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We are interested in knowing what type of manifolds are obtained by doing Dehn surgery on closed pure 3-braids in the 3-sphere. In particular, we want to determine when we get the 3-sphere by surgery on such a link. We consider links which…
Understanding entanglement remains one of the most intriguing problems in physics. While particle and site entanglement have been studied extensively, the investigation of length or energy scale entanglement, quantifying the information…
Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential…
We refine the combinatorial 1-cocycle $\mathbb{L}R_{reg}$ for regular isotopies of long knots to a 1-cocycle with values in the free $\mathbb{Z}[x,x^{-1}]$-module generated by regular isotopy classes of oriented tangles with exactly one…
We investigate to what extent renormalization can be understood as an algebraic manipulation on concatenated one-loop integrals. We find that the resulting algebra indicates a useful connection to knot theory as well as number theory and…
Suppose F is a compact orientable surface, K is a knot in F x I, and N is the 3-manifold obtained by some non-trivial surgery on K. If F x {0} compresses in N, then there is an annulus in F x I with one end K and the other end an essential…
Using Kirby Calculus, we explicitly pass from Berge's R-R descriptions of ten families of knots with lens space surgeries to surgery descriptions on the minimally twisted five chain link (MT5C). Since the MT5C admits a strong involution, we…
Suppose that $X$ is a torus bundle over a closed surface with homologically essential fibers. Let $X_K$ be the manifold obtained by Fintushel--Stern knot surgery on a fiber using a knot $K\subset S^3$. We prove that $X_K$ has a symplectic…
A knot type is exchange reducible if an arbitrary closed n-braid representative can be changed to a closed braid of minimum braid index by a finite sequence of braid isotopies, exchange moves and +/- destabilizations. In the manuscript [J…
Reconstruction of gene regulatory networks or 'reverse-engineering' is a process of identifying gene interaction networks from experimental microarray gene expression profile through computation techniques. In this paper, we tried to…
The Cyclic Surgery Theorem and Moser's work on surgeries on torus knots imply that for any non-trivial knot in $S^3$, there are at most two integer surgeries that produce a lens space. This paper investigates how many positive integer…
The three-dimensional topologies of the membrane of M-theory can be constructed by performing Dehn surgery along knot lines. We investigate membranes wrapped around a circle and the correponding subset of topologies (Seifert manifolds). The…
Cellulases hold great promise for the production of biofuels and biochemicals. However, they are modular enzymes acting on a complex heterogeneous substrate. Because of this complexity, the computational prediction of their catalytic…
Boring is an operation which converts a knot or two-component link in a 3--manifold into another knot or two-component link. It generalizes rational tangle replacement and can be described as a type of 2--handle attachment. Sutured manifold…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
Band surgery is an operation relating pairs of knots or links in the three-sphere. We prove that if two quasi-alternating knots $K$ and $K'$ of the same square-free determinant are related by a band surgery, then the absolute value of the…
We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation,…
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…
Convolutional Neural Networks (CNN) based image reconstruction methods have been intensely used for X-ray computed tomography (CT) reconstruction applications. Despite great success, good performance of this data-based approach critically…
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m…