Using a Fast Adaptive Function Approximator to calculate Protein-Filament Binding Kinetics
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arXiv
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| Hauptverfasser: | , , |
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| Format: | Preprint |
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2023
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| _version_ | 1866929337408684032 |
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| author | Zhang, Zihan Lamson, Adam R. Blackwell, Robert |
| author_facet | Zhang, Zihan Lamson, Adam R. Blackwell, Robert |
| contents | The cytoskeleton, consisting of biopolymer filaments, molecular motors, and passive crosslinking proteins, provides the internal structure of cells that facilitate movement, growth, and cell division. Understanding the microscopic motor-filament kinetics and dynamics is essential for comprehending macroscopic behaviors of reconstituted cytoskeletal assemblies, such as self-organized flow and active stress. In this study, we employ an adaptive fast Chebyshev approximator based on tree search and parallel computing to accurately recover the equilibrium distribution of crosslinking proteins. Therefore, it satisfies detailed balance in binding through kinetic Monte Carlo sampling while maintaining cost-effectiveness. Additionally, we offer expandable features, including segregating the simulation process via pre-building and allowing the free-loading of different closed-form formulations of the motor's potential energy. Overall, this research contributes to computational advancement in function approximation and has the potential to better describe the evolution of cytoskeletal active matter. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2311_03602 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Using a Fast Adaptive Function Approximator to calculate Protein-Filament Binding Kinetics Zhang, Zihan Lamson, Adam R. Blackwell, Robert Soft Condensed Matter The cytoskeleton, consisting of biopolymer filaments, molecular motors, and passive crosslinking proteins, provides the internal structure of cells that facilitate movement, growth, and cell division. Understanding the microscopic motor-filament kinetics and dynamics is essential for comprehending macroscopic behaviors of reconstituted cytoskeletal assemblies, such as self-organized flow and active stress. In this study, we employ an adaptive fast Chebyshev approximator based on tree search and parallel computing to accurately recover the equilibrium distribution of crosslinking proteins. Therefore, it satisfies detailed balance in binding through kinetic Monte Carlo sampling while maintaining cost-effectiveness. Additionally, we offer expandable features, including segregating the simulation process via pre-building and allowing the free-loading of different closed-form formulations of the motor's potential energy. Overall, this research contributes to computational advancement in function approximation and has the potential to better describe the evolution of cytoskeletal active matter. |
| title | Using a Fast Adaptive Function Approximator to calculate Protein-Filament Binding Kinetics |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2311.03602 |