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Circuit Topology
The circuit topology of a folded linear polymer refers to the arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. Proteins fold via the formation of contacts of various natures, including hydrogen bonds, disulfide bonds, and beta-beta interactions. RNA molecules fold by forming hydrogen bonds between nucleotides, forming nested or non-nested structures. Contacts in the genome are established via protein bridges including CTCF and cohesins and are measured by technologies including Chromosome conformation capture, Hi-C. Circuit topology categorises the topological arrangement of these physical contacts, that are referred to as hard contacts (or h-contacts). Furthermore, chains can fold via knotting (or the formation of "soft" contacts (s-contacts)). Circuit topology uses a similar language to categorise both "soft" and "hard" contacts, and provides a full description of a folded linear chain. In this ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Schematic Description Of Circuit Topology
A schematic, or schematic diagram, is a designed representation of the elements of a system using abstract, graphic symbols rather than realistic pictures. A schematic usually omits all details that are not relevant to the key information the schematic is intended to convey, and may include oversimplified elements in order to make this essential meaning easier to grasp, as well as additional organization of the information. For example, a subway map intended for passengers may represent a subway station with a dot. The dot is not intended to resemble the actual station at all but aims to give the viewer information without unnecessary visual clutter. A schematic diagram of a chemical process uses symbols in place of detailed representations of the vessels, piping, valves, pumps, and other equipment that compose the system, thus emphasizing the functions of the individual elements and the interconnections among them and suppresses their physical details. In an electronic circuit d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Evolution
Molecular evolution describes how Heredity, inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of Cell (biology), cells and organisms. Molecular evolution is the basis of phylogenetics, phylogenetic approaches to describing the Tree of life (biology), tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the Evolutionary developmental biology, evolution of development, and patterns and processes underlying genome, genomic changes during evolution. History The history of molecular evolution starts in the early 20th century with comparative biochemistry, and the use of "fingerprinting" methods such as immune assays, gel electrophoresis, and paper chromatography in the 1950s to explore homologous proteins. The advent of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Supramolecular Chemistry
Supramolecular chemistry refers to the branch of chemistry concerning Chemical species, chemical systems composed of a integer, discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces, electrostatics, electrostatic charge, or hydrogen bonding to strong covalent bonding, provided that the electronic coupling strength remains small relative to the energy parameters of the component. While traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules. These forces include hydrogen bonding, coordination complex, metal coordination, hydrophobic effect, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects. Important concepts advanced by supramolecular chemistry include molecular self-assembly, folding (chemistry), molecular folding, molecular recognition, host–gues ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mathematical Chemistry
Mathematical chemistry is the area of research engaged in novel applications of mathematics to chemistry; it concerns itself principally with the mathematical modeling of chemical phenomena. Mathematical chemistry has also sometimes been called computer chemistry, but should not be confused with computational chemistry. Major areas of research in mathematical chemistry include chemical graph theory, which deals with topology such as the mathematical study of isomerism and the development of topological descriptors or indices which find application in quantitative structure-property relationships; and chemical aspects of group theory, which finds applications in stereochemistry and quantum chemistry. Another important area is molecular knot theory and circuit topology that describe the topology of folded linear molecules such as proteins and nucleic acids. The history of the approach may be traced back to the 19th century. Georg Helm published a treatise titled "The Principles ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Geometry
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of a molecule, i.e. they can be understood as approximately local and hence transferable properties. Determination The molecular geometry can be determined by various spectroscopic methods and diffraction methods. IR, microwave and Raman spectroscopy can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques. X-ray crystallography, neutron diffraction and electron diffraction can g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Topology
A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Topology
Topology (from the Greek language, Greek words , and ) is the branch of mathematics concerned with the properties of a Mathematical object, geometric object that are preserved under Continuous function, continuous Deformation theory, deformations, such as Stretch factor, stretching, Torsion (mechanics), twisting, crumpling, and bending; that is, without closing holes, opening holes, tearing, gluing, or passing through itself. A topological space is a Set (mathematics), set endowed with a structure, called a ''Topology (structure), topology'', which allows defining continuous deformation of subspaces, and, more generally, all kinds of List of continuity-related mathematical topics, continuity. Euclidean spaces, and, more generally, metric spaces are examples of topological spaces, as any distance or metric defines a topology. The deformations that are considered in topology are homeomorphisms and Homotopy, homotopies. A property that is invariant under such deformations is a to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Topology (chemistry)
In chemistry, topology provides a way of describing and predicting the molecular structure within the constraints of three-dimensional (3-D) space. Given the determinants of chemical bonding and the Chemical property, chemical properties of the atoms, topology provides a model for explaining how the atoms ethereal wave functions must fit together. Molecular topology is a part of mathematical chemistry dealing with the algebraic description of chemical compounds so allowing a unique and easy characterization of them. Topology is insensitive to the details of a scalar field, and can often be determined using simplified calculations. Scalar fields such as electron density, Erwin Madelung, Madelung field, covalent field and the electrostatic potential can be used to model topology.Brown, David; Topology and Chemistry; Structural Chemistry Volume 13, Numbers 3–4, 339–355, Each scalar field has its own distinctive topology and each provides different information about the nature ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Prime Knot
In 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. Knots are characterized by their crossing numbers. The simplest prime knot is the trefoil with three crossings. The trefoil is actually a (2, 3)-torus knot. The figure-eight knot, with four crossings, is the simplest non-torus knot. For any positive integer ''n'', there are a finite number of prime knots with ''n'' crossings. The first few values for exclusively prime knots and for prime ''or'' composite k ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polymer
A polymer () is a chemical substance, substance or material that consists of very large molecules, or macromolecules, that are constituted by many repeat unit, repeating subunits derived from one or more species of monomers. Due to their broad spectrum of properties, both synthetic and natural polymers play essential and ubiquitous roles in everyday life. Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function. Polymers, both natural and synthetic, are created via polymerization of many small molecules, known as monomers. Their consequently large molecular mass, relative to small molecule compound (chemistry), compounds, produces unique physical property, physical properties including toughness, high rubber elasticity, elasticity, viscoelasticity, and a tendency to form Amorphous solid, amorphous and crystallization of polymers, semicrystalline structures rath ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Knot Theory
In topology, knot theory is the study of knot (mathematics), 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, \mathbb^3. Two mathematical knots are equivalent if one can be transformed into the other via a deformation of \mathbb^3 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. Knots can be described in various ways. Using different description methods, there may be more than one description of the same knot. For example, a common method of describing a knot is a planar diagram called a knot diagram, in which any knot can be drawn in many different ways. Therefore, a fundamental p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromosome Conformation Capture
Chromosome conformation capture techniques (often abbreviated to 3C technologies or 3C-based methods) are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of interactions between genomic loci that are nearby in 3-D space, but may be separated by many nucleotides in the linear genome. Such interactions may result from biological functions, such as promoter- enhancer interactions, or from random polymer looping, where undirected physical motion of chromatin causes loci to collide. Interaction frequencies may be analyzed directly, or they may be converted to distances and used to reconstruct 3-D structures. The chief difference between 3C-based methods is their scope. For example, when using PCR to detect interaction in a 3C experiment, the interactions between two specific fragments are quantified. In contrast, Hi-C quantifies interactions between all possible pairs of fragments simultaneously ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
