Related papers: Knots in Macromolecules in Constraint Space
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…
Knots are fascinating topological structures that have been observed in various contexts, ranging from micro-worlds to macro-systems, and are conjectured to play a fundamental role in their respective fields. In order to characterize their…
We theoretically analyse the equation of topological solitons in a chain of particles interacting via a repulsive power-law potential and confined by a periodic lattice. Starting from the discrete model, we perform a gradient expansion and…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
Ascending numbers are determined for 64 knots with at most n=10 crossings. After proving the theorem about the signature of alternating knot families, we distinguished all families of knots obtained from generating alternating knots with at…
Proteins can sometimes be knotted, and for many reasons the study of knotted proteins is rapidly becoming very important. For example, it has been proposed that a knot increases the stability of a protein. Knots may also alter enzymatic…
We consider a one-dimensional simple random walk surviving among a field of static soft traps : each time it meets a trap the walk is killed with probability 1--e --$\beta$ , where $\beta$ is a positive and fixed parameter. The positions of…
We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost…
Average block entanglement in the 1D XX-model with uncorrelated random couplings is known to grow as the logarithm of the block size, in similarity to conformal systems. In this work we study random spin chains whose couplings present long…
In the present work, four series of simulations are analyzed: entangled model networks of a) mono-disperse or b) poly-disperse weight distribution between the crosslinks, c) non-entangled phantom model networks and d) non-entangled model…
Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…
Using computer calculations and working with representatives of pretzel tangles we established general adequacy criteria for different classes of knots and links. Based on adequate graphs obtained from all Kauffman states of an alternating…
In this note microgels with and without excluded volume interactions are considered. Based on earlier exact computations on Gaussian mircogels, which are formed by self-crosslinking (with $M$ crosslinks) of polymer chains with chain length…
We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyse their range of validity by means of comprehensive Molecular…
A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We have used protein engineering and atomic force microscopy to explore…
The (ordinary) unknotting-number of 1-dimensional knots, which is defined by using the crossing-change, is a very basic and important invariant. It is very natural to consider the `unknotting-number' associated with other local-moves on…
We study several related models of self-avoiding polygons in a tubular subgraph of the simple cubic lattice, with a particular interest in the asymptotics of the knotting statistics. Polygons in a tube can be characterised by a finite…
The scaling of the bond-bond correlation function $C(s)$ along linear polymer chains is investigated with respect to the curvilinear distance, $s$, along the flexible chain and the monomer density, $\rho$, via Monte Carlo and molecular…
Consider a network of M >> 1 nodes connected by N >> 1 links, in which the distribution of the number of links per node follows a power law with exponent 0<\alpha <1. The power law is naturally truncated due to the fact that N is finite. A…
We study harmonic chains with i.i.d. random spring constants $K_n$ and i.i.d. random masses $m_n$. We introduce a new combinatorial approach which allows to derive a compact approximate expression for the complex Lyapunov exponent, in terms…