Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop DOI Open Access
Sandeep Kumar, Ranjith Padinhateeri, Snigdha Thakur

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 25, 2024

Several types of molecular machines move along biopolymers like chromatin. However, the details about microscopic activity these and how to distinguish their modes action are not well understood. We propose that such can be classified by studying looped chromatin under shear flow. Our simulations show a chromatin-like polymer with two activities (constant or local curvature dependent tangential forces) exhibits very different behavior one both measuring nature globule-to-extended coil transition, tank treading, tumbling dynamics.

Language: Английский

Machine Learning-Based Process Optimization in Biopolymer Manufacturing: A Review DOI Open Access
Ivan Malashin,

D. A. Martysyuk,

В С Тынченко

et al.

Polymers, Journal Year: 2024, Volume and Issue: 16(23), P. 3368 - 3368

Published: Nov. 29, 2024

The integration of machine learning (ML) into material manufacturing has driven advancements in optimizing biopolymer production processes. ML techniques, applied across various stages production, enable the analysis complex data generated throughout identifying patterns and insights not easily observed through traditional methods. As sustainable alternatives to petrochemical-based plastics, biopolymers present unique challenges due their reliance on variable bio-based feedstocks processing conditions. This review systematically summarizes current applications techniques aiming provide a comprehensive reference for future research while highlighting potential enhance efficiency, reduce costs, improve product quality. also shows role algorithms, including supervised, unsupervised, deep

Language: Английский

Citations

5

Knotting and adsorption of end-grafted active polymers DOI
Yifan Shen, Meng‐Bo Luo

Soft Matter, Journal Year: 2025, Volume and Issue: 21(10), P. 1873 - 1883

Published: Jan. 1, 2025

The adsorption of end-grafted active polymers is significantly influenced by the presence knots in polymer. In this study, composed an head and passive chain investigated using Langevin dynamics simulations. relationship between checked varying rotational inertia J head. effect becomes more pronounced at larger as persistence time force on increased increasing J. As a result, polymer hindered critical surface attraction strength with rising results are primarily attributed to probability Pknot leads obvious decrease number adsorbed monomers. Furthermore, we find that knotting process slower than influence relatively weaker strength. Our simulation reveal increase can thus weaken

Language: Английский

Citations

0

Langevin dynamics simulations for the critical adsorption of end-grafted active polymers DOI
Meng‐Bo Luo, Yifan Shen

Soft Matter, Journal Year: 2024, Volume and Issue: 20(26), P. 5113 - 5121

Published: Jan. 1, 2024

The critical adsorption of end-grafted active polymer chains on an attractive surface is studied using Langevin dynamics simulations. polymers are composed particle located at the head and a sequential passive chain. Results show that force exerted by pulls away from surface. Consequently, hindered, attraction strength, , increases proportionally to square force,

Language: Английский

Citations

3

Delayed Excitations Induce Polymer Looping and Coherent Motion DOI
Andriy Goychuk, Deepti Kannan, Mehran Kardar

et al.

Physical Review Letters, Journal Year: 2024, Volume and Issue: 133(7)

Published: Aug. 15, 2024

We consider inhomogeneous polymers driven by energy-consuming active processes which encode temporal patterns of athermal kicks. find that such excitation programs, propagated tension along the polymer, can effectively couple distinct polymer loci. Consequently, distant loci exhibit correlated motions fold into specific conformations, as set local actions and their distribution polymer. Interestingly, kicks are canceled out a time-delayed echo induce strong compaction

Language: Английский

Citations

2

Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop DOI
Sandeep Kumar, Ranjith Padinhateeri, Snigdha Thakur

et al.

Soft Matter, Journal Year: 2024, Volume and Issue: 20(32), P. 6500 - 6506

Published: Jan. 1, 2024

Active chromatin loops with different activity class but same structural transitions can be distinguished using shear experiment.

Language: Английский

Citations

1

Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop DOI Open Access
Sandeep Kumar, Ranjith Padinhateeri, Snigdha Thakur

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 25, 2024

Several types of molecular machines move along biopolymers like chromatin. However, the details about microscopic activity these and how to distinguish their modes action are not well understood. We propose that such can be classified by studying looped chromatin under shear flow. Our simulations show a chromatin-like polymer with two activities (constant or local curvature dependent tangential forces) exhibits very different behavior one both measuring nature globule-to-extended coil transition, tank treading, tumbling dynamics.

Language: Английский

Citations

0