相关论文: Classification of (uncolored) bonded knots and lin…
A polynomial is presented that models a topological knot in a unique manner. It distinguishes all types of knots including the orientation and has a group theory interpretation. The topologies may be labeled via a number, which upon a base…
In this paper we present a detailed study of \emph{bonded knots} and their related structures, integrating recent developments into a single framework. Bonded knots are classical knots endowed with embedded bonding arcs modeling physical or…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…
We model proteins with intramolecular bonds, such as disulfide bridges, using the concept of bonded knots -- closed loops in three-dimensional space equipped with additional bonds that connect different segments of the knot. We extend the…
Bonded knots arise naturally in topological protein modeling, where intramolecular interactions such as disulfide bridges stabilize folded configurations. These structures extend classical knot theory by incorporating embedded graphs, and…
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular…
We present a complete classification of spherical knotoids with up to six crossings and conjecture that our classification up to seven crossings is complete. Our work extends the tradition of knot tabulation to the setting of knotoids…
We introduce a monoid corresponding to knotted surfaces in four space, from its hyperbolic splitting represented by marked diagram in braid like form. It has four types of generators: two standard braid generators and two of singular type.…
The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the…
We equip a knot $K$ with a set of colored bonds, that is, colored intervals properly embedded into $\mathbb{R}^3 \setminus K$. Such a construction can be viewed as a structure that topologically models a closed protein chain including any…
The aim of this paper is to define certain algebraic structures coming from generalized Reidemeister moves of singular knot theory. We give examples, show that the set of colorings by these algebraic structures is an invariant of singular…
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…
This paper gives new and elementary combinatorial topological proofs of the classification of unoriented and oriented rational knots and links. These proofs are based on the known classification of alternating knots through flyping, and the…
Sutured manifolds defined by Gabai are useful in the geometrical study of knots and 3-dimensional manifolds. On the other hand, homology cylinders are in an important position in the recent theory of homology cobordisms of surfaces and…
We introduce topological invariants of knots and braid conjugacy classes, in the form of differential graded algebras, and present an explicit combinatorial formulation for these invariants. The algebras conjecturally give the relative…
Folded linear molecular chains are ubiquitous in biology. Folding is mediated by intra-chain interactions that "glue" two or more regions of a chain. The resulting fold topology is widely believed to be a determinant of biomolecular…
The conventional topological description given by the fundamental group of nematic order parameter does not adequately explain the entangled defect line structures that have been observed in nematic colloids. We introduce a new topological…
Arborescent knots are the ones which can be represented in terms of double fat graphs or equivalently as tree Feynman diagrams. This is the class of knots for which the present knowledge is enough for lifting topological description to the…
A special class of braids, called woven, is introduced and it is shown that every conjugation class of the braid group contains woven braids. In consequence, links can be presented as plats or closures of woven braids. Restricting on knots,…