Related papers: How cooperatively folding are homopolymer molecula…
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…
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…
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…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
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…
An extensive study of single block copolymer knots containing two kinds of monomers $A$ and $B$ is presented. The knots are in a solution and their monomers are subjected to short range interactions that can be attractive or repulsive. In…
We present a molecular dynamics study of the influence of knot complexity and molecular mass on glass formation upon cooling in knotted ring polymer melts. We find that cooperative motion, rigidity, and glassy dynamics can be tuned over a…
We investigate the thermal and structural properties of knotted diblock copolymer rings using a coarse-grained lattice model in an implicit solvent. The system is studied by means of the Wang--Landau Monte Carlo algorithm, allowing us to…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
In this work the thermodynamic properties of short polymer knots (up to 120 segments) defined on a simple cubic lattice are studied with the help of the Wang-Landau Monte Carlo algorithm. The sampling process is performed using pivot…
Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here we surprisingly observed that knotting can be very effectively produced in active polymers.…
Knots are entangled structures that cannot be untangled without a cut. Topological stability of knots is one of the many examples of their important properties that can be used in information storage and transfer. Knot dynamics is important…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
A ring polymer in a confining space may exhibit at least two phases, namely an expanded (or solvent-rich phase) if its concentration is small, or a collapsed (or polymer-rich phase) when it is concentrated and compressed. These phases are…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
Helices are the quintessential geometric motif of the microscale, from alpha-helices in proteins to double helices in DNA. Assembly of the helical geometry of biopolymers is a foundational step in a hierarchy of structure that eventually…
The mechanical properties of polymer knots under stretching in a bad or good solvent are investigated by applying a given force $F$ to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…