Transition stateIn chemistry, the transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest potential energy along this reaction coordinate. It is often marked with the double dagger ‡ symbol. As an example, the transition state shown below occurs during the SN2 reaction of bromoethane with a hydroxide anion: The activated complex of a reaction can refer to either the transition state or to other states along the reaction coordinate between reactants and products, especially those close to the transition state.
Reaction coordinateIn chemistry, a reaction coordinate is an abstract one-dimensional coordinate which represents progress along a reaction pathway. It is usually a geometric parameter that changes during the conversion of one or more molecular entities. In molecular dynamics simulations, a reaction coordinate is called collective variable. These coordinates can sometimes represent a real coordinate system (such as bond length, bond angle...), although, for more complex reactions especially, this can be difficult (and non geometric parameters are used, e.
Potential energy surfaceA potential energy surface (PES) describes the energy of a system, especially a collection of atoms, in terms of certain parameters, normally the positions of the atoms. The surface might define the energy as a function of one or more coordinates; if there is only one coordinate, the surface is called a potential energy curve or . An example is the Morse/Long-range potential. It is helpful to use the analogy of a landscape: for a system with two degrees of freedom (e.g.
Distance from a point to a planeIn Euclidean space, the distance from a point to a plane is the distance between a given point and its orthogonal projection on the plane, the perpendicular distance to the nearest point on the plane. It can be found starting with a change of variables that moves the origin to coincide with the given point then finding the point on the shifted plane that is closest to the origin. The resulting point has Cartesian coordinates : The distance between the origin and the point is .
Projection (mathematics)In mathematics, a projection is an idempotent mapping of a set (or other mathematical structure) into a subset (or sub-structure). In this case, idempotent means that projecting twice is the same as projecting once. The restriction to a subspace of a projection is also called a projection, even if the idempotence property is lost. An everyday example of a projection is the casting of shadows onto a plane (sheet of paper): the projection of a point is its shadow on the sheet of paper, and the projection (shadow) of a point on the sheet of paper is that point itself (idempotency).
Chemical reactionA chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. Classically, chemical reactions encompass changes that only involve the positions of electrons in the forming and breaking of chemical bonds between atoms, with no change to the nuclei (no change to the elements present), and can often be described by a chemical equation. Nuclear chemistry is a sub-discipline of chemistry that involves the chemical reactions of unstable and radioactive elements where both electronic and nuclear changes can occur.
Image segmentationIn and computer vision, image segmentation is the process of partitioning a into multiple image segments, also known as image regions or image objects (sets of pixels). The goal of segmentation is to simplify and/or change the representation of an image into something that is more meaningful and easier to analyze. Image segmentation is typically used to locate objects and boundaries (lines, curves, etc.) in images. More precisely, image segmentation is the process of assigning a label to every pixel in an image such that pixels with the same label share certain characteristics.
Projection (linear algebra)In linear algebra and functional analysis, a projection is a linear transformation from a vector space to itself (an endomorphism) such that . That is, whenever is applied twice to any vector, it gives the same result as if it were applied once (i.e. is idempotent). It leaves its unchanged. This definition of "projection" formalizes and generalizes the idea of graphical projection. One can also consider the effect of a projection on a geometrical object by examining the effect of the projection on points in the object.
Polar coordinate systemIn mathematics, the polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a reference point and an angle from a reference direction. The reference point (analogous to the origin of a Cartesian coordinate system) is called the pole, and the ray from the pole in the reference direction is the polar axis. The distance from the pole is called the radial coordinate, radial distance or simply radius, and the angle is called the angular coordinate, polar angle, or azimuth.
Geometric transformationIn mathematics, a geometric transformation is any bijection of a set to itself (or to another such set) with some salient geometrical underpinning. More specifically, it is a function whose domain and range are sets of points — most often both or both — such that the function is bijective so that its inverse exists. The study of geometry may be approached by the study of these transformations. Geometric transformations can be classified by the dimension of their operand sets (thus distinguishing between, say, planar transformations and spatial transformations).
DimensionIn physics and mathematics, the dimension of a mathematical space (or object) is informally defined as the minimum number of coordinates needed to specify any point within it. Thus, a line has a dimension of one (1D) because only one coordinate is needed to specify a point on it - for example, the point at 5 on a number line. A surface, such as the boundary of a cylinder or sphere, has a dimension of two (2D) because two coordinates are needed to specify a point on it - for example, both a latitude and longitude are required to locate a point on the surface of a sphere.
Perpendicular distanceIn geometry, the perpendicular distance between two objects is the distance from one to the other, measured along a line that is perpendicular to one or both. The distance from a point to a line is the distance to the nearest point on that line. That is the point at which a segment from it to the given point is perpendicular to the line. Likewise, the distance from a point to a curve is measured by a line segment that is perpendicular to a tangent line to the curve at the nearest point on the curve.
Root-mean-square deviationThe root-mean-square deviation (RMSD) or root-mean-square error (RMSE) is a frequently used measure of the differences between values (sample or population values) predicted by a model or an estimator and the values observed. The RMSD represents the square root of the second sample moment of the differences between predicted values and observed values or the quadratic mean of these differences. These deviations are called residuals when the calculations are performed over the data sample that was used for estimation and are called errors (or prediction errors) when computed out-of-sample.
Transition state theoryIn chemistry, transition state theory (TST) explains the reaction rates of elementary chemical reactions. The theory assumes a special type of chemical equilibrium (quasi-equilibrium) between reactants and activated transition state complexes. TST is used primarily to understand qualitatively how chemical reactions take place.
Reaction progress kinetic analysisIn chemistry, reaction progress kinetic analysis (RPKA) is a subset of a broad range of kinetic techniques utilized to determine the rate laws of chemical reactions and to aid in elucidation of reaction mechanisms. While the concepts guiding reaction progress kinetic analysis are not new, the process was formalized by Professor Donna Blackmond (currently at Scripps Research Institute) in the late 1990s and has since seen increasingly widespread use.
Potential energyIn physics, potential energy is the energy held by an object because of its position relative to other objects, stresses within itself, its electric charge, or other factors. The term potential energy was introduced by the 19th-century Scottish engineer and physicist William Rankine, although it has links to the ancient Greek philosopher Aristotle's concept of potentiality. Common types of potential energy include the gravitational potential energy of an object, the elastic potential energy of an extended spring, and the electric potential energy of an electric charge in an electric field.
Euclidean distanceIn mathematics, the Euclidean distance between two points in Euclidean space is the length of a line segment between the two points. It can be calculated from the Cartesian coordinates of the points using the Pythagorean theorem, therefore occasionally being called the Pythagorean distance. These names come from the ancient Greek mathematicians Euclid and Pythagoras, although Euclid did not represent distances as numbers, and the connection from the Pythagorean theorem to distance calculation was not made until the 18th century.
Euclidean planeIn mathematics, a Euclidean plane is a Euclidean space of dimension two, denoted E2. It is a geometric space in which two real numbers are required to determine the position of each point. It is an affine space, which includes in particular the concept of parallel lines. It has also metrical properties induced by a distance, which allows to define circles, and angle measurement. A Euclidean plane with a chosen Cartesian coordinate system is called a Cartesian plane.
Standard deviationIn statistics, the standard deviation is a measure of the amount of variation or dispersion of a set of values. A low standard deviation indicates that the values tend to be close to the mean (also called the expected value) of the set, while a high standard deviation indicates that the values are spread out over a wider range. Standard deviation may be abbreviated SD, and is most commonly represented in mathematical texts and equations by the lower case Greek letter σ (sigma), for the population standard deviation, or the Latin letter s, for the sample standard deviation.
Scale spaceScale-space theory is a framework for multi-scale signal representation developed by the computer vision, and signal processing communities with complementary motivations from physics and biological vision. It is a formal theory for handling image structures at different scales, by representing an image as a one-parameter family of smoothed images, the scale-space representation, parametrized by the size of the smoothing kernel used for suppressing fine-scale structures.
