相关论文: Rational tangle surgery and Xer recombination on c…

Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…

We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact…

Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree…

For p=3 and for p=5 we prove that there are exactly p equivalence classes of p-coloured knots modulo (+/-1)--framed surgeries along unknots in the kernel of a p-colouring. These equivalence classes are represented by connect-sums of n…

By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend…

Deep neural network architectures often consist of repetitive structural elements. We introduce an approach that reveals these patterns and can be broadly applied to the study of deep learning. Similarly to how a power strip helps untangle…

In this paper, we study a geometric/topological measure of knots and links called the nullification number. The nullification of knots/links is believed to be biologically relevant. For example, in DNA topology, one can intuitively regard…

In this paper, we study reducible surgeries on knots in $S^3$. We develop thickness bounds for L-space knots that admit reducible surgeries, and lower bounds on the slice genus for general knots that admit reducible surgeries. The L-space…

Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…

This paper investigates the relationship between the signature and the crossing number of knots and links. We refine existing theorems and provide a comprehensive classification of links with specific properties, particularly those with…

We study knots whose $\mathrm{SL}_2(\mathbb{C})$-character varieties have a component of dimension greater than one. We call such knots $\mathcal{X}$-large and introduce two diagrammatic constructions that produce $\mathcal{X}$-large knots.…

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…

Let $K$ be a knot in a rational homology sphere $M$. This paper investigates the question of when modifying $K$ by adding $m>0$ half-twists to two oppositely-oriented strands, while keeping the rest of $K$ fixed, produces a knot isotopic to…

Closed 3-string braids admit many bandings to two-bridge links. By way of the Montesinos Trick, this allows us to construct infinite families of knots in the connected sum of lens spaces L(r,1) # L(s,1) that admit a surgery to a lens space…

Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…

We introduce the notion of rational links in the solid torus. We show that rational links in the solid torus are fully characterized by rational tangles, and hence by the continued fraction of the rational tangle. Furthermore, we generalize…

We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…

DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuations, but some experiments on strongly-bent shorter molecules…

In transmission X-ray microscopy (TXM) systems, the rotation of a scanned sample might be restricted to a limited angular range to avoid collision to other system parts or high attenuation at certain tilting angles. Image reconstruction…

In this paper, we propose a novel formulation to extend CNNs to two-dimensional (2D) manifolds using orthogonal basis functions, called Zernike polynomials. In many areas, geometric features play a key role in understanding scientific…