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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...

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Autores principales: Faran, Michael, Bisker, Gili
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
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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.
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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
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