Related papers: Topological interactions between ring polymers: Im…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…
Grasping mechanisms must both create and subsequently hold grasps that permit safe and effective object manipulation. Existing mechanisms address the different functional requirements of grasp creation and grasp holding using a single…
Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non-equilibrium materials, which exhibit time-varying rheological properties, are topics of intense investigation. Here, we push composites of circular…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
Polymers adopt extended coil and compact globule states according to the balance between entropy and interaction energies. The transition of a polymer between an extended coil state and compact globule state can be induced by changing…
Unlike most human-engineered systems, many biological systems rely on emergent behaviors from low-level interactions, enabling greater diversity and superior adaptation to complex, dynamic environments. This study explores emergent…
Via large-scale molecular dynamics simulations, we observe the melting of a topological glass of stiff ring polymers by incorporating flexible ring polymers, along an isobaric path. As more flexible ring polymers are introduced, cluster…
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
Multiple loop formation in polymer macromolecules is an important feature of the chromatin organization and DNA compactification in the nuclei. We analyze the size and shape characteristics of complex polymer structures, containing in…
In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of…
Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of…
We study of the dynamics of ring polymers confined to diffuse in a background gel at low concentrations. We do this in order to probe the inter-play between topology and dynamics in ring polymers. We develop an algorithm that takes into…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…
Polymer composites are ubiquitous in biology and industry alike, owing to their emergent desirable mechanical properties not attainable in single-species systems. At the same time, polymer topology has been shown to play a key role in…
This study investigates the probability of threading in star catenanes under good solvent conditions using molecular dynamics simulations, emphasizing the influence of ring rigidity. Threading in these systems arises from the interplay…
We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are…