Related papers: Polynomial Invariant of Molecular Circuit Topology
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…
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…
Circuit topology employs fundamental units of entanglement, known as soft contacts, for constructing knots from the bottom up, utilising circuit topology relations, namely parallel, series, cross, and concerted relations. In this article,…
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 extend knot contact homology to a theory over the ring $\mathbb{Z}[\lambda^{\pm 1},\mu^{\pm 1}]$, with the invariant given topologically and combinatorially. The improved invariant, which is defined for framed knots in $S^3$ and can be…
Knot theory provides a powerful tool for the understanding of topological matters in biology, chemistry, and physics. Here knot theory is introduced to describe topological phases in the quantum spin system. Exactly solvable models with…
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…
We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to circuit topology, which specifically applies to single…
The classification of electron systems according to their topology has been at the forefront of condensed matter research in recent years. It has been found that systems of the same symmetry, previously thought of as equivalent, may in fact…
Circuit topology refers to the arrangement of interactions between objects belonging to a linearly ordered object set. Linearly ordered set of objects are common in nature and occur in a wide range of applications in economics, computer…
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…
We summarize recent work on a combinatorial knot invariant called knot contact homology. We also discuss the origins of this invariant in symplectic topology, via holomorphic curves and a conormal bundle naturally associated to the knot.
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…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
Cyclically ordered graphs, or cogs, sit between abstract graphs and cellularly embedded graphs. They arise naturally in topological graph theory, knot theory, and mathematical biology. We develop a formal theory of cogs and establish a…
Finite-order invariants of knots in arbitrary 3-manifolds (including non-orientable ones) are constructed and studied by methods of the topology of discriminant sets. Obstructions to the integrability of admissible weight systems to…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…
Knot and link polynomials are topological invariants calculated from the expectation value of loop operators in topological field theories. In 3D Chern-Simons theory, these invariants can be found from crossing and braiding matrices of…
The subject of this work is a three-dimensional topological field theory with a non-semisimple group of gauge symmetry with observables consisting in the holonomies of connections around three closed loops. The connections are a linear…
We introduce new topological quantum invariants of compact oriented 3-manifolds with boundary where the boundary is a disjoint union of two identical surfaces. The invariants are constructed via surgery on manifolds of the form $F \times I$…