Knot polynomials of open and closed curves.

In this manuscript, we introduce a method to measure entanglement of curves in 3-space that extends the notion of knot and link polynomials to open curves. We define the bracket polynomial of curves in 3-space and show that it has real coefficients and is a continuous function of the curve coordinates. This is used to define the Jones polynomial in a way that it is applicable to both open and closed curves in 3-space. For open curves, the Jones polynomial has real coefficients and it is a continuous function of the curve coordinates and as the endpoints of the curve tend to coincide, the Jones polynomial of the open curve tends to that of the resulting knot. For closed curves, it is a topological invariant, as the classical Jones polynomial. We show how these measures attain a simpler expression for polygonal curves and provide a finite form for their computation in the case of polygonal curves of 3 and 4 edges.

Non-Commutative Worlds and Classical Constraints.

This paper reviews results about discrete physics and non-commutative worlds and explores further the structure and consequences of constraints linking classical calculus and discrete calculus formulated via commutators. In particular, we review how the formalism of generalized non-commutative electromagnetism follows from a first order constraint and how, via the Kilmister equation, relationships with general relativity follow from a second order constraint. It is remarkable that a second order constraint, based on interlacing the commutative and non-commutative worlds, leads to an equivalent tensor equation at the pole of geodesic coordinates for general relativity.

A Knot Polynomial Invariant for Analysis of Topology of RNA Stems and Protein Disulfide Bonds.

Knot polynomials have been used to detect and classify knots in biomolecules. Computation of knot polynomials in DNA and protein molecules have revealed the existence of knotted structures, and provided important insight into their topological structures. However, conventional knot polynomials are not well suited to study RNA molecules, as RNA structures are determined by stem regions which are not taken into account in conventional knot polynomials. In this study, we develop a new class of knot polynomials specifically designed to study RNA molecules, which considers stem regions. We demonstrate that our knot polynomials have direct structural relation with RNA molecules, and can be used to classify the topology of RNA secondary structures. Furthermore, we point out that these knot polynomials can be used to model the topological effects of disulfide bonds in protein molecules.

Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids.

In this paper we introduce a method that offers a detailed overview of the entanglement of an open protein chain. Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. To this end, we implemented the concepts of planar knotoids and bonded knotoids. We show that the planar knotoids technique provides more refined information regarding the knottedness of a protein when compared to established methods in the literature. Moreover, we demonstrate that our topological model for bonded proteins is robust enough to distinguish all types of lassos in proteins.

The mysterious connection between mathematics and physics.

The essay is in the form of a dialogue between the two authors. We take John Wheeler's idea of "It from Bit" as an essential clue and we rework the structure of the bit not to the qubit, but to a logical particle that is its own anti-particle, a logical Marjorana particle. This is our key example of the amphibian nature of mathematics and the external world. We emphasize that mathematics is a combination of calculation and concept. At the conceptual level, mathematics is structured to be independent of time and multiplicity. Mathematics in this way occurs before number and counting. From this timeless domain, mathematics and mathematicians can explore worlds of multiplicity and infinity beyond the apparent limitations of the physical world and see that among these possible worlds there are coincidences with what is observed.

Self-reference, biologic and the structure of reproduction.

In this paper we explore the boundary shared by biology and formal systems.

Control aspects of quantum computing using pure and mixed states.

Steering quantum dynamics such that the target states solve classically hard problems is paramount to quantum simulation and computation. And beyond, quantum control is also essential to pave the way to quantum technologies. Here, important control techniques are reviewed and presented in a unified frame covering quantum computational gate synthesis and spectroscopic state transfer alike. We emphasize that it does not matter whether the quantum states of interest are pure or not. While pure states underly the design of quantum circuits, ensemble mixtures of quantum states can be exploited in a more recent class of algorithms: it is illustrated by characterizing the Jones polynomial in order to distinguish between different (classes of) knots. Further applications include Josephson elements, cavity grids, ion traps and nitrogen vacancy centres in scenarios of closed as well as open quantum systems.

Nuclear-magnetic-resonance quantum calculations of the Jones polynomial.

The repertoire of problems theoretically solvable by a quantum computer recently expanded to include the approximate evaluation of knot invariants, specifically the Jones polynomial. The experimental implementation of this evaluation, however, involves many known experimental challenges. Here we present experimental results for small-scale approximate evaluation of the Jones polynomial by nuclear magnetic resonance (NMR); in addition, we show how to escape from the limitations of NMR approaches that employ pseudopure states. Specifically, we use two spin-1/2 nuclei of natural abundance chloroform and apply a sequence of unitary transforms representing the trefoil knot, the figure-eight knot, and the Borromean rings. After measuring the nuclear spin state of the molecule in each case, we are able to estimate the value of the Jones polynomial for each of the knots.