Molecular knotIn chemistry, a molecular knot is a mechanically interlocked molecular architecture that is analogous to a macroscopic knot. Naturally-forming molecular knots are found in organic molecules like DNA, RNA, and proteins. It is not certain that naturally occurring knots are evolutionarily advantageous to nucleic acids or proteins, though knotting is thought to play a role in the structure, stability, and function of knotted biological molecules.
Molecular machineMolecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors. Naturally occurring or biological molecular machines are responsible for vital living processes such as DNA replication and ATP synthesis. Kinesins and ribosomes are examples of molecular machines, and they often take the form of multi-protein complexes.
TopologyIn mathematics, topology (from the Greek words τόπος, and λόγος) is concerned with the properties of a geometric object that are preserved under continuous deformations, such as stretching, twisting, crumpling, and bending; that is, without closing holes, opening holes, tearing, gluing, or passing through itself. A topological space is a set endowed with a structure, called a topology, which allows defining continuous deformation of subspaces, and, more generally, all kinds of continuity.
Molecular self-assemblyIn chemistry and materials science, molecular self-assembly is the process by which molecules adopt a defined arrangement without guidance or management from an outside source. There are two types of self-assembly: intermolecular and intramolecular. Commonly, the term molecular self-assembly refers to the former, while the latter is more commonly called folding. Molecular self-assembly is a key concept in supramolecular chemistry. This is because assembly of molecules in such systems is directed through non-covalent interactions (e.
Trefoil knotIn knot theory, a branch of mathematics, the trefoil knot is the simplest example of a nontrivial knot. The trefoil can be obtained by joining together the two loose ends of a common overhand knot, resulting in a knotted loop. As the simplest knot, the trefoil is fundamental to the study of mathematical knot theory. The trefoil knot is named after the three-leaf clover (or trefoil) plant. The trefoil knot can be defined as the curve obtained from the following parametric equations: The (2,3)-torus knot is also a trefoil knot.
Knot theoryIn topology, knot theory is the study of mathematical knots. While inspired by knots which appear in daily life, such as those in shoelaces and rope, a mathematical knot differs in that the ends are joined so it cannot be undone, the simplest knot being a ring (or "unknot"). In mathematical language, a knot is an embedding of a circle in 3-dimensional Euclidean space, . Two mathematical knots are equivalent if one can be transformed into the other via a deformation of upon itself (known as an ambient isotopy); these transformations correspond to manipulations of a knotted string that do not involve cutting it or passing it through itself.
Self-assemblySelf-assembly is a process in which a disordered system of pre-existing components forms an organized structure or pattern as a consequence of specific, local interactions among the components themselves, without external direction. When the constitutive components are molecules, the process is termed molecular self-assembly. Self-assembly can be classified as either static or dynamic. In static self-assembly, the ordered state forms as a system approaches equilibrium, reducing its free energy.
Molecular motorMolecular motors are natural (biological) or artificial molecular machines that are the essential agents of movement in living organisms. In general terms, a motor is a device that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work. In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors.
Molecular assemblerA molecular assembler, as defined by K. Eric Drexler, is a "proposed device able to guide chemical reactions by positioning reactive molecules with atomic precision". A molecular assembler is a kind of molecular machine. Some biological molecules such as ribosomes fit this definition. This is because they receive instructions from messenger RNA and then assemble specific sequences of amino acids to construct protein molecules. However, the term "molecular assembler" usually refers to theoretical human-made devices.
Synthetic molecular motorSynthetic molecular motors are molecular machines capable of continuous directional rotation under an energy input. Although the term "molecular motor" has traditionally referred to a naturally occurring protein that induces motion (via protein dynamics), some groups also use the term when referring to non-biological, non-peptide synthetic motors. Many chemists are pursuing the synthesis of such molecular motors. The basic requirements for a synthetic motor are repetitive 360° motion, the consumption of energy and unidirectional rotation.
Chiral knotIn the mathematical field of knot theory, a chiral knot is a knot that is not equivalent to its mirror image (when identical while reversed). An oriented knot that is equivalent to its mirror image is an amphicheiral knot, also called an achiral knot. The chirality of a knot is a knot invariant. A knot's chirality can be further classified depending on whether or not it is invertible. There are only five knot symmetry types, indicated by chirality and invertibility: fully chiral, invertible, positively amphicheiral noninvertible, negatively amphicheiral noninvertible, and fully amphicheiral invertible.
Molecular propellerMolecular propeller is a molecule that can propel fluids when rotated, due to its special shape that is designed in analogy to macroscopic propellers: it has several molecular-scale blades attached at a certain pitch angle around the circumference of a shaft, aligned along the rotational axis. The molecular propellers designed in the group of Prof. Petr Král from the University of Illinois at Chicago have their blades formed by planar aromatic molecules and the shaft is a carbon nanotube.
Supramolecular assemblyIn chemistry, a supramolecular assembly is a complex of molecules held together by noncovalent bonds. While a supramolecular assembly can be simply composed of two molecules (e.g., a DNA double helix or an inclusion compound), or a defined number of stoichiometrically interacting molecules within a quaternary complex, it is more often used to denote larger complexes composed of indefinite numbers of molecules that form sphere-, rod-, or sheet-like species.
Prime knotIn knot theory, a prime knot or prime link is a knot that is, in a certain sense, indecomposable. Specifically, it is a non-trivial knot which cannot be written as the knot sum of two non-trivial knots. Knots that are not prime are said to be composite knots or composite links. It can be a nontrivial problem to determine whether a given knot is prime or not. A family of examples of prime knots are the torus knots. These are formed by wrapping a circle around a torus p times in one direction and q times in the other, where p and q are coprime integers.
Molecular nanotechnologyMolecular nanotechnology (MNT) is a technology based on the ability to build structures to complex, atomic specifications by means of mechanosynthesis. This is distinct from nanoscale materials. Based on Richard Feynman's vision of miniature factories using nanomachines to build complex products (including additional nanomachines), this advanced form of nanotechnology (or molecular manufacturing) would make use of positionally-controlled mechanosynthesis guided by molecular machine systems.
Knot (mathematics)In mathematics, a knot is an embedding of the circle S^1 into three-dimensional Euclidean space, R3 (also known as E3). Often two knots are considered equivalent if they are ambient isotopic, that is, if there exists a continuous deformation of R3 which takes one knot to the other. A crucial difference between the standard mathematical and conventional notions of a knot is that mathematical knots are closed — there are no ends to tie or untie on a mathematical knot.
Self-assembly of nanoparticlesNanoparticles are classified as having at least one of three dimensions be in the range of 1-100 nm. The small size of nanoparticles allows them to have unique characteristics which may not be possible on the macro-scale. Self-assembly is the spontaneous organization of smaller subunits to form larger, well-organized patterns. For nanoparticles, this spontaneous assembly is a consequence of interactions between the particles aimed at achieving a thermodynamic equilibrium and reducing the system’s free energy.
Brunnian linkIn knot theory, a branch of topology, a Brunnian link is a nontrivial link that becomes a set of trivial unlinked circles if any one component is removed. In other words, cutting any loop frees all the other loops (so that no two loops can be directly linked). The name Brunnian is after Hermann Brunn. Brunn's 1892 article Über Verkettung included examples of such links. The best-known and simplest possible Brunnian link is the Borromean rings, a link of three unknots.
Knot polynomialIn the mathematical field of knot theory, a knot polynomial is a knot invariant in the form of a polynomial whose coefficients encode some of the properties of a given knot. The first knot polynomial, the Alexander polynomial, was introduced by James Waddell Alexander II in 1923. Other knot polynomials were not found until almost 60 years later. In the 1960s, John Conway came up with a skein relation for a version of the Alexander polynomial, usually referred to as the Alexander–Conway polynomial.
UnlinkIn the mathematical field of knot theory, an unlink is a link that is equivalent (under ambient isotopy) to finitely many disjoint circles in the plane. An n-component link L ⊂ S3 is an unlink if and only if there exists n disjointly embedded discs Di ⊂ S3 such that L = ∪i∂Di. A link with one component is an unlink if and only if it is the unknot. The link group of an n-component unlink is the free group on n generators, and is used in classifying Brunnian links. The Hopf link is a simple example of a link with two components that is not an unlink.
