相关论文: Recent advances on the non-coherent band surgery m…
The study of knots and links from a probabilistic viewpoint provides insight into the behavior of "typical" knots, and opens avenues for new constructions of knots and other topological objects with interesting properties. The knotting of…
A triangulation is called $z$-knotted if it has a single zigzag (up to reversing). A $z$-orientation on a triangulation is a minimal collection of zigzags which double covers the set of edges. An edge is of type I if zigzags from the…
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
We define a deformation of our earlier link homologies for fundamental representations of sl_m. The deformed homology of a link is isomorphic to the deformed homology of the disjoint union of its components. Moreover, there exists a…
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…
Protein-ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Tasks…
The local analysis is an established approach to the study of singularities and mobility of linkages. Key result of such analyses is a local picture of the finite motion through a configuration. This reveals the finite mobility at that…
We show that any of the new knot invariants obtained from Chern-Simons theory based on an arbitrary non-abelian gauge group do not distinguish isotopically inequivalent mutant knots and links. In an attempt to distinguish these knots and…
Given a knot, we ask how its Khovanov and Khovanov-Rozansky homologies change under the operation of introducing twists in a pair of strands. We obtain long exact sequences in homology and further algebraic structure which is then used to…
Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or…
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…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
This paper presents the methods that have participated in the SHREC 2022 contest on protein-ligand binding site recognition. The prediction of protein-ligand binding regions is an active research domain in computational biophysics and…
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 derive new existence results for tight contact structures on certain 3-manifolds which can be presented as surgery along specific knots in S^3. Indeed, we extend our earlier results on knots with maximal Thurston-Bennequin number being…
We analyze the single-photon band structure and the transport of a single photon in a one-dimensional coupled-spinning-resonator chain. The time-reversal symmetry of the resonators chain is broken by the spinning of the resonators, instead…
An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the…