Cargando…
Nonequilibrium Self-Assembly Time Forecasting by the Stochastic Landscape Method
[Image: see text] Many biological systems rely on the ability to self-assemble target structures from different molecular building blocks using nonequilibrium drives, stemming, for example, from chemical potential gradients. The complex interactions between the different components give rise to a ru...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
|
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10350916/ https://www.ncbi.nlm.nih.gov/pubmed/37403408 http://dx.doi.org/10.1021/acs.jpcb.3c01376 |
_version_ | 1785074240865697792 |
---|---|
author | Faran, Michael Bisker, Gili |
author_facet | Faran, Michael Bisker, Gili |
author_sort | Faran, Michael |
collection | PubMed |
description | [Image: see text] Many biological systems rely on the ability to self-assemble target structures from different molecular building blocks using nonequilibrium drives, stemming, for example, from chemical potential gradients. The complex interactions between the different components give rise to a rugged energy landscape with a plethora of local minima on the dynamic pathway to the target assembly. Exploring a toy physical model of multicomponents nonequilibrium self-assembly, we demonstrate that a segmented description of the system dynamics can be used to provide predictions of the first assembly times. We show that for a wide range of values of the nonequilibrium drive, a log-normal distribution emerges for the first assembly time statistics. Based on data segmentation by a Bayesian estimator of abrupt changes (BEAST), we further present a general data-based algorithmic scheme, namely, the stochastic landscape method (SLM), for assembly time predictions. We demonstrate that this scheme can be implemented for the first assembly time forecast during a nonequilibrium self-assembly process, with improved prediction power compared to a naïve guess based on the mean remaining time to the first assembly. Our results can be used to establish a general quantitative framework for nonequilibrium systems and to improve control protocols of nonequilibrium self-assembly processes. |
format | Online Article Text |
id | pubmed-10350916 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-103509162023-07-18 Nonequilibrium Self-Assembly Time Forecasting by the Stochastic Landscape Method Faran, Michael Bisker, Gili J Phys Chem B [Image: see text] Many biological systems rely on the ability to self-assemble target structures from different molecular building blocks using nonequilibrium drives, stemming, for example, from chemical potential gradients. The complex interactions between the different components give rise to a rugged energy landscape with a plethora of local minima on the dynamic pathway to the target assembly. Exploring a toy physical model of multicomponents nonequilibrium self-assembly, we demonstrate that a segmented description of the system dynamics can be used to provide predictions of the first assembly times. We show that for a wide range of values of the nonequilibrium drive, a log-normal distribution emerges for the first assembly time statistics. Based on data segmentation by a Bayesian estimator of abrupt changes (BEAST), we further present a general data-based algorithmic scheme, namely, the stochastic landscape method (SLM), for assembly time predictions. We demonstrate that this scheme can be implemented for the first assembly time forecast during a nonequilibrium self-assembly process, with improved prediction power compared to a naïve guess based on the mean remaining time to the first assembly. Our results can be used to establish a general quantitative framework for nonequilibrium systems and to improve control protocols of nonequilibrium self-assembly processes. American Chemical Society 2023-07-05 /pmc/articles/PMC10350916/ /pubmed/37403408 http://dx.doi.org/10.1021/acs.jpcb.3c01376 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Faran, Michael Bisker, Gili Nonequilibrium Self-Assembly Time Forecasting by the Stochastic Landscape Method |
title | Nonequilibrium
Self-Assembly Time Forecasting by the
Stochastic Landscape Method |
title_full | Nonequilibrium
Self-Assembly Time Forecasting by the
Stochastic Landscape Method |
title_fullStr | Nonequilibrium
Self-Assembly Time Forecasting by the
Stochastic Landscape Method |
title_full_unstemmed | Nonequilibrium
Self-Assembly Time Forecasting by the
Stochastic Landscape Method |
title_short | Nonequilibrium
Self-Assembly Time Forecasting by the
Stochastic Landscape Method |
title_sort | nonequilibrium
self-assembly time forecasting by the
stochastic landscape method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10350916/ https://www.ncbi.nlm.nih.gov/pubmed/37403408 http://dx.doi.org/10.1021/acs.jpcb.3c01376 |
work_keys_str_mv | AT faranmichael nonequilibriumselfassemblytimeforecastingbythestochasticlandscapemethod AT biskergili nonequilibriumselfassemblytimeforecastingbythestochasticlandscapemethod |