Topological comparison of flexible and semiflexible chains in polymer melts with θ-chains DOI
Maurice Schmitt, Sarah Wettermann, Kostas Ch. Daoulas

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 161(14)

Published: Oct. 10, 2024

A central paradigm of polymer physics states that chains in melts behave like random walks as intra- and interchain interactions effectively cancel each other out. Likewise, θ-chains, i.e., at the transition from a swollen coil to globular phase, are also thought ideal chains, attractive forces counterbalanced by repulsive entropic contributions. While simple mapping an equivalent Kuhn chain works rather well most scenarios with corrections scaling, do not accurately capture topology knots, particularly for flexible chains. In this paper, we demonstrate Monte Carlo molecular dynamics simulations θ-chains only agree on structural level range stiffnesses but topologically. They exhibit similar knotting probabilities knot sizes, both which captured representations. This discrepancy comes suppression small knots real is strongest very because excluded volume effects still active locally become weaker increasing semiflexibility. Our findings suggest behavior indeed two structure melt can be approximately reproduced corresponding θ-chain.

Language: Английский

Topological linking determines elasticity in limited valence networks DOI Creative Commons
Giorgia Palombo,

Simon Weir,

Davide Michieletto

et al.

Nature Materials, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

Understanding the relationship between microscopic structure and topology of a material its macroscopic properties is fundamental challenge across wide range systems. Here we investigate viscoelasticity DNA nanostar hydrogels-a model system for physical networks with limited valence-by coupling rheology measurements, confocal imaging molecular dynamics simulations. We discover that these display large degree interpenetration loops within network are topologically linked, forming percolating network-within-network structure. Below overlapping concentration, fraction branching points pore size determine high-frequency elasticity gels. At higher concentrations, this elastic response dictated by abundance topological links looped motifs in gel. Our findings highlight emergence 'topological elasticity' as previously overlooked mechanism generic network-forming liquids gels inform design controllable behaviours.

Language: Английский

Citations

2
Metareview: a survey of active matter reviews DOI Creative Commons
Michael te Vrugt, Raphael Wittkowski

The European Physical Journal E, Journal Year: 2025, Volume and Issue: 48(2)

Published: Feb. 1, 2025

In the past years, amount of research on active matter has grown extremely rapidly, a fact that is reflected in particular by existence more than 1000 reviews this topic. Moreover, field become very diverse, ranging from theoretical studies statistical mechanics particles to applied work medical applications microrobots and biological systems artificial swimmers. This makes it difficult get an overview over as whole. Here, we provide such form metareview article surveys existing review articles books matter. Thereby, provides useful starting point for finding literature about specific

Language: Английский

Citations

2
Topological foundations of ferroelectricity DOI Creative Commons
Igor Lukyanchuk, A. G. Razumnaya, Svitlana Kondovych

et al.

Physics Reports, Journal Year: 2025, Volume and Issue: 1110, P. 1 - 56

Published: Jan. 31, 2025

Language: Английский

Citations

1
Tracking topological defects in a plasma state of a quenched colloidal ice DOI
Mattia Ostinato, Pietro Tierno

Physical review. B./Physical review. B, Journal Year: 2025, Volume and Issue: 111(1)

Published: Jan. 10, 2025

In frustrated spin systems, creation and annihilation of topological defects are processes that hard to characterize information about them is often extracted by measuring averaged quantities without direct visualization their dynamics. Here we show that, in a quenched colloidal ice, an external force can be used generate plasma state which continuously created destroyed with bias-dependent rates. By developing general tracking algorithm extended other artificial fully the statistical properties kinetics generation-recombination process at steady state, both regime far from it. Further, determine defects' waiting survival time distributions unveil maximum lifetime where string tension minimized. locked icon Physics Subject Headings (PhySH)Topological defectsMagnetic colloidsSpin iceBrownian dynamics

Language: Английский

Citations

0
Folding of a tandemly knotted protein: Evidence that a polypeptide chain can get out of deep kinetic traps DOI Creative Commons
Hongyu Zhang, Sophie Jackson

Protein Science, Journal Year: 2025, Volume and Issue: 34(3)

Published: Feb. 19, 2025

Abstract It is hard to imagine how proteins can thread and form knots in their polypeptide chains, but they do. These topologically complex structures have challenged the traditional protein folding views of simple funnel‐shaped energy landscapes. Previous experimental studies on mechanisms deeply knotted with a single trefoil knot yielded evidence that this topology has more complicated landscape than other simpler proteins. However, date, there been no attempts study any which multiple threading events are needed create one within chain. Here, we report construction characterization an artificial tandemly protein. We find compelling both domains similar stabilities parent trefoil‐knotted In addition, show pathway additional very slow phases propose correspond formation second system. also during gets transiently trapped deep kinetic traps, however, majority chains (>90%) manage partially unfold acquire native tandem‐knot topology. This work highlights fact Nature tolerate topologies thought, despite considerable misfolding folding, way state even absence molecular chaperones.

Language: Английский

Citations

0
Entropic Repulsion and Local Order in Doubly Tethered Polymers on a Surface DOI Creative Commons

Min Cheol Chu,

Dieter W. Heermann

Macromolecular Theory and Simulations, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 20, 2025

Abstract The behavior of (athermal) mobile doubly tethered polymers (ring‐like in 3D) is investigated, on a 2D substrate using the bond fluctuation model. end‐monomers can move laterally within constrained distance range. Conformational properties loop are analyzed and specifically ordering system end‐monomers. For this, director considered between for local ordering. As tethering density increases, transition from mushroom‐like conformations to nearly upright structures observed, as case linear grafted polymers. effects repulsion explored, i.e., entropic repulsion, order parameter orientational correlations directors 2D. Despite lack global phase transition, emerges due interactions 3D.

Language: Английский

Citations

0
Recent Advances in Soft Matter DOI Open Access
Ingo Dierking

Materials, Journal Year: 2025, Volume and Issue: 18(7), P. 1440 - 1440

Published: March 25, 2025

As the current Section Editor for Soft Matter of Materials, I am delighted to be able present a Special Issue journal:

Language: Английский

Citations

0
Discrepant Effects of Hydrated and Neat Reline on the Conformational Stability of a Knotted Protein DOI
Sanjib Thakuria, Sandip Paul

The Journal of Physical Chemistry B, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Although knotted proteins are rare in number, their peculiar topology has long intrigued the scientific community. In this study, we have explored conformational stability of a trefoil-knotted protein, YbeA, reline (choline chloride:urea 1:2 ratio), well-characterized deep eutectic solvent, using classical molecular dynamics simulation. Deep solvents (DESs) as reliable alternative to conventional solvents, effectively altering protein's structural and activity, either stabilizing its native state or disordering conformation depending on relevant interactions involved. Here, pure hydrated concentrations reline, observe conflicting effect DES stability. Our studies at room temperature elevated temperatures show that protein is conformationally stable rigid. contrast, tends lose integrity reline. The also gets untied solvated exposed an temperature. Using Minimum Distance Distribution Functions Kirkwood-Buff Integrals, analyzed solvation pattern constituents around protein. We expect study will lead more effective strategies developing tailored solvent systems for comprehending behavior proteins.

Language: Английский

Citations

0
Super‐Tough Silk: The Potential of Knots in Evolved Spiders DOI Creative Commons
Nicola M. Pugno

Advanced Functional Materials, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 7, 2025

Abstract Spider silk is renowned for its exceptional mechanical properties, combining low density with high tensile strength and extensibility thus very toughness modulus ( t ., i.e., dissipated energy per unit mass). However, the potential of spider can be significantly enhanced if spiders evolved ‐currently absent/undiscovered‐ ability to tie knots in their silk. This advancement will allow a new level gigantic T ) revealing today “hidden toughness”, mimicking human engineering techniques particular related proposal by author used realizing world's toughest fibers. Indeed, knotting provide additional dissipation via friction, enabling construct webs traps unprecedented efficiency. To quantify this scenario, calculates 393 real virtually assumed evolving knot‐making behaviors, showing gain G = / about one or two orders magnitude. The resulting “super‐tough silk” benefit natural habitats suggests perspective on how serve as key innovation evolution Biology general.

Language: Английский

Citations

0
Influence of topology on rheological properties of polymer ring melts DOI
Ranajay Datta, Peter Virnau

The Journal of Chemical Physics, Journal Year: 2025, Volume and Issue: 162(9)

Published: March 5, 2025

We investigate with numerical simulations the influence of topology and stiffness on macroscopic rheological properties polymer melts consisting unknotted, knotted, or concatenated rings. While flexible, knotted oligomer rings tend to be significantly more viscous than their unknotted counterparts, differences vanish in a low shear rate scenario increasing degree polymerization. Melts catenanes two other hand are consistently unconcatenated counterparts. These topology-based can exploited segregate mixtures otherwise chemically similar polymers, e.g., microfluidic devices, which is demonstrated by exposing blend flexible channel flow.

Language: Английский

Citations

0