相关论文: Classification of Tangle Solutions for Integrases,…
We study two systems of tangle equations that arise when modeling the action of the Integrase family of proteins on DNA. These two systems--direct and inverted repeats--correspond to two different possibilities for the initial DNA sequence.…
We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA…
The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into another knot is normally mathematically modeled by band surgery. Band surgeries on a 2-bridge knot N((4mn-1)/(2m))…
We study systems of $2$-tangle equations which play an important role in the analysis of enzyme actions on DNA strands. We show that every system of framed tangle equations has at most one framed rational solution. Furthermore, we show that…
Higher order tensor inversion is possible for even order. We have shown that a tensor group endowed with the Einstein (contracted) product is isomorphic to the general linear group of degree $n$. With the isomorphic group structures, we…
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…
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…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
A natural generalization of a crossing change is a rational subtangle replacement (RSR). We characterize the fundamental situation of the rational tangles obtained from a given rational tangle via RSR, building on work of Berge and Gabai,…
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
In this paper we define novel topological invariants of doubly periodic tangles (DP tangles). DP tangles are embeddings of curves in the thickened plane with translational symmetries in two independent directions. We first organize the…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
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…
Accurately evaluating configurational integrals for dense solids remains a central and difficult challenge in the statistical mechanics of condensed systems. Here, we present a novel tensor network approach that reformulates the…
We show how the tangent bundle decomposition generated by a system of ordinary differential equations may be generalized to the case of a system of second order PDEs `of connection type'. Whereas for ODEs the decomposition is intrinsic, for…
Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II Topoisomerase (TopoII) enzymes play an important role in…
Nonlinear second-order ordinary differential equations are common in various fields of science, such as physics, mechanics and biology. Here we provide a new family of integrable second-order ordinary differential equations by considering…
This paper is an introduction to rational tangles, rational knots and links and their applications to DNA. The paper can be read as an introduction to our more technical papers on rational tangles (math.GT/0311499) and on rational knots…
We give a new geometrical interpretation of the local analytic solutions to a differential system, which we call a tautological system $\tau$, arising from the universal family of Calabi-Yau hypersurfaces $Y_a$ in a $G$-variety $X$ of…