Related papers: Activity-driven polymer knotting for macromolecula…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
Understanding how to produce forces using biomolecular building blocks is essential for the development of adaptive synthetic cells and living materials. Here we ask whether a dynamic polymer system can generate deformation forces in soft…
Hydrodynamic interactions as modeled by Multi-Particle Collision Dynamics can dramatically influence the dynamics of fully flexible, ring-shaped polymers in ways not known for any other polymer architecture or topology. We show that steady…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance' to the knot. The influence of knots on…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
Motivated by chromosomes enclosed in nucleus and the recently discovered active topological glass, we study a spherically confined melt of long nonconcatenated active polymer rings. Without activity, the rings exhibit the same average…
Traditional robotic mechanisms contain a series of rigid links connected by rotational joints that provide powered motion, all of which is controlled by a central processor. By contrast, analogous mechanisms found in nature, such as octopus…
The thermal properties of coarse grained knotted polymers containing two kinds of monomers $A$ and $B$ fluctuating in a solution are investigated on a simple cubic lattice using the Wang-Landau MC algorithm. These knots have a more complex…
Molecular motors are essential to the living, they generate additional fluctuations that boost transport and assist assembly. Self-propelled colloids, that consume energy to move, hold similar potential for the man-made assembly of…
The characterization of the interactions between two fully flexible self-avoiding polymers is one of the classic and most important problems in polymer physics. In this paper we measure these interactions in the presence of active…
Biological organisms often have elongated, flexible structures with some degree of chirality in their bodies or movements. In nature, these organisms frequently take advantage of self-encapsulation mechanisms that create folded…
Ring polymers are prevalent in natural and engineered systems, including circular bacterial DNA, crown ethers for cation chelation, and mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and…
Reconstituted filamentous actin networks with myosin motor proteins form active gels, in which motor proteins generate forces that drive the network far from equilibrium. This motor activity can also strongly affect the network elasticity;…
We use a computational phase-field model together with analytical analysis to study how inter-cellular active forces can mediate individual cell morphology and collective motion in a confluent cell monolayer. Contractile inter-cellular…