Related papers: RNA foldings and Stuck Knots
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate…
We define a new topological invariant of line arrangements in the complex projective plane. This invariant is a root of unity defined under some combinatorial restrictions for arrangements endowed with some special torsion character on the…
The altenating knots, links and twists projected on the S_2 sphere are identified with the phase Space of a Hamiltonian dynamic system of one degree of freedom. The saddles of the system correspond to the crossing points, the edges, to the…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
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.…
We establish inequalities that constrain the genera of smooth cobordisms between knots in 4-dimensional cobordisms. These "relative adjunction inequalities" improve the adjunction inequalities for closed surfaces which have been…
We study petal diagrams of knots, which provide a method of describing knots in terms of permutations in a symmetric group $S_{2n+1}$. We define two classes of moves on such permutations, called trivial petal additions and crossing…
We define an invariant of tangles and framed tangles given a finite crossed module and a pair of functions, called a Reidemeister pair, satisfying natural properties. We give several examples of Reidemeister pairs derived from racks,…
Knots have a twisted history in quantum physics. They were abandoned as failed models of atoms. Only much later was the connection between knot invariants and Wilson loops in topological quantum field theory discovered. Here we show that…
Ng constructed an invariant of knots in ${\mathbb{R}}^3$, a combinatorial knot contact homology. Extending his study, we construct an invariant of surface-knots in ${\mathbb{R}}^4$ using diagrams in ${\mathbb{R}}^3$.
We study random knots and links in R^3 using the Petaluma model, which is based on the petal projections developed by Adams et al. (2012). In this model we obtain a formula for the distribution of the linking number of a random…
Tied links and the tied braid monoid were introduced recently by the authors and used to define new invariants for classical links. Here, we give a version purely algebraic-combinatoric of tied links. With this new version we prove that the…
Recent progress in string theory has led to a reformulation of quantum-group polynomial invariants for knots and links into new polynomial invariants whose coefficients can be understood in topological terms. We describe in detail how to…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
We study Coxeter racks over $\mathbb{Z}_n$ and the knot and link invariants they define. We exploit the module structure of these racks to enhance the rack counting invariants and give examples showing that these enhanced invariants are…
We present a topological interpretation of knot and braid contact homology in degree zero, in terms of cords and skein relations. This interpretation allows us to extend the knot invariant to embedded graphs and higher-dimensional knots. We…
We offer a pedestrian level review of the wall-crossing invariants. The story begins from the scattering theory in quantum mechanics where the spectrum reshuffling can be related to permutations of S-matrices. In non-trivial situations,…