Related papers: Activity-driven polymer knotting for macromolecula…
In the presented work we study, by means of numerical simulations, the behaviour of a suspension of active ring polymers in the bulk and under lateral confinement. When changing the separation between the confining planes and the polymers'…
In this work, we compare the structural and dynamic behavior of active filaments in two dimensions using tangential and push-pull models, including a variant with passive end monomers. These models serve as valuable frameworks for…
The topological effects on the thermal properties of several knot configurations are investigated using Monte Carlo simulations. In order to check if the topology of the knots is preserved during the thermal fluctuations we propose a method…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
Active colloidal particles typically exhibit a pronounced affinity for accumulating and being captured at boundaries. Here, we engineer long-range repulsive interactions between colloids that self-propel under an electric field and…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
Indentation is a common experimental technique to study the mechanics of polymeric materials. The main advantage of using indentation is because this provides a direct correlation between the microstructure and the small-scale mechanical…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…
Activity and renewability are distinctive features of living matter, and constitute a new class of materials that we term renewable active matter. A striking example is the cell cytoskeleton, where myosin filaments bind to the actin…
Active dynamic processes of cells are largely driven by the cytoskeleton, a complex and adaptable semiflexible polymer network, motorized by mechanoenzymes. Small dimensions, confined geome- tries and hierarchical structures make it…
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate…
Evolution in time-varying environments naturally leads to adaptable biological systems that can easily switch functionalities. Advances in the synthesis of environmentally-responsive materials therefore open up the possibility of creating a…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
Tangentially driven active polymers (TDAPs), model systems for motor-driven filaments, have been extensively studied in uniform activity fields. Here, we show that an activity gradient breaks fore-aft symmetry, generating net body forces…
We explore the effect of Couette flow on knotted linear polymer chains with extensive Molecular Dynamics (MD) simulations. Hydrodynamic interactions are accounted for by means of Multi-Particle Collision Dynamics (MPCD). The polymer chain,…
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…