In physical knot theory, a knot energy is a functional on the space of all knot conformations. A conformation of a knot is a particular embedding of a circle into three-dimensional space. Depending on the needs of the energy function, the space of conformations is restricted to a sufficiently nicely behaved class. For example, one may consider only polygonal circles or C2 functions. A property of the functional often requires that evolution of the knot under gradient descent does not change knot type.
Physical knot theory is the study of mathematical models of knotting phenomena, often motivated by considerations from biology, chemistry, and physics. Physical knot theory is used to study how geometric and topological characteristics of filamentary structures, such as magnetic flux tubes, vortex filaments, polymers, DNAs, influence their physical properties and functions. It has applications in various fields of science, including topological fluid dynamics, structural complexity analysis and DNA biology.
In mathematics, the term functional has at least two meanings.
Gradient descent is a first-order iterative optimization algorithm for finding the minimum of a function. To find a local minimum of a function using gradient descent, one takes steps proportional to the negative of the gradient of the function at the current point. If, instead, one takes steps proportional to the positive of the gradient, one approaches a local maximum of that function; the procedure is then known as gradient ascent.
The most common type of knot energy comes from the intuition of the knot as electrically charged. Coulomb's law states that two electric charges of the same sign will repel each other as the inverse square of the distance. Thus the knot will evolve under gradient descent according to the electric potential to an ideal configuration that minimizes the electrostatic energy. Naively defined, the integral for the energy will diverge and a regularization trick from physics, subtracting off a term from the energy, is necessary. In addition the knot could change knot type under evolution unless self-intersections are prevented.
Coulomb's law, or Coulomb's inverse-square law, is an experimental law of physics that quantifies the amount of force between two stationary, electrically charged particles. The electric force between charged bodies at rest is conventionally called electrostatic force or Coulomb force. The quantity of electrostatic force between stationary charges is always described by Coulomb’s law. The law was first published in 1785 by French physicist Charles-Augustin de Coulomb, and was essential to the development of the theory of electromagnetism, maybe even its starting point, because it was now possible to discuss quantity of electric charge in a meaningful way.
The inverse-square law, in physics, is any physical law stating that a specified physical quantity or intensity is inversely proportional to the square of the distance from the source of that physical quantity. The fundamental cause for this can be understood as geometric dilution corresponding to point-source radiation into three-dimensional space.
An electric potential is the amount of work needed to move a unit of positive charge from a reference point to a specific point inside the field without producing an acceleration. Typically, the reference point is the Earth or a point at infinity, although any point beyond the influence of the electric field charge can be used.
An electrostatic energy of polygonal knots was studied by Fukuhara in 1987 [1] and shortly after a different, geometric energy was studied by Sakuma. [2] [3] In 1988, Jun O'Hara defined a knot energy based on electrostatic energy, Möbius energy. [4] A fundamental property of the O'Hara energy function is that infinite energy barriers exist for passing the knot through itself. With some additional restrictions, O'Hara showed there were only finitely many knot types with energies less than a given bound. Later, Freedman, He, and Wang removed these restrictions. [5]
Jun O'Hara, legally named Jun Imai, is a Japanese mathematician who works on the fields of low-dimensional topology and knot theory. He is a professor at Tokyo Metropolitan University.
In mathematics, the Möbius energy of a knot is a particular knot energy, i.e., a functional on the space of knots. It was discovered by Jun O'Hara, who demonstrated that the energy blows up as the knot's strands get close to one another. This is a useful property because it prevents self-intersection and ensures the result under gradient descent is of the same knot type.
In topology, a surface is a two-dimensional manifold. Some surfaces arise as the boundaries of three-dimensional solids; for example, the sphere is the boundary of the solid ball. Other surfaces arise as graphs of functions of two variables; see the figure at right. However, surfaces can also be defined abstractly, without reference to any ambient space. For example, the Klein bottle is a surface that cannot be embedded in three-dimensional Euclidean space.
In mathematics, topology is concerned with the properties of space that are preserved under continuous deformations, such as stretching, twisting, crumpling and bending, but not tearing or gluing.
A Möbius strip, Möbius band, or Möbius loop, also spelled Mobius or Moebius, is a surface with only one side and only one boundary. The Möbius strip has the mathematical property of being unorientable. It can be realized as a ruled surface. Its discovery is attributed to the German mathematicians August Ferdinand Möbius and Johann Benedict Listing in 1858, though a structure similar to the Möbius strip can be seen in Roman mosaics dated circa 200–250 AD.
In mathematics, a topological group is a group G together with a topology on G such that the group's binary operation and the group's inverse function are continuous functions with respect to the topology. A topological group is a mathematical object with both an algebraic structure and a topological structure. Thus, one may perform algebraic operations, because of the group structure, and one may talk about continuous functions, because of the topology.
In mathematics, a function space is a set of functions between two fixed sets. Often, the domain and/or codomain will have additional structure which is inherited by the function space. For example, the set of functions from any set X into a vector space have a natural vector space structure given by pointwise addition and scalar multiplication. In other scenarios, the function space might inherit a topological or metric structure, hence the name function space.
In mathematical analysis, a space-filling curve is a curve whose range contains the entire 2-dimensional unit square. Because Giuseppe Peano (1858–1932) was the first to discover one, space-filling curves in the 2-dimensional plane are sometimes called Peano curves, but that phrase also refers to the Peano curve, the specific example of a space-filling curve found by Peano.
A topological quantum field theory is a quantum field theory which computes topological invariants.
In mathematics, contact geometry is the study of a geometric structure on smooth manifolds given by a hyperplane distribution in the tangent bundle satisfying a condition called 'complete non-integrability'. Equivalently, such a distribution may be given as the kernel of a differential one-form, and the non-integrability condition translates into a maximal non-degeneracy condition on the form. These conditions are opposite to two equivalent conditions for 'complete integrability' of a hyperplane distribution, i.e. that it be tangent to a codimension one foliation on the manifold, whose equivalence is the content of the Frobenius theorem.
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
In mathematics, low-dimensional topology is the branch of topology that studies manifolds, or more generally topological spaces, of four or fewer dimensions. Representative topics are the structure theory of 3-manifolds and 4-manifolds, knot theory, and braid groups. It can be regarded as a part of geometric topology. It may also be used to refer to the study of topological spaces of dimension 1, though this is more typically considered part of continuum theory.
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit, or explicitly modelling electrons of each atom.
A lens space is an example of a topological space, considered in mathematics. The term often refers to a specific class of 3-manifolds, but in general can be defined for higher dimensions.
Cotransporters are a subcategory of membrane transport proteins (transporters) that couple the favorable movement of one molecule with its concentration gradient and unfavorable movement of another molecule against its concentration gradient. They enable cotransport and include antiporters and symporters. In general, cotransporters consist of two out of the three classes of integral membrane proteins known as transporters that move molecules and ions across biomembranes. Uniporters are also transporters but move only one type of molecule down its concentration gradient and are not classified as cotransporters.
In mathematics, a manifold is a topological space that locally resembles Euclidean space near each point. More precisely, each point of an n-dimensional manifold has a neighbourhood that is homeomorphic to the Euclidean space of dimension n. In this more precise terminology, a manifold is referred to as an n-manifold.
In mathematics, Floer homology is a tool for studying symplectic geometry and low-dimensional topology. Floer homology is a novel invariant that arises as an infinite-dimensional analog of finite-dimensional Morse homology. Andreas Floer introduced the first version of Floer homology, now called Hamiltonian Floer homology, in his proof of the Arnold conjecture in symplectic geometry. Floer also developed a closely related theory for Lagrangian submanifolds of a symplectic manifold. A third construction, also due to Floer, associates homology groups to closed three-dimensional manifolds using the Yang–Mills functional. These constructions and their descendants play a fundamental role in current investigations into the topology of symplectic and contact manifolds as well as (smooth) three- and four-dimensional manifolds.
In organic chemistry, Möbius aromaticity is a special type of aromaticity believed to exist in a number of organic molecules. In terms of molecular orbital theory these compounds have in common a monocyclic array of molecular orbitals in which there is an odd number of out-of-phase overlaps, the opposite pattern compared to the aromatic character to Hückel systems. The nodal plane of the orbitals, viewed as a ribbon, is a Möbius strip, rather than a cylinder, hence the name. The pattern of orbital energies is given by a rotated Frost circle (with the edge of the polygon on the bottom instead of a vertex), so systems with 4n electrons are aromatic, while those with 4n + 2 electrons are anti-aromatic/non-aromatic. Due to incrementally twisted nature of the orbitals of a Möbius aromatic system, stable Möbius aromatic molecules need to contain at least 8 electrons, although 4 electron Möbius aromatic transition states are well known in the context of the Dewar-Zimmerman framework for pericyclic reactions. Möbius molecular systems were considered in 1964 by Edgar Heilbronner by application of the Hückel method, but the first such isolable compound was not synthesized until 2003 by the group of Rainer Herges. However, the fleeting trans-C9H9+ cation, one conformation of which is shown on the right, was proposed to be Möbius aromatic in 1998 based on computational and experimental data.
Surface Evolver is an interactive program for the study of surfaces shaped by surface tension and other energies, and subject to various constraints. A surface is implemented as a simplicial complex. The user defines an initial surface in a datafile. The Evolver evolves the surface toward minimal energy by a gradient descent method. The aim can be to find a minimal energy surface, or to model the process of evolution by mean curvature. The energy in the Evolver can be a combination of surface tension, gravitational energy, squared mean curvature, user-defined surface integrals, or knot energies. The Evolver can handle arbitrary topology, volume constraints, boundary constraints, boundary contact angles, prescribed mean curvature, crystalline integrands, gravity, and constraints expressed as surface integrals. The surface can be in an ambient space of arbitrary dimension, which can have a Riemannian metric, and the ambient space can be a quotient space under a group action.