Related papers: Circuit topology for bottom-up engineering of mole…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
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…
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,…
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…
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…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
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…
Apart from the knots formed by the main-chain, the proteins can form numerous topological structures, when included the covalent and ion-mediated interactions. In this work, we define the protein non-trivial $\theta$-curves and identify 7…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
Although rare, an increasing number of proteins have been observed to contain entanglements in their native structures. To gain more insight into the significance of protein knotting, researchers have been investigating protein knot…
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…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
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…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
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…
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 present a systematic classification of uncolored bonded knots with singularity number at most seven. Bonded knots provide a topological model for closed protein chains with intramolecular bridges, such as disulfide bonds. Following the…
These notes review a description of quantum mechanics in terms of the topology of spaces, basing on the axioms of Topological Quantum Field Theory and path integral formalism. In this description quantum states and operators are encoded by…
A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past…
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…