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In these lecture notes we review the original work of Riemann on multi-valued functions, Kelvin’s application to Green’s potential theory, and the result of Gauss on the interpretation of the magnetic potential in terms of solid angle to show the relevance of these earlier results in modern topological field theory. This is done by considering some particular case studies. First we re-derive the Biot-Savart induction law in terms of solid angle, and we discuss the interplay of topology and physics in the context of the celebrated Aharonov-Bohm experiment. By showing how the helicity is made gauge invariant in a multiply connected domain, we demonstrate how Riemann’s cuts are re-interpreted in terms of modern homological concepts. Finally, by considering Kleinert’s multi-valued gauge theory for defects we show how direct application of the theory of currents help to correct results in the hydrodynamic interpretation of vortex defects in condensed matter physics.

The last years have witnessed remarkable advances in our understanding of the emergence and consequences of topological constraints in biological and soft matter. Examples are abundant in relation to (bio)polymeric systems and range from the characterization of knots in single polymers and proteins to that of whole chromosomes and polymer melts. At the same time, considerable advances have been made in the description of the interplay between topological and physical properties in complex fluids, with the development of techniques that now allow researchers to control the formation of and interaction between defects in diverse classes of liquid crystals. Thanks to technological progress and the integration of experiments with increasingly sophisticated numerical simulations, topological biological and soft matter is a vibrant area of research attracting scientists from a broad range of disciplines. However, owing to the high degree of specialization of modern science, many results have remained confined to their own particular fields, with different jargon making it difficult for researchers to share ideas and work together towards a comprehensive view of the diverse phenomena at play. Compelled by these motivations, here we present a comprehensive overview of topological effects in systems ranging from DNA and genome organization to entangled proteins, polymeric materials, liquid crystals, and theoretical physics, with the intention of reducing the barriers between different fields of soft matter and biophysics. Particular care has been taken in providing a coherent formal introduction to the topological properties of polymers and of continuum materials and in highlighting the underlying common aspects concerning the emergence, characterization, and effects of topological objects in different systems. The second half of the review is dedicated to the presentation of the latest results in selected problems, specifically, the effects of topological constraints on the

Here we review some recent developments in the topological study of vortex knots and links. We start from fundamental properties of kinetic helicity, a conserved quantity of ideal fluid mechanics, focusing on the topological interpretation in terms of linking numbers. Then we proceed to consider the derivation from helicity of the Jones and HOMFLYPT knot polynomials, showing that their adapted formulation can be expressed in terms of writhe and twist helicity. Through explicit computations and examples, we also show that these adapted polynomials provide useful information to quantify the topological cascade of reconnecting vortex knots and links in relation to energy. In an effort to establish direct relationships between topological complexity and energy contents, we highlight the role of ropelength in the energy relaxation of magnetic knots. Optimal pathways of decaying vortex knots are re-considered by a new approach based on the interpretation of geodesic flows in an appropriate knot polynomial space. This novel approach proves to be useful to determine the probability associated with each topological state, and the topological degeneration of fluid structures undergoing a change of topology. As an example, we consider the numerical simulation of the decay of 3 vortex loops linked together to form a system of Borromean rings. The evolution of such system is governed by the Gross-Pitaevskii equation, and preliminary results of this test case are analysed in terms of energy transfers.

Here we illustrate how Jones' polynomials are derived from the kinetic helicity of vortical flows, and how they can be used to measure the topological complexity of fluid knots by numerical values. Relying on this new findings, we show how to use our adapted Jones polynomial in a new framework by introducing a knot polynomial space whose discrete points are the adapted Jones polynomials of fluid knots, interpreting the topological simplification associated with the natural decay of reconnecting fluid knots as geodesic flows on this space.

In this note we provide an analytical proof of the zero helicity condition for systems governed by the Gross-Pitaevskii equation (GPE). The proof is based on the hydrodynamic interpretation of the GPE, and the direct use of Noether's theorem by applying Kleinert's multi-valued gauge theory. As a by-product we also demonstrate the conservation and quantization of the circulation for the GPE.

Here we show that the Gross-Pitaevskii equation (GPE) for Bose-Einstein condensates (BECs) admits hydrodynamic interpretation in a general Riemannian metric, and show that in this metric the momentum equation has a new term that is associated with local curvature and density distribution profile. In particular conditions of steady state a new Einstein's field equation is determined in presence of negative curvature. Since GPE governs BECs defects that are useful, analogue models in cosmology, a relativistic form of GPE is also considered to show connection with models of analogue gravity, thus providing further grounds for future investigations of black hole dynamics in cosmology.

In this paper, we determine the instability effects of a phase twist superposed on a quantum vortex defect governed by the Gross–Pitaevskii equation. For this, we consider the modified form of the equation in two cases: when a uniform phase twist is present everywhere in the condensate, and when the defect is subject to a localized phase twist confined to the defect healing region. In the first case, we show that a secondary, new defect is produced as manifestation of an Aharonov–Bohm type effect. In the second case, we prove that due to energy minimization, the defect changes its configurational energy by converting localized twist to writhe. This mechanism, typical of classical elastic systems, is shown to occur also in quantum defects, and it may find useful applications in science and technology.

Using an improved numerical code we investigate the creation and evolution of quantum knots and links as defects of the Gross-Pitaevskii equation. The particular constraints put on quantum hydrodynamics make this an ideal context for application of geometric and topological methods to investigate dynamical properties. Evolutionary processes are classified into three generic scenarios representing (i) direct topological cascade and collapse, (ii) structural and topological cycles, and (iii) inverse topological cascade of complex structures. Several examples and test cases are studied; the head-on collision of quantum vortex rings and the creation of a trefoil knot from initially unlinked, unknotted loops are realized for the first time. Each type of scenario is studied by carrying out a detailed evaluation of fundamental geometric and dynamical properties associated with evolution. Direct topological cascade that governs the decay of complex structures to small-scale vortex rings is identified by writhe measures, while picks of total curvature are found to provide a clear signature of reconnection events. We demonstrate that isophase minimal surfaces spanning knots and links have a privileged role in the decay process by detecting surface energy relaxation of complex structures. Minimal surfaces are shown to be critical markers for energy and prove to be appropriate detectors for the evolution of complex systems.

Line defects are one-dimensional phase singularities (forming knots and links) that arise in a variety of physical systems. In these systems, isophase surfaces (Seifert surfaces) have the phase defects as boundary, and these Seifert surfaces define a framing of the normal bundle of each link component. We define the individual helicity for each component of a link singularity, and prove that each individual helicity is zero if and only if there exists a Seifert framing for the link. We extend these results to multi-armed defects. We prove that under anti-parallel reconnection of defect strands total twist is conserved.

Topological fluid mechanics is a crucial area of classical mechanics, with remarkable theoretical significance and wide applications in practice. In this paper, we expect to present an introductory review of the direction, for the purpose of attracting more domestic researchers of China to enter into this important area. Our emphasis is placed on the topological essence of fluid helicity. We will give the relationship between helicity and mathematical knotted field theory (i.e., that between helicity and the mutual- and self-linking numbers, as well as the fluid knot polynomial topological invariants constructed in terms of helicity recently discovered by the authors), and give an introduction to the international research on energy-structural complexity relationship for a fluid vortex knot ensemble. Moreover, typical numerical methods are also demonstrated through examples of reconnections occurring in superfluid vortex knots/links. Expectedly, a combination of the theoretical framework and numerical techniques may contribute to the reader a comprehensive understanding of the main target, research methodology and potential technical difficulties in practice in this interdisciplinary field of cutting-edge research world-wide.

Physical knots observed in various contexts – from DNA biology to vortex dynamics and condensed matter physics – are found to undergo topological simplification through iterated recombination of knot strands following a common, qualitative pattern that bears remarkable similarities across fields. Here, by interpreting evolutionary processes as geodesic flows in a suitably defined knot polynomial space, we show that a new measure of topological complexity allows accurate quantification of the probability of decay pathways by selecting the optimal unlinking pathways. We also show that these optimal pathways are captured by a logarithmic best-fit curve related to the distribution of minimum energy states of tight knots. This preliminary approach shows great potential for establishing new relations between topological simplification pathways and energy cascade processes in nature.

The equations governing the evolution of quantum vortex defects subject to twist are derived in standard hydrodynamic form. Vortex defects emerge as solutions of the Gross-Pitaevskii equation, that by Madelung transformation admits a hydrodynamic description. Here, we consider a vortex defect subject to superposed twist due to the rotation of the phase of the wave function. We prove that, when twist is present, the corresponding Hamiltonian is non-Hermitian and determine the effect of twist on the energy expectation value of the system. We show how twist diffusion may trigger linear instability, a property directly related to the non-Hermiticity of the Hamiltonian. We derive the correct continuity equation and, by applying defect theory, we obtain the correct momentum equation. Finally, by coupling twist kinematics and vortex dynamics we determine the full set of hydrodynamic equations governing quantum vortex evolution subject to twist.

In this paper we determine the effects of winding number on the dynamics of vortex torus knots and unknots in the context of classical, ideal fluid mechanics. We prove that the winding number — a topological invariant of torus knots — has a primary effect on vortex motion. This is done by applying the Moore-Saffman desingularization technique to the full Biot-Savart induction law, determining the influence of winding number on the 3 components of the induced velocity. Results have been obtained for 56 knots and unknots up to 51 crossings. In agreement with previous numerical results we prove that in general the propagation speed increases with the number of toroidal coils, but we notice that the number of poloidal coils may greatly modify the motion. Indeed we prove that for increasing aspect ratio and number of poloidal coils vortex motion can be even reversed, in agreement with previous numerical observations. These results demonstrate the importance of three-dimensional features in vortex dynamics and find useful applications to understand helicity and energy transfers across scales in vortical flows.

In this paper we demonstrate that new phase defects of the Gross-Pitaevskii equation (GPE) can be produced as a Aharonov-Bohm effect resulting from pure phase twist injection on existing defects. This is a phenomenon that has physical justification in the hydrodynamic interpretation of GPE. Here we give an analytical proof of its effects by using Fermi-Walker transport and Biot-Savart induction law. An analytical derivation of the dispersion relation is derived from the superposition of phase twist on the fundamental state. Since the extra twist corresponds to a topological change of the total linking number of the system, we show that the production of new defects is just another manifestation of the Aharonov-Bohm effect. We propose a laboratory experiment for Bose-Einstein condensates to test this phenomenon and to show that it can have useful applications in science and technology.

Here we show how to apply a recently introduced method based on the geometric interpretation of linear momentum of vortex lines to determine dynamical properties of a network of knots and links. To show how the method works and to prove its feasibility, we consider the evolution of quantum vortices governed by the Gross-Pitaevskii equation. Accurate estimates of the momentum of interacting and reconnecting vortex rings, links, and knots are determined. The method is of general validity and it proves particularly useful in practical situations where no analytical information is available. It can be easily adapted to situations where morphological information can be extracted from experimental or computational data, thus providing a powerful tool for real-time diagnostics of vortex filaments or other networks of filamentary structures.

In this paper we review recent results on the groundstate energy spectra of magnetic knots and links and compare these results with new results on bending energy of tight knots and links obtained by using RIDGERUNNER data on curvature. Remarkable similarities between the two systems are found. Comparative analysis between magnetic and bending energy at groundstate energy level shows that information based on bending energy provides a very good proxy for magnetic end-states.

By considering steady magnetic fields in the shape of torus knots and unknots in ideal magnetohydrodynamics, we compute some fundamental geometric and physical properties to provide estimates for magnetic energy and helicity. By making use of an appropriate parametrization, we show that knots with dominant toroidal coils that are a good model for solar coronal loops have negligible total torsion contribution to magnetic helicity while writhing number provides a good proxy. Hence, by the algebraic definition of writhe based on crossing numbers, we show that the estimated values of writhe based on image analysis provide reliable information for the exact values of helicity. We also show that magnetic energy is linearly related to helicity, and the effect of the confinement of magnetic field can be expressed in terms of geometric information. These results can find useful application in solar and plasma physics, where braided structures are often present.

In this paper we show that twist, defined in terms of rotation of the phase associated with quantum vortices and other physical defects effectively deprived of internal structure, is a property that has observable effects in terms of induced axial flow. For this we consider quantum vortices governed by the Gross–Pitaevskii equation (GPE) and perform a number of test cases to investigate and compare the effects of twist in two different contexts: (i) when this is artificially superimposed on an initially untwisted vortex ring; (ii) when it is naturally produced on the ring by the simultaneous presence of a central straight vortex. In the first case large amplitude perturbations quickly develop, generated by the unnatural setting of the initial condition that is not an analytical solution of the GPE. In the second case much milder perturbations emerge, signature of a genuine physical process. This scenario is confirmed by other test cases performed at higher twist values. Since the second setting corresponds to essential linking, these results provide new evidence of the influence of topology on physics.

In this paper we derive and compare numerical sequences obtained by adapted polynomials such as HOMFLYPT, Jones and Alexander-Conway for the topological cascade of vortex torus knots and links that progressively untie by a single reconnection event at a time. Two cases are considered: the alternate sequence of knots and co-oriented links (with positive crossings) and the sequence of two-component links with oppositely oriented components (negative crossings). New recurrence equations are derived and sequences of numerical values are computed. In all cases the adapted HOMFLYPT polynomial proves to be the best quantifier for the topological cascade of torus knots and links.

Geometric and topological aspects associated with induction effects of field lines in the shape of torus knots/unknots are examined and discussed in detail. Knots are assumed to lie on a mathematical torus of circular cross-section and are parametrized by standard equations. The induced field is computed by direct integration of the Biot-Savart law. Field line patterns of the induced field are obtained and several properties are examined for a large family of knots/unknots up to 51 crossings. The intensity of the induced field at the origin of the reference system (center of the torus) is found to depend linearly on the number of toroidal coils and reaches maximum values near the boundary of the mathematical torus. New analytical estimates and bounds on energy and helicity are established in terms of winding number and minimum crossing number. These results find useful applications in several contexts when the source field is either vorticity, electric current or magnetic field, from vortex dynamics to astrophysics and plasma physics, where highly braided magnetic fields and currents are present.

By numerically solving the three-dimensional Gross-Pitaevskii equation we analyze the cascade process associated with the evolution and decay of a pair of linked vortex rings. The system decays through a series of reconnections to produce finally three unlinked, unfolded, almost planar vortex loops. Total helicity, initially zero, remains unchanged throughout the process. The gradual transfer from writhe (due to initial linking) to twist helicity, followed by a continuous relaxation of twist across scales during the evolution is shown to be a generic mechanism that consistently takes place on each individual component

A comprehensive study of geometric and topological properties of torus knots and unknots is presented. Torus knots/unknots are particularly symmetric, closed, space curves, that wrap the surface of a mathematical torus a number of times in the longitudinal and meridian direction. By using a standard parametrization, new results on local and global properties are found. In particular, we demonstrate the existence of inflection points for a given critical aspect ratio, determine the location and prescribe the regularization condition to remove the local singularity associated with torsion. Since to first approximation total length grows linearly with the number of coils, its nondimensional counterpart is proportional to the topological crossing number of the knot type. We analyze several global geometric quantities, such as total curvature, writhing number, total torsion, and geometric 'energies' given by total squared curvature and torsion, in relation to knot complexity measured by the winding number. We conclude with a brief presentation of research topics, where geometric and topological information on torus knots/unknots finds useful application.

Due to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems.

The process of vortex cascade through continuous reduction of topological complexity by stepwise unlinking, that has been observed experimentally in the production of vortex knots (Kleckner & Irvine, 2013), is shown to be reproduced in the branching of the skein relations of knot polynomials (Liu & Ricca, 2015) used to identify topological complexity of vortex systems. This observation can be usefully exploited for predictions of energy-complexity estimates for fluid flows.

Reconnection is a fundamental event in many areas of science, from the interaction of vortices in classical and quantum fluids, and magnetic flux tubes in magnetohydrodynamics and plasma physics, to the recombination in polymer physics and DNA biology. By using fundamental results in topological fluid mechanics, the helicity of a flux tube can be calculated in terms of writhe and twist contributions. Here we show that the writhe is conserved under anti-parallel reconnection. Hence, for a pair of interacting flux tubes of equal flux, if the twist of the reconnected tube is the sum of the original twists of the interacting tubes, then helicity is conserved during reconnection. Thus, any deviation from helicity conservation is entirely due to the intrinsic twist inserted or deleted locally at the reconnection site. This result has important implications for helicity and energy considerations in various physical contexts.

By using and extending earlier results (Liu & Ricca, J. Phys. A, vol. 45, 2012, 205501), we derive the skein relations of the HOMFLYPT polynomial for ideal fluid knots from helicity, thus providing a rigorous proof that the HOMFLYPT polynomial is a new, powerful invariant of topological fluid mechanics. Since this invariant is a two-variable polynomial, the skein relations are derived from two independent equations expressed in terms of writhe and twist contributions. Writhe is given by addition/subtraction of imaginary local paths, and twist by Dehn's surgery. HOMFLYPT then becomes a function of knot topology and field strength. For illustration we derive explicit expressions for some elementary cases and apply these results to homogeneous vortex tangles. By examining some particular examples we show how numerical implementation of the HOMFLYPT polynomial can provide new insight into fluid-mechanical behaviour of real fluid flows.

Here we show that under quantum reconnection, simulated by using the three-dimensional Gross-Pitaevskii equation, self-helicity of a system of two interacting vortex rings remains conserved. By resolving the fine structure of the vortex cores, we demonstrate that the total length of the vortex system reaches a maximum at the reconnection time, while both writhe helicity and twist helicity remain separately unchanged throughout the process. Self-helicity is computed by two independent methods, and topological information is based on the extraction and analysis of geometric quantities such as writhe, total torsion, and intrinsic twist of the reconnecting vortex rings.

By using analytical results for the constrained minimum energy of magnetic knots we determine the influence of internal twist on the minimum magnetic energy levels of knots and links, and by using ropelength data from the RIDGERUNNER tightening algorithm (Ashton et al 2011 Exp. Math. 20 57-90) we obtain the groundstate energy spectra of the first 250 prime knots and 130 prime links. The two spectra are found to follow an almost identical logarithmic law. By assuming that the number of knot types grows exponentially with the topological crossing number, we show that this generic behavior can be justified by a general relationship between ropelength and crossing number, which is in good agreement with former analytical estimates (Buck and Simon 1999 Topol. Appl. 91 245-57, Diao 2003 J. Knot Theory Ramifications 12 1-16). Moreover, by considering the ropelength averaged over a given knot family, we establish a new connection between the averaged ropelength and the topological crossing number of magnetic knots

In this paper I present and discuss with examples new techniques based on the use of geometric and topological information to quantify dynamical information and determine new relationships between structural complexity and dynamical properties of vortex flows. New means to determine linear and angular momenta from standard diagram analysis of vortex tangles are provided, and the Jones polynomial, derived from the skein relations of knot theory is introduced as a new knot invariant of topological fluid mechanics. For illustration several explicit computations are carried out for elementary vortex configurations. These new techniques are discussed in the context of ideal fluid flows, but they can be equally applied in the case of dissipative systems, where vortex topology is no longer conserved. In this case, a direct implementation of adaptive methods in a real-time diagnostics of real vortex dynamics may offer a new, powerful tool to analyze energy-complexity relations and estimate energy transfers in highly turbulent flows. These methods have general validity, and they can be used in many systems that display a similar degree of self-organization and adaptivity.

A new method based on the use of the Jones polynomial, a well-known topological invariant of knot theory, is introduced to tackle and quantify topological aspects of structural complexity of vortex tangles in ideal fluids. By re-writing the Jones polynomial in terms of helicity, the resulting polynomial becomes then function of knot topology and vortex circulation, providing thus a new invariant of topological fluid dynamics. Explicit computations of the Jones polynomial for some standard configurations, including the Whitehead link and the Borromean rings (whose linking numbers are zero), are presented for illustration. In the case of a homogeneous, isotropic tangle of vortex filaments with same circulation, the new Jones polynomial reduces to some simple algebraic expression, that can be easily computed by numerical methods. This shows that this technique may offer a new setting and a powerful tool to detect and compute topological complexity and to investigate relations with energy, by tackling fundamental aspects of turbulence research.

In this paper I extend the area interpretation of linear and angular momenta of ideal vortex filaments to complex tangles of filaments in space. A method based on the extraction of area information from diagram projections is presented to evaluate the impulse of vortex knots and links. The method relies on the estimate of the signed areas of sub-regions of the graph resulting from the projection of the vortex axes on the plane of the graph. Some examples based on vortex rings interaction, vortex knots and links are considered for illustration. This method provides a complementary tool to estimate dynamical properties of complex fluid flows and it can be easily implemented in real-time diagnostics to investigate fluid dynamical properties of complex vortex flows.

In this paper we examine certain geometric and topological aspects of the dynamics and energetics of vortex torus knots and un-knots. The knots are given by small-amplitude torus knot solutions in the local induction approximation (LIA). Vortex evolution is then studied in the context of the Euler equations by direct numerical integration of the Biot-Savart law and the velocity, helicity and kinetic energy of different vortex knots and unknots are presented for comparison. Vortex complexity is parametrized by the winding number w given by the ratio of the number of meridian wraps to longitudinal wraps. We find that for w < 1, vortex knots and toroidal coils move faster and carry more energy than a reference vortex ring of the same size and circulation, whereas for w > 1, knots and poloidal coils have approximately the same speed and energy as the reference vortex ring. Kinetic helicity is dominated by writhe contributions and increases with knot complexity. All torus knots and unknots tested under Biot-Savart show much stronger permanence than under LIA.

By making simple, heuristic assumptions, a new method based on the derivation of the Jones polynomial invariant of knot theory to tackle and quantify structural complexity of vortex filaments in ideal fluids is presented. First, we show that the topology of a vortex tangle made by knots and links can be described by means of the Jones polynomial expressed in terms of kinetic helicity. Then, for the sake of illustration, explicit calculations of the Jones polynomial for the left-handed and right-handed trefoil knot and for the Whitehead link via the figure-of-eight knot are considered. The resulting polynomials are thus function of the topology of the knot type and vortex circulation and we provide several examples of those. While this heuristic approach extends the use of helicity in terms of linking numbers to the much richer context of knot polynomials, it gives also rise to new interesting problems in mathematical physics and it offers new tools to perform real-time numerical diagnostics of complex flows.