In mathematics, orthogonality is the generalization of the geometric notion of perpendicularity . Whereas perpendicular is typically followed by to when relating two lines to one another (e.g., "line A is perpendicular to line B"), [1] orthogonal is commonly used without to (e.g., "orthogonal lines A and B"). [2]
Orthogonality is also used with various meanings that are often weakly related or not related at all with the mathematical meanings.
The word comes from the Ancient Greek ὀρθός (orthós), meaning "upright", [3] and γωνία (gōnía), meaning "angle". [4]
The Ancient Greek ὀρθογώνιον (orthogṓnion) and Classical Latin orthogonium originally denoted a rectangle. [5] Later, they came to mean a right triangle. In the 12th century, the post-classical Latin word orthogonalis came to mean a right angle or something related to a right angle. [6]
In mathematics, orthogonality is the generalization of the geometric notion of perpendicularity to the linear algebra of bilinear forms.
Two elements u and v of a vector space with bilinear form are orthogonal when . Depending on the bilinear form, the vector space may contain null vectors, non-zero self-orthogonal vectors, in which case perpendicularity is replaced with hyperbolic orthogonality.
In the case of function spaces, families of functions are used to form an orthogonal basis, such as in the contexts of orthogonal polynomials, orthogonal functions, and combinatorics.
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In optics, polarization states are said to be orthogonal when they propagate independently of each other, as in vertical and horizontal linear polarization or right- and left-handed circular polarization.
In special relativity, a time axis determined by a rapidity of motion is hyperbolic-orthogonal to a space axis of simultaneous events, also determined by the rapidity. The theory features relativity of simultaneity.
In quantum mechanics, a sufficient (but not necessary) condition that two eigenstates of a Hermitian operator, and , are orthogonal is that they correspond to different eigenvalues. This means, in Dirac notation, that if and correspond to different eigenvalues. This follows from the fact that Schrödinger's equation is a Sturm–Liouville equation (in Schrödinger's formulation) or that observables are given by Hermitian operators (in Heisenberg's formulation).[ citation needed ]
In art, the perspective (imaginary) lines pointing to the vanishing point are referred to as "orthogonal lines". The term "orthogonal line" often has a quite different meaning in the literature of modern art criticism. Many works by painters such as Piet Mondrian and Burgoyne Diller are noted for their exclusive use of "orthogonal lines" — not, however, with reference to perspective, but rather referring to lines that are straight and exclusively horizontal or vertical, forming right angles where they intersect. For example, an essay at the web site of the Thyssen-Bornemisza Museum states that "Mondrian ... dedicated his entire oeuvre to the investigation of the balance between orthogonal lines and primary colours." Archived 2009-01-31 at the Wayback Machine
Orthogonality in programming language design is the ability to use various language features in arbitrary combinations with consistent results. [8] This usage was introduced by Van Wijngaarden in the design of Algol 68:
The number of independent primitive concepts has been minimized in order that the language be easy to describe, to learn, and to implement. On the other hand, these concepts have been applied “orthogonally” in order to maximize the expressive power of the language while trying to avoid deleterious superfluities. [9]
Orthogonality is a system design property which guarantees that modifying the technical effect produced by a component of a system neither creates nor propagates side effects to other components of the system. Typically this is achieved through the separation of concerns and encapsulation, and it is essential for feasible and compact designs of complex systems. The emergent behavior of a system consisting of components should be controlled strictly by formal definitions of its logic and not by side effects resulting from poor integration, i.e., non-orthogonal design of modules and interfaces. Orthogonality reduces testing and development time because it is easier to verify designs that neither cause side effects nor depend on them.
An instruction set is said to be orthogonal if it lacks redundancy (i.e., there is only a single instruction that can be used to accomplish a given task) [10] and is designed such that instructions can use any register in any addressing mode. This terminology results from considering an instruction as a vector whose components are the instruction fields. One field identifies the registers to be operated upon and another specifies the addressing mode. An orthogonal instruction set uniquely encodes all combinations of registers and addressing modes. [11]
In telecommunications, multiple access schemes are orthogonal when an ideal receiver can completely reject arbitrarily strong unwanted signals from the desired signal using different basis functions. One such scheme is time-division multiple access (TDMA), where the orthogonal basis functions are nonoverlapping rectangular pulses ("time slots").
Another scheme is orthogonal frequency-division multiplexing (OFDM), which refers to the use, by a single transmitter, of a set of frequency multiplexed signals with the exact minimum frequency spacing needed to make them orthogonal so that they do not interfere with each other. Well known examples include (a, g, and n) versions of 802.11 Wi-Fi; WiMAX; ITU-T G.hn, DVB-T, the terrestrial digital TV broadcast system used in most of the world outside North America; and DMT (Discrete Multi Tone), the standard form of ADSL.
In OFDM, the subcarrier frequencies are chosen[ how? ] so that the subcarriers are orthogonal to each other, meaning that crosstalk between the subchannels is eliminated and intercarrier guard bands are not required. This greatly simplifies the design of both the transmitter and the receiver. In conventional FDM, a separate filter for each subchannel is required.
When performing statistical analysis, independent variables that affect a particular dependent variable are said to be orthogonal if they are uncorrelated, [12] since the covariance forms an inner product. In this case the same results are obtained for the effect of any of the independent variables upon the dependent variable, regardless of whether one models the effects of the variables individually with simple regression or simultaneously with multiple regression. If correlation is present, the factors are not orthogonal and different results are obtained by the two methods. This usage arises from the fact that if centered by subtracting the expected value (the mean), uncorrelated variables are orthogonal in the geometric sense discussed above, both as observed data (i.e., vectors) and as random variables (i.e., density functions). One econometric formalism that is alternative to the maximum likelihood framework, the Generalized Method of Moments, relies on orthogonality conditions. In particular, the Ordinary Least Squares estimator may be easily derived from an orthogonality condition between the explanatory variables and model residuals.
In taxonomy, an orthogonal classification is one in which no item is a member of more than one group, that is, the classifications are mutually exclusive.
In chemistry and biochemistry, an orthogonal interaction occurs when there are two pairs of substances and each substance can interact with their respective partner, but does not interact with either substance of the other pair. For example, DNA has two orthogonal pairs: cytosine and guanine form a base-pair, and adenine and thymine form another base-pair, but other base-pair combinations are strongly disfavored. As a chemical example, tetrazine reacts with transcyclooctene and azide reacts with cyclooctyne without any cross-reaction, so these are mutually orthogonal reactions, and so, can be performed simultaneously and selectively. [13]
In organic synthesis, orthogonal protection is a strategy allowing the deprotection of functional groups independently of each other.
In supramolecular chemistry the notion of orthogonality refers to the possibility of two or more supramolecular, often non-covalent, interactions being compatible; reversibly forming without interference from the other.
In analytical chemistry, analyses are "orthogonal" if they make a measurement or identification in completely different ways, thus increasing the reliability of the measurement. Orthogonal testing thus can be viewed as "cross-checking" of results, and the "cross" notion corresponds to the etymologic origin of orthogonality. Orthogonal testing is often required as a part of a new drug application.
In the field of system reliability orthogonal redundancy is that form of redundancy where the form of backup device or method is completely different from the prone to error device or method. The failure mode of an orthogonally redundant back-up device or method does not intersect with and is completely different from the failure mode of the device or method in need of redundancy to safeguard the total system against catastrophic failure.
In neuroscience, a sensory map in the brain which has overlapping stimulus coding (e.g. location and quality) is called an orthogonal map.
In philosophy, two topics, authors, or pieces of writing are said to be "orthogonal" to each other when they do not substantively cover what could be considered potentially overlapping or competing claims. Thus, texts in philosophy can either support and complement one another, they can offer competing explanations or systems, or they can be orthogonal to each other in cases where the scope, content, and purpose of the pieces of writing are entirely unrelated.
In board games such as chess which feature a grid of squares, 'orthogonal' is used to mean "in the same row/'rank' or column/'file'". This is the counterpart to squares which are "diagonally adjacent". [27] In the ancient Chinese board game Go a player can capture the stones of an opponent by occupying all orthogonally adjacent points.
In law, orthogonality can refer to interests in a proceeding that are not aligned, but also bear no correlation or effect on each other, so as not to create a conflict of interest.
Stereo vinyl records encode both the left and right stereo channels in a single groove. The V-shaped groove in the vinyl has walls that are 90 degrees to each other, with variations in each wall separately encoding one of the two analogue channels that make up the stereo signal. The cartridge senses the motion of the stylus following the groove in two orthogonal directions: 45 degrees from vertical to either side. [28] A pure horizontal motion corresponds to a mono signal, equivalent to a stereo signal in which both channels carry identical (in-phase) signals.
The 1,3-dipolar cycloaddition is a chemical reaction between a 1,3-dipole and a dipolarophile to form a five-membered ring. The earliest 1,3-dipolar cycloadditions were described in the late 19th century to the early 20th century, following the discovery of 1,3-dipoles. Mechanistic investigation and synthetic application were established in the 1960s, primarily through the work of Rolf Huisgen. Hence, the reaction is sometimes referred to as the Huisgen cycloaddition. 1,3-dipolar cycloaddition is an important route to the regio- and stereoselective synthesis of five-membered heterocycles and their ring-opened acyclic derivatives. The dipolarophile is typically an alkene or alkyne, but can be other pi systems. When the dipolarophile is an alkyne, aromatic rings are generally produced.
Chemical biology is a scientific discipline between the fields of chemistry and biology. The discipline involves the application of chemical techniques, analysis, and often small molecules produced through synthetic chemistry, to the study and manipulation of biological systems. Although often confused with biochemistry, which studies the chemistry of biomolecules and regulation of biochemical pathways within and between cells, chemical biology remains distinct by focusing on the application of chemical tools to address biological questions.
An isocyanide is an organic compound with the functional group –N+≡C−. It is the isomer of the related nitrile (–C≡N), hence the prefix is isocyano. The organic fragment is connected to the isocyanide group through the nitrogen atom, not via the carbon. They are used as building blocks for the synthesis of other compounds.
Click chemistry is an approach to chemical synthesis that emphasizes efficiency, simplicity, selectivity, and modularity in chemical processes used to join molecular building blocks. It includes both the development and use of "click reactions", a set of simple, biocompatible chemical reactions that meet specific criteria like high yield, fast reaction rates, and minimal byproducts. It was first fully described by K. Barry Sharpless, Hartmuth C. Kolb, and M. G. Finn of The Scripps Research Institute in 2001. In this seminal paper, Sharpless argued that synthetic chemistry could emulate the way nature constructs complex molecules, using efficient reactions to join together simple, non-toxic building blocks.
In chemical biology, bioorthogonal chemical reporter is a non-native chemical functionality that is introduced into the naturally occurring biomolecules of a living system, generally through metabolic or protein engineering. These functional groups are subsequently utilized for tagging and visualizing biomolecules. Jennifer Prescher and Carolyn R. Bertozzi, the developers of bioorthogonal chemistry, defined bioorthogonal chemical reporters as "non-native, non-perturbing chemical handles that can be modified in living systems through highly selective reactions with exogenously delivered probes." It has been used to enrich proteins and to conduct proteomic analysis.
In organic chemistry, a cycloalkyne is the cyclic analog of an alkyne. A cycloalkyne consists of a closed ring of carbon atoms containing one or more triple bonds. Cycloalkynes have a general formula CnH2n−4. Because of the linear nature of the C−C≡C−C alkyne unit, cycloalkynes can be highly strained and can only exist when the number of carbon atoms in the ring is great enough to provide the flexibility necessary to accommodate this geometry. Large alkyne-containing carbocycles may be virtually unstrained, while the smallest constituents of this class of molecules may experience so much strain that they have yet to be observed experimentally. Cyclooctyne is the smallest cycloalkyne capable of being isolated and stored as a stable compound. Despite this, smaller cycloalkynes can be produced and trapped through reactions with other organic molecules or through complexation to transition metals.
Carolyn Ruth Bertozzi is an American chemist and Nobel laureate, known for her wide-ranging work spanning both chemistry and biology. She coined the term "bioorthogonal chemistry" for chemical reactions compatible with living systems. Her recent efforts include synthesis of chemical tools to study cell surface sugars called glycans and how they affect diseases such as cancer, inflammation, and viral infections like COVID-19. At Stanford University, she holds the Anne T. and Robert M. Bass Professorship in the School of Humanities and Sciences. Bertozzi is also an Investigator at the Howard Hughes Medical Institute (HHMI) and is the former director of the Molecular Foundry, a nanoscience research center at Lawrence Berkeley National Laboratory.
Bioconjugation is a chemical strategy to form a stable covalent link between two molecules, at least one of which is a biomolecule. Methods to conjugate biomolecules are applied in various field, including medicine, diagnostics, biocatalysis and materials. Synthetically modified biomolecules can have diverse functionalities, such as tracking cellular events, revealing enzyme function, determining protein biodistribution, imaging specific biomarkers, and delivering drugs to targeted cells.
A frustrated Lewis pair (FLP) is a compound or mixture containing a Lewis acid and a Lewis base that, because of steric hindrance, cannot combine to form a classical adduct. Many kinds of FLPs have been devised, and many simple substrates exhibit activation.
Morten Peter Meldal is a Danish chemist and Nobel laureate. He is a professor of chemistry at the University of Copenhagen in Copenhagen, Denmark. He is best known for developing the CuAAC-click reaction, concurrently with but independent of Valery V. Fokin and K. Barry Sharpless.
The term bioorthogonal chemistry refers to any chemical reaction that can occur inside of living systems without interfering with native biochemical processes. The term was coined by Carolyn R. Bertozzi in 2003. Since its introduction, the concept of the bioorthogonal reaction has enabled the study of biomolecules such as glycans, proteins, and lipids in real time in living systems without cellular toxicity. A number of chemical ligation strategies have been developed that fulfill the requirements of bioorthogonality, including the 1,3-dipolar cycloaddition between azides and cyclooctynes, between nitrones and cyclooctynes, oxime/hydrazone formation from aldehydes and ketones, the tetrazine ligation, the isocyanide-based click reaction, and most recently, the quadricyclane ligation.
Copper-free click chemistry is a bioorthogonal reaction as a variant of an azide-alkyne Huisgen cycloaddition. By eliminating cytotoxic copper catalysts, the reaction proceeds without live-cell toxicity. It was developed as a faster alternative to the Staudinger ligation with the first generation of Cu-free click chemistry, producing rate constants over 63 times faster.
An aldehyde tag is a short peptide tag that can be further modified to add fluorophores, glycans, PEG chains, or reactive groups for further synthesis. A short, genetically-encoded peptide with a consensus sequence LCxPxR is introduced into fusion proteins, and by subsequent treatment with the formylglycine-generating enzyme (FGE), the cysteine of the tag is converted to a reactive aldehyde group. This electrophilic group can be targeted by an array of aldehyde-specific reagents, such as aminooxy- or hydrazide-functionalized compounds.
The SpyTag/SpyCatcher system is a technology for irreversible conjugation of recombinant proteins. The peptide SpyTag spontaneously reacts with the protein SpyCatcher to form an intermolecular isopeptide bond between the pair. DNA sequence encoding either SpyTag or SpyCatcher can be recombinantly introduced into the DNA sequence encoding a protein of interest, forming a fusion protein. These fusion proteins can be covalently linked when mixed in a reaction through the SpyTag/SpyCatcher system.
Ramesh Jasti is a professor of organic chemistry at the University of Oregon. He was the first person to synthesize the elusive cycloparaphenylene in 2008 during post doctoral work in the laboratory of Professor Carolyn Bertozzi. He started his laboratory at Boston University where he was the recipient of the NSF CAREER award. His early lab repeatedly broke the record for the synthesis of the smallest cycloparaphenylene known. In 2014, he moved his laboratory to the University of Oregon where he expanded his focus to apply the molecules he discovered in the areas of organic materials, mechanically interlocked molecules, and biology. He is the Director of the Materials Science Institute at the University of Oregon.
Ellen Sletten is an American chemist who is the John McTague Career Development Chair at University of California, Los Angeles. Her research considers the use of physical organic chemistry for diagnostics and medical therapies.
Intrinsic bond orbitals (IBO) are localized molecular orbitals giving exact and non-empirical representations of wave functions. They are obtained by unitary transformation and form an orthogonal set of orbitals localized on a minimal number of atoms. IBOs present an intuitive and unbiased interpretation of chemical bonding with naturally arising Lewis structures. For this reason IBOs have been successfully employed for the elucidation of molecular structures and electron flow along the intrinsic reaction coordinate (IRC). IBOs have also found application as Wannier functions in the study of solids.
Jennifer Ann Prescher is an American chemist who is a professor of chemistry at the University of California, Irvine. Her research considers the development of bioorthogonal, bioluminescent tools for the noninvasive, real-time imaging of immunometabolism. She was recognized with the 2023 American Chemical Society Arthur C. Cope Scholar Award.
Neal K. Devaraj is an American chemist and professor at the University of California, San Diego (UCSD). His research interests include artificial cells, lipid membranes, and bioconjugation.
Cyclooctyne is the cycloalkyne with a formula C
8H
12. Its molecule has a ring of 8 carbon atoms, connected by seven single bonds and one triple bond.