubule highway.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- CellDynaMo-stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly.PLoS computational biology · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Interaction of cytoskeletal filaments, motor proteins, and crosslinking proteins drives important cellular processes such as cell division and cell movement. Cytoskeletal networks also exhibit nonequilibrium self-assembly in reconstituted systems. An emerging problem in cytoskeletal modeling and simulation is spatiotemporal alteration of the dynamics of filaments, motors, and associated proteins. This can occur due to motor crowding, obstacles along the filament, motor interactions and direction switching, and changes, defects, or heterogeneity in the filament binding lattice. How such spatiotemporally varying cytoskeletal filaments and motor interactions affect their collective properties is not fully understood. We developed the Cytoskeleton Lattice-based Kinetic Simulator (CyLaKS) to investigate such problems. The simulation model builds on previous work by incorporating motor mechanochemistry into a simulation with many interacting motors and/or associated proteins on a discretized lattice. CyLaKS also includes detailed balance in binding kinetics, movement, and lattice heterogeneity. The simulation framework is flexible and extensible for future modeling work and is available on GitHub for others to freely use or build upon. Here we illustrate the use of CyLaKS to study long-range motor interactions, microtubule lattice heterogeneity, motion of a heterodimeric motor, and how changing crosslinker number affects filament separation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.