Fluctuating Chromatin Facilitates Enhancer–Promoter Communication by Regulating Transcriptional Clustering Dynamics

The Journal of Physical Chemistry Letters, Journal Year: 2024, Volume and Issue: 15(45), P. 11428 - 11436

Published: Nov. 7, 2024

Enhancers regulate gene expression by forming contacts with distant promoters. Phase-separated condensates or clusters formed transcription factors (TFs) and cofactors are thought to facilitate these enhancer-promoter (E-P) interactions. Using polymer physics, we developed distinct coarse-grained chromatin models that produce similar ensemble-averaged Hi-C maps but "stable" "dynamic" characteristics. Our findings, consistent recent experiments, reveal a multistep E-P communication process. The dynamic model facilitates proximity enhancing TF clustering subsequently promotes direct interactions destabilizing the through chain flexibility. study physical understanding of molecular mechanisms governing in transcriptional regulation.

Language: Английский

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Data efficiency of classification strategies for chemical and materials design

Digital Discovery, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

We benchmark the performance of space-filling and active learning algorithms on classification problems in materials science, revealing trends optimally data-efficient algorithms.

Language: Английский

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Accelerating Multicomponent Phase-Coexistence Calculations with Physics-informed Neural Networks

Molecular Systems Design & Engineering, Journal Year: 2024, Volume and Issue: 10(2), P. 89 - 101

Published: Dec. 24, 2024

We develop a physics-informed machine learning workflow that accelerates multicomponent phase-coexistence calculations on the number, composition, and abundance of phases. The is demonstrated for systems described by Flory–Huggins theory.

Language: Английский

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