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terrestrial inputs (e.g. soil organic matter, leaf litterfall), submerged or floating aquatic vegetation, or autochthonous production of algae (living or detrital). Each source of POM has its own chemical composition that affects its lability, or accessibility to the food web. Algal-derived POM is thought to be most labile, but there is growing evidence that terrestrially-derived POM can supplement the diets of micro-organisms such as zooplankton when primary productivity is limited. === The biological carbon pump === The dynamics of the particulate organic carbon (POC) pool in the ocean are central to the marine carbon cycle. POC is the link between surface primary production, the deep ocean, and sediments. The rate at which POC is degraded in the dark ocean can impact atmospheric CO2 concentration. Therefore, a central focus of marine organic geochemistry studies is to improve the understanding of POC distribution, composition, and cycling. The last few decades have seen improvements in analytical techniques that have greatly expanded what can be measured, both in terms of organic compound structural diversity and isotopic composition, and complementary molecular omics studies. As illustrated in the diagram, phytoplankton fix carbon dioxide in the euphotic zone using solar energy and produce POC. POC formed in the euphotic zone is processed by marine microorganisms (microbes), zooplankton and their consumers into organic aggregates (marine snow), which is then exported to the mesopelagic (200–1000 m depth) and bathypelagic zones by sinking and vertical migration by zooplankton and fish. The biological carbon pump describes the collection of biogeochemical processes associated with the production, sinking, and remineralization of organic carbon in the ocean. In brief, photosynthesis by microorganisms in the upper tens of meters of the water column fix inorganic carbon (any of the chemical species of dissolved carbon dioxide) into biomass. When this biomass sinks to the deep ocean,
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"page_id": 49090922,
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"title": "Particulate organic matter"
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a portion of it fuels the metabolism of the organisms living there, including deep-sea fish and benthic organisms. Zooplankton play a critical role in shaping particle flux through ingestion and fragmentation of particles, production of fast-sinking fecal material and active vertical migration. Besides the importance of "exported" organic carbon as a food source for deep ocean organisms, the biological carbon pump provides a valuable ecosystem function: Exported organic carbon transports an estimated 5–20 Gt C each year to the deep ocean, where some of it (~0.2–0.5 Gt C) is sequestered for several millennia. The biological carbon pump is hence of similar magnitude to current carbon emissions from fossil fuels (~10 Gt C year−1). Any changes in its magnitude caused by a warming world may have direct implications for both deep-sea organisms and atmospheric carbon dioxide concentrations. The magnitude and efficiency (amount of carbon sequestered relative to primary production) of the biological carbon pump, hence ocean carbon storage, is partly determined by the amount of organic matter exported and the rate at which it is remineralized (i.e., the rate with which sinking organic matter is reworked and respired in the mesopelagic zone region. Especially particle size and composition are important parameters determining how fast a particle sinks, how much material it contains, and which organisms can find and utilize it. Sinking particles can be phytoplankton, zooplankton, detritus, fecal pellets, or a mix of these. They range in size from a few micrometers to several centimeters, with particles of a diameter of >0.5 mm being referred to as marine snow. In general, particles in a fluid are thought to sink once their densities are higher than the ambient fluid, i.e., when excess densities are larger than zero. Larger individual phytoplankton cells can thus contribute to sedimentary fluxes. For example, large diatom cells
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and diatom chains with a diameter of >5 μm have been shown to sink at rates up to several 10 s meters per day, though this is only possible owing to the heavy ballast of a silica frustule. Both size and density affect particle sinking velocity; for example, for sinking velocities that follow Stokes' Law, doubling the size of the particle increases the sinking speed by a factor of 4. However, the highly porous nature of many marine particles means that they do not obey Stokes' Law because small changes in particle density (i.e., compactness) can have a large impact on their sinking velocities. Large sinking particles are typically of two types: (1) aggregates formed from a number of primary particles, including phytoplankton, bacteria, fecal pellets, live protozoa and zooplankton and debris, and (2) zooplankton fecal pellets, which can dominate particle flux events and sink at velocities exceeding 1,000 m d−1. Knowing the size, abundance, structure and composition (e.g. carbon content) of settling particles is important as these characteristics impose fundamental constraints on the biogeochemical cycling of carbon. For example, changes in climate are expected to facilitate a shift in species composition in a manner that alters the elemental composition of particulate matter, cell size and the trajectory of carbon through the food web, influencing the proportion of biomass exported to depth. As such, any climate-induced change in the structure or function of phytoplankton communities is likely to alter the efficiency of the biological carbon pump, with feedbacks on the rate of climate change. === Bioluminescent shunt hypothesis === The consumption of the bioluminescent POC by fish can lead to the emission of bioluminescent fecal pellets (repackaging), which can also be produced with non-bioluminescent POC if the fish gut is already charged with bioluminescent bacteria. In the diagram on the
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"page_id": 49090922,
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"title": "Particulate organic matter"
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right, the sinking POC is moving downward followed by a chemical plume. The plain white arrows represent the carbon flow. Panel (a) represents the classical view of a non-bioluminescent particle. The length of the plume is identified by the scale on the side. Panel (b) represents the case of a glowing particle in the bioluminescence shunt hypothesis. Bioluminescent bacteria are represented aggregated onto the particle. Their light emission is shown as a bluish cloud around it. Blue dotted arrows represent the visual detection and the movement toward the particle of the consumer organisms. Increasing the visual detection allows a better detection by upper trophic levels, potentially leading to the fragmentation of sinking POC into suspended POC due to sloppy feeding. == See also == Microbial loop Particulate matter Total organic carbon == References ==
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{
"page_id": 49090922,
"source": null,
"title": "Particulate organic matter"
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Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a parasexual mode of reproduction in bacteria. It is a mechanism of horizontal gene transfer as are transformation and transduction although these two other mechanisms do not involve cell-to-cell contact. Classical E. coli bacterial conjugation is often regarded as the bacterial equivalent of sexual reproduction or mating, since it involves the exchange of genetic material. However, it is not sexual reproduction, since no exchange of gamete occurs, and indeed no generation of a new organism: instead, an existing organism is transformed. During classical E. coli conjugation, the donor cell provides a conjugative or mobilizable genetic element that is most often a plasmid or transposon. Most conjugative plasmids have systems ensuring that the recipient cell does not already contain a similar element. The genetic information transferred is often beneficial to the recipient. Benefits may include antibiotic resistance, xenobiotic tolerance or the ability to use new metabolites. Other elements can be detrimental, and may be viewed as bacterial parasites. Conjugation in Escherichia coli by spontaneous zygogenesis and in Mycobacterium smegmatis by distributive conjugal transfer differ from the better studied classical E. coli conjugation in that these cases involve substantial blending of the parental genomes. == History == The process was discovered by Joshua Lederberg and Edward Tatum in 1946. == Mechanism == Conjugation diagram Donor cell produces pilus. Pilus attaches to recipient cell and brings the two cells together. The mobile plasmid is nicked and a single strand of DNA is then transferred to the recipient cell. Both cells synthesize a complementary strand to produce a double stranded circular plasmid and also reproduce pili; both cells are now viable donor for
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the F-factor. The F-factor is an episome (a plasmid that can integrate itself into the bacterial chromosome by homologous recombination) with a length of about 100 kb. It carries its own origin of replication, the oriV, and an origin of transfer, or oriT. There can only be one copy of the F-plasmid in a given bacterium, either free or integrated, and bacteria that possess a copy are called F-positive or F-plus (denoted F+). Cells that lack F plasmids are called F-negative or F-minus (F−) and as such can function as recipient cells. Among other genetic information, the F-plasmid carries a tra and trb locus, which together are about 33 kb long and consist of about 40 genes. The tra locus includes the pilin gene and regulatory genes, which together form pili on the cell surface. The locus also includes the genes for the proteins that attach themselves to the surface of F− bacteria and initiate conjugation. Though there is some debate on the exact mechanism of conjugation it seems that the pili are the structures through which DNA exchange occurs. The F-pili are extremely resistant to mechanical and thermochemical stress, which guarantees successful conjugation in a variety of environments. Several proteins coded for in the tra or trb locus seem to open a channel between the bacteria and it is thought that the traD enzyme, located at the base of the pilus, initiates membrane fusion. When conjugation is initiated by a signal, the relaxase enzyme creates a nick in one of the strands of the conjugative plasmid at the oriT. Relaxase may work alone, or in a complex of over a dozen proteins known collectively as a relaxosome. In the F-plasmid system, the relaxase enzyme is called TraI and the relaxosome consists of TraI, TraY, TraM and the integrated host
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{
"page_id": 4460,
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factor IHF. The nicked strand, or T-strand, is then unwound from the unbroken strand and transferred to the recipient cell in a 5'-terminus to 3'-terminus direction. The remaining strand is replicated either independent of conjugative action (vegetative replication beginning at the oriV) or in concert with conjugation (conjugative replication similar to the rolling circle replication of lambda phage). Conjugative replication may require a second nick before successful transfer can occur. A recent report claims to have inhibited conjugation with chemicals that mimic an intermediate step of this second nicking event. If the F-plasmid that is transferred has previously been integrated into the donor's genome (producing an Hfr strain ["High Frequency of Recombination"]) some of the donor's chromosomal DNA may also be transferred with the plasmid DNA. The amount of chromosomal DNA that is transferred depends on how long the two conjugating bacteria remain in contact. In common laboratory strains of E. coli the transfer of the entire bacterial chromosome takes about 100 minutes. The transferred DNA can then be integrated into the recipient genome via homologous recombination. A cell culture that contains in its population cells with non-integrated F-plasmids usually also contains a few cells that have accidentally integrated their plasmids. It is these cells that are responsible for the low-frequency chromosomal gene transfers that occur in such cultures. Some strains of bacteria with an integrated F-plasmid can be isolated and grown in pure culture. Because such strains transfer chromosomal genes very efficiently they are called Hfr (high frequency of recombination). The E. coli genome was originally mapped by interrupted mating experiments in which various Hfr cells in the process of conjugation were sheared from recipients after less than 100 minutes (initially using a Waring blender). The genes that were transferred were then investigated. Since integration of the F-plasmid into
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the E. coli chromosome is a rare spontaneous occurrence, and since the numerous genes promoting DNA transfer are in the plasmid genome rather than in the bacterial genome, it has been argued that conjugative bacterial gene transfer, as it occurs in the E. coli Hfr system, is not an evolutionary adaptation of the bacterial host, nor is it likely ancestral to eukaryotic sex. Spontaneous zygogenesis in E. coli In addition to classical bacterial conjugation described above for E. coli, a form of conjugation referred to as spontaneous zygogenesis (Z-mating for short) is observed in certain strains of E. coli. In Z-mating there is complete genetic mixing, and unstable diploids are formed that throw off phenotypically haploid cells, of which some show a parental phenotype and some are true recombinants. == Conjugal transfer in mycobacteria == Conjugation in Mycobacteria smegmatis, like conjugation in E. coli, requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient chromosome by homologous recombination. However, unlike E. coli Hfr conjugation, mycobacterial conjugation is chromosome rather than plasmid based. Furthermore, in contrast to E. coli Hfr conjugation, in M. smegmatis all regions of the chromosome are transferred with comparable efficiencies. The lengths of the donor segments vary widely, but have an average length of 44.2kb. Since a mean of 13 tracts are transferred, the average total of transferred DNA per genome is 575kb. This process is referred to as "Distributive conjugal transfer." Gray et al. found substantial blending of the parental genomes as a result of conjugation and regarded this blending as reminiscent of that seen in the meiotic products of sexual reproduction. == Conjugation-like DNA transfer in hyperthermophilic archaea == Hyperthermophilic archaea encode pili structurally similar to the bacterial conjugative pili. However,
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"page_id": 4460,
"source": null,
"title": "Bacterial conjugation"
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unlike in bacteria, where conjugation apparatus typically mediates the transfer of mobile genetic elements, such as plasmids or transposons, the conjugative machinery of hyperthermophilic archaea, called Ced (Crenarchaeal system for exchange of DNA) and Ted (Thermoproteales system for exchange of DNA), appears to be responsible for the transfer of cellular DNA between members of the same species. It has been suggested that in these archaea the conjugation machinery has been fully domesticated for promoting DNA repair through homologous recombination rather than spread of mobile genetic elements. In addition to the VirB2-like conjugative pilus, the Ced and Ted systems include components for the VirB6-like transmembrane mating pore and the VirB4-like ATPase. == Inter-kingdom transfer == Bacteria related to the nitrogen fixing Rhizobia are an interesting case of inter-kingdom conjugation. For example, the tumor-inducing (Ti) plasmid of Agrobacterium and the root-tumor inducing (Ri) plasmid of A. rhizogenes contain genes that are capable of transferring to plant cells. The expression of these genes effectively transforms the plant cells into opine-producing factories. Opines are used by the bacteria as sources of nitrogen and energy. Infected cells form crown gall or root tumors. The Ti and Ri plasmids are thus endosymbionts of the bacteria, which are in turn endosymbionts (or parasites) of the infected plant. The Ti and Ri plasmids can also be transferred between bacteria using a system (the tra, or transfer, operon) that is different and independent of the system used for inter-kingdom transfer (the vir, or virulence, operon). Such transfers create virulent strains from previously avirulent strains. == Genetic engineering applications == Conjugation is a convenient means for transferring genetic material to a variety of targets. In laboratories, successful transfers have been reported from bacteria to yeast, plants, mammalian cells, diatoms and isolated mammalian mitochondria. Conjugation has advantages over other forms of
|
{
"page_id": 4460,
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"title": "Bacterial conjugation"
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genetic transfer including minimal disruption of the target's cellular envelope and the ability to transfer relatively large amounts of genetic material (see the above discussion of E. coli chromosome transfer). In plant engineering, Agrobacterium-like conjugation complements other standard vehicles such as tobacco mosaic virus (TMV). While TMV is capable of infecting many plant families these are primarily herbaceous dicots. Agrobacterium-like conjugation is also primarily used for dicots, but monocot recipients are not uncommon. == See also == Sexual conjugation in algae and ciliates Transfection Triparental mating Zygotic induction == References == == External links == Bacterial conjugation (a Flash animation)
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"page_id": 4460,
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"title": "Bacterial conjugation"
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Chemical Agent Detector Paper is a type of paper used for detecting the presence of chemical agents, including nerve agents, mustard agents, and blister agents. The paper typically change color in the presence of a chemical agent. The U.S. Military and first responders typically use the paper. == M8 Detector Paper == M8 Detector Paper is used to detect the presence of V and G type nerve agents and H type blister agents. It works by detecting chemical agents from a liquid splash. Each sheet of paper has three separate detection dyes. The yellow color appears when exposed to G nerve agents, the dark green color appears when exposed to V nerve agents, and the red color appears when exposed to H blister agents. The M8 detector paper does not detect agents in the form of aerosols or vapors. The M8 was a Canadian invention, being first standardized in 1963. By 1964 it entered US service as part of the M15A2 Chemical Agent Detector Kit, with about 67,000 of these kits being produced from 1965-1969, with most other NATO nations also purchasing the M8. == M9 Detector Tape == M9 Detector Tape or paper is used to detect the presence of nerve (V- and G- types) and mustard (H, HD, HN, and HT) agents. It cannot identify what particular agent it is being exposed to. The tape is typically a dull cream color when not exposed to chemical agents, but will turn red in the presence of chemical agents. The tape is made from Mylar, which is the sticky backing, and a red agent detection dye. The detector tape does have false positives, which can be caused by antifreeze, petroleum-based products, and liquid insecticide. The M9 was adopted by the US Army in 1980, although prior testing showed the dye
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{
"page_id": 67309930,
"source": null,
"title": "Chemical Agent Detector Paper"
}
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used in the tape was mutagenic and possibly carcinogenic. Adoption nonetheless proceeded and the Army was able to find a replacement dye that was not mutagenic. == Chemical Detection Kit == The M256/M256A1 Chemical Detection Kits include not only M8 Detector Paper for detecting the presence of toxins, but also enzyme-based "tickets" for identifying which agent is present. The M18 kit includes M8 sheets, "tickets", and test tubes loaded with colorimetric reagents for measuring the concentration of toxins. == References ==
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{
"page_id": 67309930,
"source": null,
"title": "Chemical Agent Detector Paper"
}
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Cryptobiosis or anabiosis is a metabolic state in extremophilic organisms in response to adverse environmental conditions such as desiccation, freezing, and oxygen deficiency. In the cryptobiotic state, all measurable metabolic processes stop, preventing reproduction, development, and repair. When environmental conditions return to being hospitable, the organism will return to its metabolic state of life as it was prior to cryptobiosis. == Forms == === Anhydrobiosis === Anhydrobiosis is the most studied form of cryptobiosis and occurs in situations of extreme desiccation. The term anhydrobiosis derives from the Greek for "life without water" and is most commonly used for the desiccation tolerance observed in certain invertebrate animals such as bdelloid rotifers, tardigrades, brine shrimp, nematodes, and at least one insect, a species of chironomid (Polypedilum vanderplanki). However, other life forms exhibit desiccation tolerance. These include the resurrection plant Craterostigma plantagineum, the majority of plant seeds, and many microorganisms such as bakers' yeast. Studies have shown that some anhydrobiotic organisms can survive for decades, even centuries, in the dry state. Invertebrates undergoing anhydrobiosis often contract into a smaller shape and some proceed to form a sugar called trehalose, a disaccharide consisting of two molecules of glucose with high water retention capabilities. Desiccation tolerance in plants is associated with the production of another sugar, sucrose. These sugars are thought to protect the organism from desiccation damage. In some creatures, such as bdelloid rotifers, no trehalose has been found, which has led scientists to propose other mechanisms of anhydrobiosis, possibly involving intrinsically disordered proteins. In 2011, Caenorhabditis elegans, a nematode that is also one of the best-studied model organisms, was shown to undergo anhydrobiosis in the dauer larva stage. Further research taking advantage of genetic and biochemical tools available for this organism revealed that in addition to trehalose biosynthesis, a set of other functional
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{
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"source": null,
"title": "Cryptobiosis"
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pathways is involved in anhydrobiosis at the molecular level. These are mainly defense mechanisms against reactive oxygen species and xenobiotics, expression of heat shock proteins and intrinsically disordered proteins as well as biosynthesis of polyunsaturated fatty acids and polyamines. Some of them are conserved among anhydrobiotic plants and animals, suggesting that anhydrobiotic ability may depend on a set of common mechanisms. Understanding these mechanisms in detail might enable modification of non-anhydrobiotic cells, tissues, organs or even organisms so that they can be preserved in a dried state of suspended animation over long time periods. As of 2004, such an application of anhydrobiosis is being applied to vaccines. In vaccines, the process can produce a dry vaccine that reactivates once it is injected into the body. In theory, dry-vaccine technology could be used on any vaccine, including live vaccines such as the one for measles. It could also potentially be adapted to allow a vaccine's slow release, eliminating the need for boosters. This proposes to eliminate the need for refrigerating vaccines, thus making dry vaccines more widely available throughout the developing world where refrigeration, electricity, and proper storage are less accessible. Based on similar principles, lyopreservation has been developed as a technique for preservation of biological samples at ambient temperatures. Lyopreservation is a biomimetic strategy based on anhydrobiosis to preserve cells at ambient temperatures. It has been explored as an alternative technique for cryopreservation. The technique has the advantages of being able to preserve biological samples at ambient temperatures, without the need for refrigeration or use of cryogenic temperatures. === Anoxybiosis === In situations lacking oxygen (a.k.a., anoxia), many cryptobionts (such as M. tardigradum) take in water and become turgid and immobile, but can survive for prolonged periods of time. Some ectothermic vertebrates and some invertebrates, such as brine shrimps, copepods,
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{
"page_id": 1708398,
"source": null,
"title": "Cryptobiosis"
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nematodes, and sponge gemmules, are capable of surviving in a seemingly inactive state during anoxic conditions for months to decades. Studies of the metabolic activity of these idling organisms during anoxia have been mostly inconclusive. This is because it is difficult to measure very small degrees of metabolic activity reliably enough to prove a cryptobiotic state rather than ordinary metabolic rate depression (MRD). Many experts are skeptical of the biological feasibility of anoxybiosis, as the organism is managing to prevent damage to its cellular structures from the environmental negative free energy, despite being both surrounded by plenty of water and thermal energy and without using any free energy of its own. However, there is evidence that the stress-induced protein p26 may act as a protein chaperone that requires no energy in cystic Artemia franciscana (sea monkey) embryos, and most likely an extremely specialized and slow guanine polynucleotide pathway continues to provide metabolic free energy to the A. franciscana embryos during anoxic conditions. It seems that A. franciscana approaches but does not reach true anoxybiosis. === Chemobiosis === Chemobiosis is the cryptobiotic response to high levels of environmental toxins. It has been observed in tardigrades. === Cryobiosis === Cryobiosis is a form of cryptobiosis that takes place in reaction to decreased temperature. Cryobiosis begins when the water surrounding the organism's cells has been frozen. Stopping molecule mobility allows the organism to endure the freezing temperatures until more hospitable conditions return. Organisms capable of enduring these conditions typically feature molecules that facilitate freezing of water in preferential locations while also prohibiting the growth of large ice crystals that could otherwise damage cells. Examples of such organisms include lobster and nematodes. === Osmobiosis === Osmobiosis is the least studied of all types of cryptobiosis. Osmobiosis occurs in response to increased solute concentration in
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{
"page_id": 1708398,
"source": null,
"title": "Cryptobiosis"
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the solution the organism lives in. Little is known for certain, other than that osmobiosis appears to involve a cessation of metabolism. == Examples == The brine shrimp Artemia salina, which can be found in the Makgadikgadi Pans in Botswana, survives over the dry season when the water of the pans evaporates, leaving a virtually desiccated lake bed. The tardigrade, or water bear, can undergo all five types of cryptobiosis. While in a cryptobiotic state, its metabolism reduces to less than 0.01% of what is normal, and its water content can drop to 1% of normal. It can withstand extreme temperature, radiation, and pressure while in a cryptobiotic state. Some nematodes and rotifers can also undergo cryptobiosis. == See also == Biostasis – Coping with environmental changes without adapting Cryobiology – Study of effects of extreme low temperatures on life Cryonics – Freezing of a corpse with the intent of future revival Cryptobiotic soil – Communities of living organisms on the soil surface in arid and semi-arid ecosystemsPages displaying short descriptions of redirect targets Hibernation – Physiological state of dormant inactivity in order to pass the winter season Lyopreservation – Metabolic state of lifePages displaying short descriptions of redirect targets == References == == Further reading == David A. Wharton, Life at the Limits: Organisms in Extreme Environments, Cambridge University Press, 2002, hardcover, ISBN 0-521-78212-0
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{
"page_id": 1708398,
"source": null,
"title": "Cryptobiosis"
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A lithium atom is an atom of the chemical element lithium. Stable lithium is composed of three electrons bound by the electromagnetic force to a nucleus containing three protons along with either three or four neutrons, depending on the isotope, held together by the strong force. Similarly to the case of the helium atom, a closed-form solution to the Schrödinger equation for the lithium atom has not been found. However, various approximations, such as the Hartree–Fock method, can be used to estimate the ground state energy and wavefunction of the atom. The quantum defect is a value that describes the deviation from hydrogenic energy levels. == Further reading == W. Zheng et al. / Appl. Math. Comput. 153 (2004) 685–695 "Numerical solutions of the Schrödinger equation for the ground lithium by the finite element method"
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{
"page_id": 43979118,
"source": null,
"title": "Lithium atom"
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In the history of chemistry, the chemical revolution, also called the first chemical revolution, was the reformulation of chemistry during the seventeenth and eighteenth centuries, which culminated in the law of conservation of mass and the oxygen theory of combustion. During the 19th and 20th century, this transformation was credited to the work of the French chemist Antoine Lavoisier (the "father of modern chemistry"). However, recent work on the history of early modern chemistry considers the chemical revolution to consist of gradual changes in chemical theory and practice that emerged over a period of two centuries. The so-called Scientific Revolution took place during the sixteenth and seventeenth centuries whereas the chemical revolution took place during the seventeenth and eighteenth centuries. == Primary factors == Several factors led to the first chemical revolution. First, there were the forms of gravimetric analysis that emerged from alchemy and new kinds of instruments that were developed in medical and industrial contexts. In these settings, chemists increasingly challenged hypotheses that had already been presented by the ancient Greeks. For example, chemists began to assert that all structures were composed of more than the four elements of the Greeks or the eight elements of the medieval alchemists. The Irish alchemist, Robert Boyle, laid the foundations for the Chemical Revolution, with his mechanical corpuscular philosophy, which in turn relied heavily on the alchemical corpuscular theory and experimental method dating back to pseudo-Geber. Earlier works by chemists such as Jan Baptist van Helmont helped to shift the belief in theory that air existed as a single element to that of one in which air existed as a composition of a mixture of distinct kinds of gasses. Van Helmont's data analysis also suggests that he had a general understanding of the law of conservation of mass in the 17th
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{
"page_id": 3543408,
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"title": "Chemical revolution"
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century. Furthermore, work by Jean Rey in the early 17th century with metals like tin and lead and their oxidation in the presence of air and water helped pinpoint the contribution and existence of oxygen in the oxidation process. Other factors included new experimental techniques and the discovery of 'fixed air' (carbon dioxide) by Joseph Black in the middle of the 18th century. This discovery was particularly important because it empirically proved that 'air' did not consist of only one substance and because it established 'gas' as an important experimental substance. Nearer the end of the 18th century, the experiments by Henry Cavendish and Joseph Priestley further proved that air is not an element and is instead composed of several different gases. Lavoisier also translated the names of chemical substance into a new nomenclatural language more appealing to scientists of the nineteenth century. Such changes took place in an atmosphere in which the Industrial Revolution increased public interest in learning and practicing chemistry. When describing the task of reinventing chemical nomenclature, Lavoisier attempted to harness the new centrality of chemistry by making the rather hyperbolic claim that: We must clean house thoroughly, for they have made use of an enigmatical language peculiar to themselves, which in general presents one meaning for the adepts and another meaning for the vulgar, and at the same time contains nothing that is rationally intelligible either for the one or for the other. === Precision instruments === Much of the reasoning behind Antoine Lavoisier being named the "father of modern chemistry" and the start of the chemical revolution lay in his ability to mathematize the field, pushing chemistry to use the experimental methods utilized in other "more exact sciences." Lavoisier changed the field of chemistry by keeping meticulous balance sheets in his research, attempting to
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{
"page_id": 3543408,
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"title": "Chemical revolution"
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show that through the transformation of chemical species the total amount of substance was conserved. Lavoisier used instrumentation for thermometric and barometric measurements in his experiments, and collaborated with Pierre Simon de Laplace in the invention of the calorimeter, an instrument for measuring heat changes in a reaction. In attempting to dismantle phlogiston theory and implement his own theory of combustion, Lavoisier utilized multiple apparatuses. These included a red-hot iron gun barrel which was designed to have water run through it and decompose, and an alteration of the apparatus which implemented a pneumatic trough at one end, a thermometer, and a barometer. The precision of his measurements was a requirement in convincing opposition of his theories about water as a compound, with instrumentation designed by himself implemented in his research. Despite having precise measurements for his work, Lavoisier faced a large amount of opposition in his research. Proponents of phlogiston theory, such as Keir and Priestley, claimed that demonstration of facts was only applicable for raw phenomena, and that interpretation of these facts did not imply accuracy in theories. They stated that Lavoisier was attempting to impose order on observed phenomena, whereas a secondary source of validity would be required to give definitive proof of the composition of water and non-existence of phlogiston. == Antoine Lavoisier == The latter stages of the revolution was fuelled by the 1789 publication of Lavoisier's Traité Élémentaire de Chimie (Elements of Chemistry). Beginning with this publication and others to follow, Lavoisier synthesised the work of others and coined the term "oxygen". Antoine Lavoisier represented the chemical revolution not only in his publications, but also in the way he practiced chemistry. Lavoisier's work was characterized by his systematic determination of weights and his strong emphasis on precision and accuracy. While it has been postulated that
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{
"page_id": 3543408,
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the law of conservation of mass was discovered by Lavoisier, this claim has been refuted by scientist Marcellin Berthelot. Earlier use of the law of conservation of mass has been suggested by Henry Guerlac, noting that scientist Jan Baptist van Helmont had implicitly applied the methodology to his work in the 16th and 17th centuries. Earlier references of the law of conservation of mass and its use were made by Jean Rey in 1630. Although the law of conservation of mass was not explicitly discovered by Lavoisier, his work with a wider array of materials than what most scientists had available at the time allowed his work to greatly expand the boundaries of the principle and its fundamentals. Lavoisier also contributed to chemistry a method of understanding combustion and respiration and proof of the composition of water by decomposition into its constituent parts. He explained the theory of combustion, and challenged the phlogiston theory with his views on caloric. The Traité incorporates notions of a "new chemistry" and describes the experiments and reasoning that led to his conclusions. Like Newton's Principia, which was the high point of the Scientific Revolution, Lavoisier's Traité can be seen as the culmination of the Chemical Revolution. Lavoisier's work was not immediately accepted and it took several decades for it gain momentum. This transition was aided by the work of Jöns Jakob Berzelius, who came up with a simplified shorthand to describe chemical compounds based on John Dalton's theory of atomic weights. Many people credit Lavoisier and his overthrow of phlogiston theory as the traditional chemical revolution, with Lavoisier marking the beginning of the revolution and John Dalton marking its culmination. === Méthode de nomenclature chimique === Antoine Lavoisier, in a collaborative effort with Louis Bernard Guyton de Morveau, Claude Louis Berthollet, and Antoine François
|
{
"page_id": 3543408,
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"title": "Chemical revolution"
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de Fourcroy, published Méthode de nomenclature chimique in 1787. This work established a terminology for the "new chemistry" which Lavoisier was creating, which focused on a standardized set of terms, establishment of new elements, and experimental work. Méthode established 55 elements which were substances that could not be broken down into simpler composite parts at the time of publishing. By introducing new terminology into the field, Lavoisier encouraged other chemists to adopt his theories and practices in order to use his terms and stay current in chemistry. === Traité élémentaire de chimie === One of Lavoisier's main influences was Étienne Bonnet, abbé de Condillac. Condillac's approach to scientific research, which was the basis of Lavoisier's approach in Traité, was to demonstrate that human beings could create a mental representation of the world using gathered evidence. In Lavoisier's preface to Traité, he statesIt is a maxim universally admitted in geometry, and indeed in every branch of knowledge, that, in the progress of investigation, we should proceed from known facts to what is unknown. ... In this manner, from a series of sensations, observations, and analyses, a successive train of ideas arises, so linked together, that an attentive observer may trace back to a certain point the order and connection of the whole sum of human knowledge.Lavoisier clearly ties his ideas in with those of Condillac, seeking to reform the field of chemistry. His goal in Traité was to associate the field with direct experience and observation, rather than assumption. His work defined a new foundation for the basis of chemical ideas and set a direction for the future course of chemistry. == Humphry Davy == Humphry Davy was an English chemist and a professor of chemistry at the London's Royal Institution in the early 1800s. There he performed experiments that cast
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doubt upon some of Lavoisier's key ideas such as the acidity of oxygen and the idea of a caloric element. Davy was able to show that acidity was not due to the presence of oxygen using muriatic acid (hydrochloric acid) as proof. He also proved that the compound oxymuriatic acid contained no oxygen and was instead an element, which he named chlorine. Through his use of electric batteries at the Royal Institution Davy first isolated chlorine, followed by the isolation of elemental iodine in 1813. Using the batteries Davy was also able to isolate the elements sodium and potassium. From these experiments Davy concluded that the forces that join chemical elements together must be electrical in nature. Davy also opposed the idea that caloric was an immaterial fluid, arguing instead that heat was a type of motion. == John Dalton == John Dalton was an English chemist who developed the idea of atomic theory of chemical elements. Dalton's atomic theory of chemical elements assumed that each element had unique atoms associated with and specific to that atom. This was in opposition to Lavoisier's definition of elements which was that elements are substances that chemists could not break down further into simpler parts. Dalton's idea also differed from the idea of corpuscular theory of matter, which believed that all atoms were the same, and had been a supported theory since the 17th century. To help support his idea, Dalton worked on defining the relative weights of atoms in chemicals in his work New System of Chemical Philosophy, published in 1808. His text showed calculations to determine the relative atomic weights of Lavoisier's different elements based on experimental data pertaining to the relative amounts of different elements in chemical combinations. Dalton argued that elements would combine in the simplest form possible. Water
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was known to be a combination of hydrogen and oxygen, thus Dalton believed water to be a binary compound containing one hydrogen and one oxygen. Dalton was able to accurately compute the relative quantity of gases in atmospheric air. He used the specific gravity of azotic (nitrogen), oxygenous, carbonic acid (carbon dioxide), and hydrogenous gases as well as aqueous vapor determined by Lavoisier and Davy to determine the proportional weights of each as a percent of a whole volume of atmospheric air. Dalton determined that atmospheric air contains 75.55% azotic gas, 23.32% oxygenous gas, 1.03% aqueous vapor, and 0.10% carbonic acid gas. == Jöns Jacob Berzelius == Jöns Jacob Berzelius was a Swedish chemist who studied medicine at the University of Uppsala and was a professor of chemistry in Stockholm. He drew on the ideas of both Davy and Dalton to create an electrochemical view of how elements combined together. Berzelius classified elements into two groups, electronegative and electropositive depending which pole of a galvanic battery they were released from when decomposed. He created a scale of charge with oxygen being the most electronegative element and potassium the most electropositive. This scale signified that some elements had positive and negative charges associated with them and the position of an element on this scale and the element's charge determined how that element combined with others. Berzelius's work on electrochemical atomic theory was published in 1818 as Essai sur la théorie des proportions chimiques et sur l'influence chimique de l'électricité. He also introduced a new chemical nomenclature into chemistry by representing elements with letters and abbreviations, such as O for oxygen and Fe for iron. Combinations of elements were represented as sequences of these symbols and the number of atoms were represented at first by superscripts and then later subscripts. == References
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== == Further reading == William B. Jensen, "Logic, History, and the Chemistry Textbook: III. One Chemical Revolution or Three?", Journal of Chemical Education, Vol. 75, No. 8, August 1998 John G. McEvoy (2010). Historiography of the Chemical Revolution: Patterns of Interpretation in the History of Science. Pickering & Chatto. ISBN 978-1-84893-030-8. See also book review by Seymour Mauskopf in HYLE--International Journal for Philosophy of Chemistry, Vol. 17, No.1 (2011), pp. 41–46. == External links == Chemistry :: The chemical revolution – Encyclopædia Britannica A bibliography on the chemical revolution Archived 2008-04-22 at the Wayback Machine – University of Valencia
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Amphipathic Lipid Packing Sensor (ALPS) motifs were first identified in 2005 in ARFGAP1 and have been reviewed. The curving of a phospholipid bilayer, for example into a liposome, causes disturbances to the packing of the lipids on the side of the bilayer that has the larger surface area (the outside of a liposome for example). The less "ordered" or "looser" packing of the lipids is recognized by ALPS motifs. ALPS motifs are 20 to 40 amino acid long portions of proteins that have important collections of types of amino acid residues. Bulky hydrophobic amino acid residues, such as Phenylalanine, Leucine, and Tryptophan are present every 3 or 4 positions, with many polar but uncharged amino acid residues such as Glycine, Serine and Threonine between. The ALPS is unstructured in solution but folds as an alpha helix when associated with the membrane bilayer, such that the hydrophobic residues insert between loosely packed lipids and the polar residues point toward the aqueous cytoplasm. == References ==
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Continuous reactors (alternatively referred to as flow reactors) carry chemical materials as a flowing stream. Reactants are continuously fed into the reactor and emerge as continuous stream of product. Continuous reactors are used for a wide variety of chemical and biological processes within the food, chemical and pharmaceutical industries. A survey of the continuous reactor market will throw up a daunting variety of shapes and types of machine. Beneath this variation however lies a relatively small number of key design features which determine the capabilities of the reactor. When classifying continuous reactors, it can be more helpful to look at these design features rather than the whole system. == Batch versus continuous == Reactors can be divided into two broad categories, batch reactors and continuous reactors. Batch reactors are stirred tanks sufficiently large to handle the full inventory of a complete batch cycle. In some cases, batch reactors may be operated in semi batch mode where one chemical is charged to the vessel and a second chemical is added slowly. Continuous reactors are generally smaller than batch reactors and handle the product as a flowing stream. Continuous reactors may be designed as pipes with or without baffles or a series of interconnected stages. The advantages of the two options are considered below. === Benefits of batch reactors === Batch reactors are very versatile and are used for a variety for different unit operations (batch distillation, storage, crystallisation, liquid-liquid extraction etc.) in addition to chemical reactions. There is a large installed base of batch reactors within industry and their method of use is well established. Batch reactors are excellent at handling difficult materials like slurries or products with a tendency to foul. Batch reactors represent an effective and economic solution for many types of slow reactions. === Benefits of continuous reactors
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=== The rate of many chemical reactions is dependent on reactant concentration. Continuous reactors are generally able to cope with much higher reactant concentrations due to their superior heat transfer capacities. Plug flow reactors have the additional advantage of greater separation between reactants and products giving a better concentration profile. The small size of continuous reactors makes higher mixing rates possible. The output from a continuous reactor can be altered by varying the run time. This increases operating flexibility for manufacturers. == Heat transfer capacity == The rate of heat transfer within a reactor can be determined from the following relationship: q x = U A ( T p − T j ) {\displaystyle q_{x}=UA(T_{p}-T_{j})} where: qx: the heat liberated or absorbed by the process (W) U: the heat transfer coefficient of the heat exchanger (W/(m2K)) A: the heat transfer area (m2) Tp: process temperature (K) Tj: jacket temperature (K) From a reactor design perspective, heat transfer capacity is heavily influenced by channel size since this determines the heat transfer area per unit volume. Channel size can be categorised in various ways however in broadest terms, the categories are as follows: Industrial batch reactors: 1–10 m2/m3 (depending on reactor capacity) Laboratory batch reactors: 10–100 m2/m3 (depending on reactor capacity) Continuous reactors (non-micro): 100–5,000 m2/m3 (depending on channel size) Micro reactors: 5,000–50,000 m2/m3 (depending on channel size) Small diameter channels have the advantage of high heat transfer capacity. Against this however they have lower flow capacity, higher pressure drop and an increased tendency to block. In many cases, the physical structure and fabrication techniques for micro reactors make cleaning and unblocking very difficult to achieve. == Temperature control == Temperature control is one of the key functions of a chemical reactor. Poor temperature control can severely affect both yield and product
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"page_id": 18289011,
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quality. It can also lead to boiling or freezing within the reactor which may stop the reactor from working altogether. In extreme cases, poor temperature control can lead to severe over pressure which can be destructive on the equipment and potentially dangerous. === Single stage systems with high heating or cooling flux === In a batch reactor, good temperature control is achieved when the heat added or removed by the heat exchange surface (qx) equals the heat generated or absorbed by the process material (qp). For flowing reactors made up of tubes or plates, satisfying the relationship qx = qp does not deliver good temperature control since the rate of process heat liberation/absorption varies at different points within the reactor. Controlling the outlet temperature does not prevent hot/cold spots within the reactor. Hot or cold spots caused by exothermic or endothermic activity can be eliminated by relocating the temperature sensor (T) to the point where the hot/cold spots exists. This however leads to overheating or overcooling downstream of the temperature sensor. Many different types of plate or tube reactors use simple feed back control of the product temperature. From a user’s perspective, this approach is only suitable for processes where the effects of hot/cold spots do not compromise safety, quality or yield. === Single stage systems with low heating or cooling flux === Micro reactors can be tube or plates and have the key feature of small diameter flow channels (typically less than <1 mm). The significance of micro reactors is that the heat transfer area (A) per unit volume (of product) is very large. A large heat transfer area means that high values of qx can be achieved with low values of Tp – Tj. The low value of Tp – Tj limits the extent of over cooling that
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can occur. Thus the product temperature can be controlled by regulating the temperature of the heat transfer fluid (or the product). The feedback signal for controlling the process temperature can be the product temperature or the heat transfer fluid temperature. It is often more practical to control the temperature of the heat transfer fluid. Although micro reactors are efficient heat transfer devices, the narrow channels can result in high pressure drops, limited flow capacity and a tendency to block. They are also often fabricated in a manner which makes cleaning and dismantling difficult or impossible. === Multistage systems with high heating or cooling flux === Conditions within a continuous reactor change as the product passes along the flow channel. In an ideal reactor the design of the flow channel is optimised to cope with this change. In practice, this is achieved by breaking the reactor into a series of stages. Within each stage the ideal heat transfer conditions can be achieved by varying the surface to volume ratio or the cooling/heating flux. Thus stages where process heat output is very high either use extreme heat transfer fluid temperatures or have high surface to volume ratios (or both). By tackling the problem as a series of stages, extreme cooling/heating conditions to be employed at the hot/cold spots without suffering overheating or overcooling elsewhere. The significance of this is that larger flow channels can be used. Larger flow channels are generally desirable as they permit higher rate, lower pressure drop and a reduced tendency to block. == Mixing == Mixing is another important classifying feature for continuous reactors. Good mixing improves the efficiency of heat and mass transfer. In terms of trajectory through the reactor, the ideal flow condition for a continuous reactor is plug flow (since this delivers uniform residence time
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within the reactor). There is however a measure of conflict between good mixing and plug flow since mixing generates axial as well as radial movement of the fluid. In tube type reactors (with or without static mixing), adequate mixing can be achieved without seriously compromising plug flow. For this reason, these types of reactor are sometimes referred to as plug flow reactors. Continuous reactors can be classified in terms of the mixing mechanism as follows: === Mixing by diffusion === Diffusion mixing relies on concentration or temperature gradients within the product. This approach is common with micro reactors where the channel thicknesses are very small and heat can be transmitted to and from the heat transfer surface by conduction. In larger channels and for some types of reaction mixture (especially immiscible fluids), mixing by diffusion is not practical. === Mixing with the product transfer pump === In a continuous reactor, the product is continuously pumped through the reactor. This pump can also be used to promote mixing. If the fluid velocity is sufficiently high, turbulent flow conditions exist (which promotes mixing). The disadvantage with this approach is that it leads to long reactors with high pressure drops and high minimum flow rates. This is particularly true where the reaction is slow or the product has high viscosity. This problem can be reduced with the use of static mixers. Static mixers are baffles in the flow channel which are used to promote mixing. They are able to work with or without turbulent conditions. Static mixers can be effective but still require relatively long flow channels and generate relatively high pressure drops. The oscillatory baffled reactor is specialised form of static mixer where the direction of process flow is cycled. This permits static mixing with low net flow through the reactor. This
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has the benefit of allowing the reactor to be kept comparatively short. === Mixing with a mechanical agitator === Some continuous reactors use mechanical agitation for mixing (rather than the product transfer pump). Whilst this adds complexity to the reactor design, it offers significant advantages in terms of versatility and performance. With independent agitation, efficient mixing can be maintained irrespective of product throughput or viscosity. It also eliminates the need for long flow channels and high pressure drops. One less desirable feature associated with mechanical agitators is the strong axial mixing they generate. This problem can be managed by breaking up the reactor into a series of mixed stages separated by small plug flow channels. The most familiar form of continuous reactor of this type is the continuously stirred tank reactor (CSTR). This is essentially a batch reactor used in a continuous flow. The disadvantage with a single stage CSTR is that it can be relatively wasteful on product during start up and shutdown. The reactants are also added to a mixture which is rich in product. For some types of process, this can affect quality and yield. These problems are managed by using multi stage CSTRs. At the large scale, conventional batch reactors can be used for the CSTR stages. == See also == Batch reactor Chemical reactor == References == == External links == ReelReactor Continuous Chemical and Biological Reactor ThalesNano Continuous Reactors Syrris Continuous Reactors Fluitec Contiplant Continuous Reactors Uniqsis Continuous Reactors Amtechuk Continuous Reactors Alfa Laval Continuous Reactors LIST Continuous Kneader Reactors NiTech Solutions Continuous Crystallisers
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A mnemonic is a memory aid used to improve long-term memory and make the process of consolidation easier. Many chemistry aspects, rules, names of compounds, sequences of elements, their reactivity, etc., can be easily and efficiently memorized with the help of mnemonics. This article contains the list of certain mnemonics in chemistry. == Orbitals == === Sequence of orbitals === Sober Physicists Don't Find Giraffes Hiding In Kitchens. Note: After the k shell, they follow alphabetical order (skipping s and p as they came earlier). === Aufbau principle === The order of sequence of atomic orbitals (according to Madelung rule or Klechkowski rule) can be remembered by the following. == Periodic table == === Periods === ==== Periods 1, 2 and 3 ==== Hi Hello Little Beer Bottles Crack Nicely On Freddie's kNee Nasties Merge All Silly 'People Suffer Clouts Arnti Happy Henry Likes Beans Brownies and Chocolate Nuts Over Friday's News. Naughty Margaret Always Sighs, "Please Stop Clowning Around." Kind Cats Scare Tiny Vicious Creatures, Might Fear Cows & Nice Cute Zebras. Happy Henry Likes Beans Brownies and Chocolate Nuts Over Friday's News. Happy Harry/Henry Listens B B C Network Over France Nevertheless Nothing More Arose So Peter Stopped Cleaning Airgun K Ca. Ha. Healthy Little Beggar Boys Catching Newts Or Fish. Hi, Here Little Beatniks Brandish Countless Number Of Flick kNives. Nagging Maggie Always Sighs, "Please Stop Clowning Around." (adapted) Hi Helium. Little Berries Borrow Carbs, NO Fight Needed. Hi Hello! Lion Beneath the Burning Car Needs Oxygen For New life. Native Magpies Always Sit Peacefully Searching Clear Areas. Naval Magistrates Always Signal Per Siren, Claiming Adequacy. Naughty Margaret Always Sighs, "Please Stop Clowning Around." Nellie's Naughty Magpie Always Sings Pop Songs Clearly After Killing Cathy. Shoddy Magician Aligned Six Phones Successfully, Classic Art! All Silicon Ports. Superman
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Clean Argon's K-Capture. ==== Period 4 ==== Kindly Cannibals Scare Timid Visitors, 'n' Cruelly Menace Female Communist Nitwits Cuddling Zany Gabbling Geese Astride Several Brutal Kangaroos. In reverse order: Kry Brother! SeAs of Germany and Gaul sink copper ships Nice and Cold From Manx to Crimea, Vancouver to Timor, and Scandinavia to the California Koast. Kind Cats Scare Tiny Vicious Creatures, Maintaining Feline Connections Nice, Cute & Zen. Gallium Germinates As Selene Brings Krypton. ==== Period 5 ==== Ruby, Sir, Yells "Zircon Nebulas !". Most Technicians Rule Rhodes and Paddle Against Cadence". India Sent Sebastian to Tell "Io Xe. Ruby Stuck in Yuck Zoo, Nice Monk Tackled Rude Rhino. Pay Silver Coin In Tin And Tell I eXeed. === Transition metals === ==== First ==== Scary Tiny Vicious Creatures are Mean; Females Come to NightClub Zen. Scary Tiny Vicious Creatures Might Fear Cows and Nice Cute Zebras. SucTion VelCro Man Fears CoNiC uZi. ScienTist ViCroMan Iron(Fe) Comes from NiCuZan. ==== Second ==== Yes S(Z)ir, Nob. Most Technicians Ruin Rob's Pale Silver Cadillac. ==== Third ==== Lucifer's Half Taken, Wendy Reached Out H(I)er Plate Audibly, Helga. Lucky Harry Took Walk, Reached Office In Pants, After an Hour. Lucky Horned-Fox's Tail got Wet. Restless Ostrich Irrelevantly Painted Gold(AU) on Mercury(HG). === Lanthanides and actinides === ==== Lanthanides ==== Last Century Presented New Democratic Prime Minister. Smart European Government Decided To Ban Dirty Hotels Entirely To Make Yellow Buildings Luxurious. Ladies Can't Put Needles Properly in Slot-machines. Every Girl Tries Daily, However, Every Time You'd Lose. Languid Centaurs Praise Ned's Promise of Small European Garden Tubs; Dinosaurs Hobble Erratically Thrumming Yellow Lutes. Lately, Central Park Needed Primroses. Small Entire Golden Tassels Dyeing the Hollow Earth, Tempting Your Love. ==== Actinides ==== Radiant Acting Thoroughly Protects yoUr Nepotism, Plutocratic America Cures-me & Berkeley California,
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Einstein Firmly Mended Noble Lawreins. Ace Thor Protects Uranus, Neptune, and Pluto. Army Cured Bark. In California Einstein and Fermi Made Noble Laws. Actually Thor Protects Uranus, Neptune, and Pluto. Army Cured Bark. In California Einstein and Fermi Made Noble Laws. === 56 elements in sequence === Here Lies Benjamin Bones. Cry Not Oh Friend Needlessly. Nature Magnifies All Simple People Sometimes Clowns And Kings Can Scream Till Vast Crowds Moan. Fear Conquers Neither Courageous Zealous Gallant Gents. As Seen Brown Karate Robes Strip Yobs. Zurich Noble Mortals Track Ruddy Rhubarb. Paid Silver Candid Indian Sons Sobbing Tears In Xcess Cease Bawling. === Groups === ==== Group 1 (alkali metals) ==== Lithium, Sodium, Potassium, Rubidium, Caesium, Francium Little Nasty Kids Rub Cats Fur Little Naughty Kids Robs Cents From (me) Little Naughty Kids Ruin Ben's Convenient Store Forever Little Nathan Knew Rubies Cost Fortunes Little Naughty Kids Rob Crispy Fries ==== Group 2 (alkaline earth metals) ==== Beryllium, Magnesium, Calcium, Strontium, Barium, Radium Bearded Muggers Came Straight Back Rapidly. Beer Mugs Can Serve Bar Rats. Ben Meg & Casia Stroll away to Bar of Radium ==== Group 13 ==== Boron, Aluminium, Gallium, Indium, Thallium, Nihonium BAlm Game In Tail Bowler Ali Gave Instant Tea BAG IT Bears Always Gave Indians Trouble ==== Group 14 ==== Carbon, Silicon, Germanium, Tin (stannum in Latin), Lead (plumbum in Latin) CSI Gets Stan Plums (comment: plum and plumb are homophones) Can Simple Germans Snare (Tiny) Public (Lead)? Chemistry Sir Gets Snacks Publicly Can Someone Get Some Peanutbutter ? ==== Group 15 (Pnictogens) ==== Nitrogen, Phosphorus, Arsenic, Antimony, Bismuth, Moscovium. No Person can Assassinate Sebastian Billy in Moscow (place). ==== Group 16 (Chalcogens) ==== Oxygen, Sulphur, Selenium, Tellurium, Polonium Old Style Sets TemPo Old TSangpo Seems Terribly Polluted Lately. Ottoman Sultan Sends Textiles to Poor
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Ladies. ==== Group 17 (Halogens) ==== Fluorine, Chlorine, Bromine, Iodine, Astatine, Tennessine Funny Clowns Broil Innocent Ants. Fast Clouds Break In Atlantis. Father Clark B(r)lesses Ivan A(s)tlast. First Class Briyani In Australia ==== Group 18 (noble gases) ==== Helium, Neon, Argon, Krypton, Xenon, Radon. Hero Never Argues, Kryptonite Xterminates Rao Hero Needs Arguable Kryptic Xes. Right-on. He Never Arrived; Karen eXited with Ron. He Needs A Kickin', Xylophone-playin' Racehorse! (And... Oh, gee, now we need to add Oganesson (Og)!) Hey, N(e)ArK(r)s, Run, O.g! == Properties of elements == === Abundance of elements on Earth's crust === Only Strong Athletes In College Study Past Midnight Oh, see(Si), Alfie(Fe) Cannot(Na) Kiss Meg(Mg) As they are present in trace quantities they are measured in parts per million(ppm). === Activity series of metals === Please Stop Calling Me A Cute Zebra Crab I Like Her Call Smart Goat Please Stop Calling Me A Carless Zebra Crab Instead Try Learning How Copper Miners Save Gold Pit Popular Scientists Can Make A Zoo In Low Humid Climate ... Note that carbon and hydrogen are non-metals, used as a baseline. Kangaroos Naturally Muck About in Zoos For Purple Hippos Chasing Aardvarks. Katty's Naughty Cat Mingled with Alice and Zarina; Fearlessly Plundering Her Cupboard of Gold. Papa Said Call Me After Zinc Interacts Tin Leading Hydrogen Co-operate Mr. Sylvester to Gain Popularity. Pretty(Potassium) Sally(Sodium) Could(Calcium) Marry(Magnesium) A(Aluminium) Crazy(Carbon) Zulu(Zinc) IN(Iron/Nickel) Tree(Tin) Lined(Lead) House(Hydrogen) Causing(Copper) Strangely(Silver) Glancing(Gold) People(Platinum). === Electronegativity === Pronounce: FOClN BrIS CHP. (F)irst (O)ff, (Cl)ean (N)ow; (Br)ing (I)n (S)ome (C)lothes, (H)ats, and (P)ants. (First off, clean now. Bring in some caps, hats {and} pants.) === Electrochemical series === Paddy Still Could Marry A Zulu In The Lovely Honolulu Causing Strange Gazes. Passive Sarcasm Can Mutate Angry Zombies InTo Large Hypocritical Cold Sexy Guys. Poor Science Course
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Makes A Zany Idiot Totally Lose His Composure, Sir! Good! == Reactions and ions == === Redox reactions === A redox reaction is a chemical reaction in which there is a change in oxidation state of atoms participating in the reaction. === Ions === An atom (or ion) whose oxidation number increases in a redox reaction is said to be oxidized (and is called a reducing agent). It is accomplished by loss of one or more electrons. The atom whose oxidation number decreases gains (receives) one or more electrons and is said to be reduced. This relation can be remembered by the following mnemonics. Leo says Ger! or Leo the lion, Ger! can be used to represent Loss of electron is oxidation; Gain of electron is reduction. Oil Rig: Oxidation is loss; Reduction is gain (of electrons). Cations are Plussy Cats. === Cations and anions === Cations are positively (+) charged ions while anions are negatively (−) charged. This can be remembered with the help of the following mnemonics. Cats have paws ⇔ Cations are pawsitive. Ca+ion: The letter t in cation looks like a + (plus) sign. An anion is a negative ion. (Anegativeion ⇒ Anion). === Oxidation vs. reduction: electrochemical cell and electron gain/loss === AN OIL RIG CAT: At the ANode, Oxidation Involves Loss of electrons. Reduction Involves Gaining electrons at the CAThode. LOAN - Left Anode Oxidation Negative. In written representation of galvanic cell, anode is written on the left. It is the electrode where oxidation takes place. It is the negative electrode. Obviously, the opposite properties (Right/Cathode/Reduction/Positive) are found on the cathode. Hence, by remembering LOAN mnemonic, we can arrive at the corresponding properties for the cathode. LEO the lion says GER [grr]: "Loss of Electrons, Oxidation; Gain of Electrons, Reduction". === Electrodes === An
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electrode in which oxidation takes place is called an anode while in that which reduction takes place is called cathode. This applies for both electrolytic and electrochemical cells, though the charge on them reverses. The red cat and an ox mnemonics are useful to remember the same. Red cat: Reduction at cathode An ox: Anode for oxidation. PANIC : Positive Anode, Negative Is Cathode The words oxidation and anode, both begin with vowels. Also, both reduction and cathode begin with consonants. Fat Cat: electrons flow From Anode To Cathode LOAN: Left side;Oxidation;Anode;Negative. ACID: Anode Current Into Device == Compounds == === Diatomic molecules === Molecules exhibiting diatomic structures can be remembered through the following mnemonics. Have No Fear Of Ice Cold Beer. Horses Need Oats For Clear Brown Eyes (I's). Her Nana's Only Functioning Clicker Broke Instantly. BrINClHOF: say Brinkelhof. I Bring Clay For Our New House. CHINFOB === Hydrogen bonds === Hydrogen forms hydrogen bonds with three elements which are nitrogen (N), oxygen (O) and fluorine (F). The names of these elements can be remembered by the following mnemonic. Hydrogen is FON! (fun). Hydrogen likes to have FON! === Polyatomic ions: −ate and -ite ions === Super Popeye Constantly Clubbed Brutus In Nevada. Nick Brit the Camel ate an Inky Clam with Crêpes for Supper in Phoenix. Number of consonants denotes number of oxygen atoms. Number of vowels denotes negative charge quantity. Inclusion of the word "ate" signifies that each ends with the letters a-t-e. To use this for the -ite ions, simply subtract one oxygen but keep the charge the same. == Organic chemistry == === Prefixes for naming carbon chains === The prefixes for naming carbon chains containing one to four carbons. For chains containing five or more carbons, the inorganic prefixes (e.g. pent = 5, hept
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= 7) are used. Monkeys Eat Peeled Bananas For the first five chains. Many Elephants Pee Behind Plants Mom Eats Pretty Big Pears === Carboxylic acids === Common names of homogeneous aliphatic carboxylic acids, Frogs Are Polite, Being Very Courteous. === Dicarboxylic acids === The sequence of dicarboxylic acids can be remembered with following mnemonics. Oh My, Such Good Apples. Oh My Stars, Green Apples. Oh My, Such Good Apple Pie, Sweet As Sugar. Oh My Stars, Go Ahead Please OMSGAPS – is a phonetic word for the first letters of the first seven dicarboxylic acids above in sequence can be said as below. Oh My Sir, Give A Party Soon. === Aromatic compounds === ==== m-directing groups ==== Queen Elizabeth Second's Navy Commands, Controls, Communicates. ==== o,p-directing groups ==== AHA AHA P. Note: -NH2,-NHR and NR2 are para directing groups but not -NR3+ === E-Z notation for isomers === "E" for 'enemies'. i.e. higher priority groups on opposite sides. Z form has higher priority groups on same side. "Z" means 'zame zide' (same side) i.e. high priority groups on same side. === Cis–trans isomerism === Cis starts with a C and the functional groups form a C. Trans, therefore is the other one by default. === Benzene ring: order of substitutes === From R group moving around the ring: Benzene likes to ROMP. == Biochemistry == === Nutrients === The four most common elements in living organisms – carbon, hydrogen, oxygen, and nitrogen – may be remembered with the acronym CHON. To remember the elements necessary for agriculture; C (see) Hopkins CaFe, Mighty-good Man, Cu (see your) Money, hope they are Closed or out of Business. For remembering macronutrients; C. HOPKiN'S Ca Mg (C. Hopkins coffee mug). MagiCal CKN SHOP (Magical Chicken SHOP). To remember the elements comprising the
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human body; Chopin's CaFe I.P. Cohn's CaFe === Essential amino acids === PVT TIM HaLL and TT HALL Very IMPortant. These Ten Valuable Acids Have Long Preserved Life In Men MATT HILL, VP LIFT HIM KIW(V)I TV FILM HW(R)K. FM TK HW RIVL Any Help In Learning These Little Molecules Proves Truly Valuable. This method begins with the two amino acids that need some qualifications as to their requirements. === Krebs cycle === To remember the Krebs cycle (citric acid cycle, tricarboxylic acid cycle): Caesar's Armies Invaded Other Kingdoms Searching For Many Oranges. Citric Acid Is One Key Substrate For Mitochondrial Oxidation == See also == List of medical mnemonics List of mnemonics == References == == External links == "Mnemonics for the Entire Periodic Table" Science jokes and mnemonics
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In condensed matter physics, a Bose–Einstein condensate (BEC) is a state of matter that is typically formed when a gas of bosons at very low densities is cooled to temperatures very close to absolute zero, i.e. 0 K (−273.15 °C; −459.67 °F). Under such conditions, a large fraction of bosons occupy the lowest quantum state, at which microscopic quantum-mechanical phenomena, particularly wavefunction interference, become apparent macroscopically. More generally, condensation refers to the appearance of macroscopic occupation of one or several states: for example, in BCS theory, a superconductor is a condensate of Cooper pairs. As such, condensation can be associated with phase transition, and the macroscopic occupation of the state is the order parameter. Bose–Einstein condensate was first predicted, generally, in 1924–1925 by Albert Einstein, crediting a pioneering paper by Satyendra Nath Bose on the new field now known as quantum statistics. In 1995, the Bose–Einstein condensate was created by Eric Cornell and Carl Wieman of the University of Colorado Boulder using rubidium atoms. Later that year, Wolfgang Ketterle of MIT produced a BEC using sodium atoms. In 2001 Cornell, Wieman, and Ketterle shared the Nobel Prize in Physics "for the achievement of Bose–Einstein condensation in dilute gases of alkali atoms, and for early fundamental studies of the properties of the condensates". == History == Bose first sent a paper to Einstein on the quantum statistics of light quanta (now called photons), in which he derived Planck's quantum radiation law without any reference to classical physics. Einstein was impressed, translated the paper himself from English to German and submitted it for Bose to the Zeitschrift für Physik, which published it in 1924. (The Einstein manuscript, once believed to be lost, was found in a library at Leiden University in 2005.) Einstein then extended Bose's ideas to matter in two other
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papers. The result of their efforts is the concept of a Bose gas, governed by Bose–Einstein statistics, which describes the statistical distribution of identical particles with integer spin, now called bosons. Bosons are allowed to share a quantum state. Einstein proposed that cooling bosonic atoms to a very low temperature would cause them to fall (or "condense") into the lowest accessible quantum state, resulting in a new form of matter. Bosons include the photon, polaritons, magnons, some atoms and molecules (depending on the number of nucleons, see #Isotopes) such as atomic hydrogen, helium-4, lithium-7, rubidium-87 or strontium-84. In 1938, Fritz London proposed the BEC as a mechanism for superfluidity in 4He and superconductivity. The quest to produce a Bose–Einstein condensate in the laboratory was stimulated by a paper published in 1976 by two program directors at the National Science Foundation (William Stwalley and Lewis Nosanow), proposing to use spin-polarized atomic hydrogen to produce a gaseous BEC. This led to the immediate pursuit of the idea by four independent research groups; these were led by Isaac Silvera (University of Amsterdam), Walter Hardy (University of British Columbia), Thomas Greytak (Massachusetts Institute of Technology) and David Lee (Cornell University). However, cooling atomic hydrogen turned out to be technically difficult, and Bose-Einstein condensation of atomic hydrogen was only realized in 1998. On 5 June 1995, the first gaseous condensate was produced by Eric Cornell and Carl Wieman at the University of Colorado at Boulder NIST–JILA lab, in a gas of rubidium atoms cooled to 170 nanokelvins (nK). Shortly thereafter, Wolfgang Ketterle at MIT produced a Bose–Einstein Condensate in a gas of sodium atoms. For their achievements Cornell, Wieman, and Ketterle received the 2001 Nobel Prize in Physics. Bose-Einstein condensation of alkali gases is easier because they can be pre-cooled with laser cooling techniques, unlike
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atomic hydrogen at the time, which give a significant head start when performing the final forced evaporative cooling to cross the condensation threshold. These early studies founded the field of ultracold atoms, and hundreds of research groups around the world now routinely produce BECs of dilute atomic vapors in their labs. Since 1995, many other atomic species have been condensed (see #Isotopes), and BECs have also been realized using molecules, polaritons, and other quasi-particles. BECs of photons can be made, for example, in dye microcavites with wavelength-scale mirror separation, forming a two-dimensional harmonically confined photon gas with tunable chemical potential. BEC of plasmonic quasiparticles (plasmon-exciton polaritons) has been realized in periodic arrays of metal nanoparticles overlaid with dye molecules, exhibiting ultrafast sub-picosecond dynamics and long-range correlations. == Critical temperature == This transition to BEC occurs below a critical temperature, which for a uniform three-dimensional gas consisting of non-interacting particles with no apparent internal degrees of freedom is given by T c = ( n ζ ( 3 / 2 ) ) 2 / 3 2 π ℏ 2 m k B ≈ 3.3125 ℏ 2 n 2 / 3 m k B , {\displaystyle T_{\text{c}}=\left({\frac {n}{\zeta (3/2)}}\right)^{2/3}{\frac {2\pi \hbar ^{2}}{mk_{\text{B}}}}\approx 3.3125\,{\frac {\hbar ^{2}n^{2/3}}{mk_{\text{B}}}},} where: T c {\displaystyle T_{\text{c}}} is the critical temperature, n {\displaystyle n} is the particle density, m {\displaystyle m} is the mass per boson, ℏ {\displaystyle \hbar } is the reduced Planck constant, k B {\displaystyle k_{\text{B}}} is the Boltzmann constant, ζ {\displaystyle \zeta } is the Riemann zeta function ( ζ ( 3 / 2 ) ≈ 2.6124 {\displaystyle \zeta (3/2)\approx 2.6124} ). Interactions shift the value, and the corrections can be calculated by mean-field theory. This formula is derived from finding the gas degeneracy in the Bose gas using Bose–Einstein statistics. The critical temperature depends
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on the density. A more concise and experimentally relevant condition involves the phase-space density D = n λ T 3 {\displaystyle {\mathcal {D}}=n\lambda _{T}^{3}} , where λ T = ℏ 2 π m k B T {\displaystyle \lambda _{T}=\hbar {\sqrt {\frac {2\pi }{mk_{\text{B}}T}}}} is the thermal de Broglie wavelength. It is a dimensionless quantity. The transition to BEC occurs when the phase-space density is greater than critical value: D c = ζ ( 3 / 2 ) {\displaystyle {\mathcal {D}}_{\text{c}}=\zeta (3/2)} in 3D uniform space. This is equivalent to the above condition on the temperature. In a 3D harmonic potential, the critical value is instead D c = ζ ( 3 ) ≈ 1.202 {\displaystyle {\mathcal {D}}_{\text{c}}=\zeta (3)\approx 1.202} where n {\displaystyle n} has to be understood as the peak density. == Derivation == === Ideal Bose gas === For an ideal Bose gas we have the equation of state 1 v = 1 λ 3 g 3 / 2 ( f ) + 1 V f 1 − f , {\displaystyle {\frac {1}{v}}={\frac {1}{\lambda ^{3}}}g_{3/2}(f)+{\frac {1}{V}}{\frac {f}{1-f}},} where v = V / N {\displaystyle v=V/N} is the per-particle volume, λ {\displaystyle \lambda } is the thermal wavelength, f {\displaystyle f} is the fugacity, and g α ( f ) = ∑ n = 1 ∞ f n n α . {\displaystyle g_{\alpha }(f)=\sum \limits _{n=1}^{\infty }{\frac {f^{n}}{n^{\alpha }}}.} It is noticeable that g 3 / 2 {\displaystyle g_{3/2}} is a monotonically growing function of f {\displaystyle f} in f ∈ [ 0 , 1 ] {\displaystyle f\in [0,1]} , which are the only values for which the series converge. Recognizing that the second term on the right-hand side contains the expression for the average occupation number of the fundamental state ⟨ n 0 ⟩ {\displaystyle \langle n_{0}\rangle } ,
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the equation of state can be rewritten as 1 v = 1 λ 3 g 3 / 2 ( f ) + ⟨ n 0 ⟩ V ⇔ ⟨ n 0 ⟩ V λ 3 = λ 3 v − g 3 / 2 ( f ) . {\displaystyle {\frac {1}{v}}={\frac {1}{\lambda ^{3}}}g_{3/2}(f)+{\frac {\langle n_{0}\rangle }{V}}\Leftrightarrow {\frac {\langle n_{0}\rangle }{V}}\lambda ^{3}={\frac {\lambda ^{3}}{v}}-g_{3/2}(f).} Because the left term on the second equation must always be positive, λ 3 v > g 3 / 2 ( f ) {\displaystyle {\frac {\lambda ^{3}}{v}}>g_{3/2}(f)} , and because g 3 / 2 ( f ) ≤ g 3 / 2 ( 1 ) {\displaystyle g_{3/2}(f)\leq g_{3/2}(1)} , a stronger condition is λ 3 v > g 3 / 2 ( 1 ) , {\displaystyle {\frac {\lambda ^{3}}{v}}>g_{3/2}(1),} which defines a transition between a gas phase and a condensed phase. On the critical region it is possible to define a critical temperature and thermal wavelength: λ c 3 = g 3 / 2 ( 1 ) v = ζ ( 3 / 2 ) v , {\displaystyle \lambda _{c}^{3}=g_{3/2}(1)v=\zeta (3/2)v,} T c = 2 π ℏ 2 m k B λ c 2 , {\displaystyle T_{\text{c}}={\frac {2\pi \hbar ^{2}}{mk_{\text{B}}\lambda _{c}^{2}}},} recovering the value indicated on the previous section. The critical values are such that if T < T c {\displaystyle T<T_{\text{c}}} or λ > λ c {\displaystyle \lambda >\lambda _{\text{c}}} , we are in the presence of a Bose–Einstein condensate. Understanding what happens with the fraction of particles on the fundamental level is crucial. As so, write the equation of state for f = 1 {\displaystyle f=1} , obtaining ⟨ n 0 ⟩ N = 1 − ( λ c λ ) 3 {\displaystyle {\frac {\langle n_{0}\rangle }{N}}=1-\left({\frac {\lambda _{\text{c}}}{\lambda }}\right)^{3}} and equivalently ⟨ n 0
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⟩ N = 1 − ( T T c ) 3 / 2 . {\displaystyle {\frac {\langle n_{0}\rangle }{N}}=1-\left({\frac {T}{T_{\text{c}}}}\right)^{3/2}.} So, if T ≪ T c {\displaystyle T\ll T_{\text{c}}} , the fraction ⟨ n 0 ⟩ N ≈ 1 {\displaystyle {\frac {\langle n_{0}\rangle }{N}}\approx 1} , and if T ≫ T c {\displaystyle T\gg T_{\text{c}}} , the fraction ⟨ n 0 ⟩ N ≈ 0 {\displaystyle {\frac {\langle n_{0}\rangle }{N}}\approx 0} . At temperatures near to absolute 0, particles tend to condense in the fundamental state, which is the state with momentum p → = 0 {\displaystyle {\vec {p}}=0} . == Experimental observation == === Superfluid helium-4 === In 1938, Pyotr Kapitsa, John Allen and Don Misener discovered that helium-4 became a new kind of fluid, now known as a superfluid, at temperatures less than 2.17 K (the lambda point). Superfluid helium has many unusual properties, including zero viscosity (the ability to flow without dissipating energy) and the existence of quantized vortices. It was quickly believed that the superfluidity was due to partial Bose–Einstein condensation of the liquid. In fact, many properties of superfluid helium also appear in gaseous condensates created by Cornell, Wieman and Ketterle (see below). Superfluid helium-4 is a liquid rather than a gas, which means that the interactions between the atoms are relatively strong; the original theory of Bose–Einstein condensation must be heavily modified in order to describe it. Bose–Einstein condensation remains, however, fundamental to the superfluid properties of helium-4. Note that helium-3, a fermion, also enters a superfluid phase (at a much lower temperature) which can be explained by the formation of bosonic Cooper pairs of two atoms (see also fermionic condensate). === Dilute atomic gases === The first "pure" Bose–Einstein condensate was created by Eric Cornell, Carl Wieman, and co-workers at JILA on 5
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June 1995. They cooled a dilute vapor of approximately two thousand rubidium-87 atoms to below 170 nK using a combination of laser cooling (a technique that won its inventors Steven Chu, Claude Cohen-Tannoudji, and William D. Phillips the 1997 Nobel Prize in Physics) and magnetic evaporative cooling. About four months later, an independent effort led by Wolfgang Ketterle at MIT condensed sodium-23. Ketterle's condensate had a hundred times more atoms, allowing important results such as the observation of quantum mechanical interference between two different condensates. Cornell, Wieman and Ketterle won the 2001 Nobel Prize in Physics for their achievements. A group led by Randall Hulet at Rice University announced a condensate of lithium atoms only one month following the JILA work. Lithium has attractive interactions, causing the condensate to be unstable and collapse for all but a few atoms. Hulet's team subsequently showed the condensate could be stabilized by confinement quantum pressure for up to about 1000 atoms. Various isotopes have since been condensed. ==== Velocity-distribution data graph ==== In the image accompanying this article, the velocity-distribution data indicates the formation of a Bose–Einstein condensate out of a gas of rubidium atoms. The false colors indicate the number of atoms at each velocity, with red being the fewest and white being the most. The areas appearing white and light blue are at the lowest velocities. The peak is not infinitely narrow because of the Heisenberg uncertainty principle: spatially confined atoms have a minimum width velocity distribution. This width is given by the curvature of the magnetic potential in the given direction. More tightly confined directions have bigger widths in the ballistic velocity distribution. This anisotropy of the peak on the right is a purely quantum-mechanical effect and does not exist in the thermal distribution on the left. This graph served
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as the cover design for the 1999 textbook Thermal Physics by Ralph Baierlein. === Quasiparticles === Bose–Einstein condensation also applies to quasiparticles in solids. Magnons, excitons, and polaritons have integer spin which means they are bosons that can form condensates. Magnons, electron spin waves, can be controlled by a magnetic field. Densities from the limit of a dilute gas to a strongly interacting Bose liquid are possible. Magnetic ordering is the analog of superfluidity. In 1999 condensation was demonstrated in antiferromagnetic TlCuCl3, at temperatures as great as 14 K. The high transition temperature (relative to atomic gases) is due to the magnons' small mass (near that of an electron) and greater achievable density. In 2006, condensation in a ferromagnetic yttrium-iron-garnet thin film was seen even at room temperature, with optical pumping. Excitons, electron-hole pairs, were predicted to condense at low temperature and high density by Boer et al., in 1961. Bilayer system experiments first demonstrated condensation in 2003, by Hall voltage disappearance. Fast optical exciton creation was used to form condensates in sub-kelvin Cu2O in 2005 on. Polariton condensation was first detected for exciton-polaritons in a quantum well microcavity kept at 5 K. Quasiparticle BECs have been achieved at room-temperature, for example, in microcavity-coupled organic semiconductors and plasmon-exciton polaritons in periodic arrays of metal nanoparticles coupled to dye molecules. === In zero gravity === In June 2020, the Cold Atom Laboratory experiment on board the International Space Station successfully created a BEC of rubidium atoms and observed them for over a second in free-fall. Although initially just a proof of function, early results showed that, in the microgravity environment of the ISS, about half of the atoms formed into a magnetically insensitive halo-like cloud around the main body of the BEC. == Models == === Bose Einstein's non-interacting gas ===
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Consider a collection of N non-interacting particles, which can each be in one of two quantum states, | 0 ⟩ {\displaystyle |0\rangle } and | 1 ⟩ {\displaystyle |1\rangle } . If the two states are equal in energy, each different configuration is equally likely. If we can tell which particle is which, there are 2 N {\displaystyle 2^{N}} different configurations, since each particle can be in | 0 ⟩ {\displaystyle |0\rangle } or | 1 ⟩ {\displaystyle |1\rangle } independently. In almost all of the configurations, about half the particles are in | 0 ⟩ {\displaystyle |0\rangle } and the other half in | 1 ⟩ {\displaystyle |1\rangle } . The balance is a statistical effect: the number of configurations is largest when the particles are divided equally. If the particles are indistinguishable, however, there are only N + 1 {\displaystyle N+1} different configurations. If there are K {\displaystyle K} particles in state | 1 ⟩ {\displaystyle |1\rangle } , there are N − K {\displaystyle N-K} particles in state | 0 ⟩ {\displaystyle |0\rangle } . Whether any particular particle is in state | 0 ⟩ {\displaystyle |0\rangle } or in state | 1 ⟩ {\displaystyle |1\rangle } cannot be determined, so each value of K {\displaystyle K} determines a unique quantum state for the whole system. Suppose now that the energy of state | 1 ⟩ {\displaystyle |1\rangle } is slightly greater than the energy of state | 0 ⟩ {\displaystyle |0\rangle } by an amount E {\displaystyle E} . At temperature T {\displaystyle T} , a particle will have a lesser probability to be in state | 1 ⟩ {\displaystyle |1\rangle } by e − E / k T {\displaystyle e^{-E/kT}} . In the distinguishable case, the particle distribution will be biased slightly towards state |
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0 ⟩ {\displaystyle |0\rangle } . But in the indistinguishable case, since there is no statistical pressure toward equal numbers, the most-likely outcome is that most of the particles will collapse into state | 0 ⟩ {\displaystyle |0\rangle } . In the distinguishable case, for large N, the fraction in state | 0 ⟩ {\displaystyle |0\rangle } can be computed. It is the same as flipping a coin with probability proportional to exp ( − E / T ) {\displaystyle \exp {(-E/T)}} to land tails. In the indistinguishable case, each value of K {\displaystyle K} is a single state, which has its own separate Boltzmann probability. So the probability distribution is exponential: P ( K ) = C e − K E / T = C p K . {\displaystyle \,P(K)=Ce^{-KE/T}=Cp^{K}.} For large N {\displaystyle N} , the normalization constant C {\displaystyle C} is 1 − p {\displaystyle 1-p} . The expected total number of particles not in the lowest energy state, in the limit that N → ∞ {\displaystyle N\rightarrow \infty } , is equal to ∑ n > 0 C n p n = p / ( 1 − p ) {\displaystyle \sum _{n>0}Cnp^{n}=p/(1-p)} It does not grow when N is large; it just approaches a constant. This will be a negligible fraction of the total number of particles. So a collection of enough Bose particles in thermal equilibrium will mostly be in the ground state, with only a few in any excited state, no matter how small the energy difference. Consider now a gas of particles, which can be in different momentum states labeled | k ⟩ {\displaystyle |k\rangle } . If the number of particles is less than the number of thermally accessible states, for high temperatures and low densities, the particles will all be
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in different states. In this limit, the gas is classical. As the density increases or the temperature decreases, the number of accessible states per particle becomes smaller, and at some point, more particles will be forced into a single state than the maximum allowed for that state by statistical weighting. From this point on, any extra particle added will go into the ground state. To calculate the transition temperature at any density, integrate, over all momentum states, the expression for maximum number of excited particles, p / ( 1 − p ) {\displaystyle p/(1-p)} : N = V ∫ d 3 k ( 2 π ) 3 p ( k ) 1 − p ( k ) = V ∫ d 3 k ( 2 π ) 3 1 e k 2 2 m T − 1 {\displaystyle \,N=V\int {d^{3}k \over (2\pi )^{3}}{p(k) \over 1-p(k)}=V\int {d^{3}k \over (2\pi )^{3}}{1 \over e^{k^{2} \over 2mT}-1}} p ( k ) = e − k 2 2 m T . {\displaystyle \,p(k)=e^{-k^{2} \over 2mT}.} When the integral (also known as Bose–Einstein integral) is evaluated with factors of k B {\displaystyle k_{B}} and ℏ {\displaystyle \hbar } restored by dimensional analysis, it gives the critical temperature formula of the preceding section. Therefore, this integral defines the critical temperature and particle number corresponding to the conditions of negligible chemical potential μ {\displaystyle \mu } . In Bose–Einstein statistics distribution, μ {\displaystyle \mu } is actually still nonzero for BECs; however, μ {\displaystyle \mu } is less than the ground state energy. Except when specifically talking about the ground state, μ {\displaystyle \mu } can be approximated for most energy or momentum states as μ ≈ 0 {\displaystyle \mu \approx 0} . === Bogoliubov theory for weakly interacting gas === Nikolay Bogoliubov considered perturbations on the limit
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of dilute gas, finding a finite pressure at zero temperature and positive chemical potential. This leads to corrections for the ground state. The Bogoliubov state has pressure ( T = 0 ) {\displaystyle (T=0)} : P = g n 2 / 2 {\displaystyle P=gn^{2}/2} . The original interacting system can be converted to a system of non-interacting particles with a dispersion law. === Gross–Pitaevskii equation === In some simplest cases, the state of condensed particles can be described with a nonlinear Schrödinger equation, also known as Gross–Pitaevskii or Ginzburg–Landau equation. The validity of this approach is actually limited to the case of ultracold temperatures, which fits well for the most alkali atoms experiments. This approach originates from the assumption that the state of the BEC can be described by the unique wavefunction of the condensate ψ ( r → ) {\displaystyle \psi ({\vec {r}})} . For a system of this nature, | ψ ( r → ) | 2 {\displaystyle |\psi ({\vec {r}})|^{2}} is interpreted as the particle density, so the total number of atoms is N = ∫ d r → | ψ ( r → ) | 2 {\displaystyle N=\int d{\vec {r}}|\psi ({\vec {r}})|^{2}} Provided essentially all atoms are in the condensate (that is, have condensed to the ground state), and treating the bosons using mean-field theory, the energy (E) associated with the state ψ ( r → ) {\displaystyle \psi ({\vec {r}})} is: E = ∫ d r → [ ℏ 2 2 m | ∇ ψ ( r → ) | 2 + V ( r → ) | ψ ( r → ) | 2 + 1 2 U 0 | ψ ( r → ) | 4 ] {\displaystyle E=\int d{\vec {r}}\left[{\frac {\hbar ^{2}}{2m}}|\nabla \psi ({\vec {r}})|^{2}+V({\vec {r}})|\psi ({\vec {r}})|^{2}+{\frac {1}{2}}U_{0}|\psi ({\vec {r}})|^{4}\right]} Minimizing
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this energy with respect to infinitesimal variations in ψ ( r → ) {\displaystyle \psi ({\vec {r}})} , and holding the number of atoms constant, yields the Gross–Pitaevski equation (GPE) (also a non-linear Schrödinger equation): i ℏ ∂ ψ ( r → ) ∂ t = ( − ℏ 2 ∇ 2 2 m + V ( r → ) + U 0 | ψ ( r → ) | 2 ) ψ ( r → ) {\displaystyle i\hbar {\frac {\partial \psi ({\vec {r}})}{\partial t}}=\left(-{\frac {\hbar ^{2}\nabla ^{2}}{2m}}+V({\vec {r}})+U_{0}|\psi ({\vec {r}})|^{2}\right)\psi ({\vec {r}})} where: In the case of zero external potential, the dispersion law of interacting Bose–Einstein-condensed particles is given by so-called Bogoliubov spectrum (for T = 0 {\displaystyle \ T=0} ): ω p = p 2 2 m ( p 2 2 m + 2 U 0 n 0 ) {\displaystyle {\omega _{p}}={\sqrt {{\frac {p^{2}}{2m}}\left({{\frac {p^{2}}{2m}}+2{U_{0}}{n_{0}}}\right)}}} The Gross-Pitaevskii equation (GPE) provides a relatively good description of the behavior of atomic BEC's. However, GPE does not take into account the temperature dependence of dynamical variables, and is therefore valid only for T = 0 {\displaystyle \ T=0} . It is not applicable, for example, for the condensates of excitons, magnons and photons, where the critical temperature is comparable to room temperature. ==== Numerical solution ==== The Gross-Pitaevskii equation is a partial differential equation in space and time variables. Usually it does not have analytic solution and different numerical methods, such as split-step Crank–Nicolson and Fourier spectral methods, are used for its solution. There are different Fortran and C programs for its solution for contact interaction and long-range dipolar interaction which can be freely used. ==== Weaknesses of Gross–Pitaevskii model ==== The Gross–Pitaevskii model of BEC is a physical approximation valid for certain classes of BECs. By construction, the GPE uses
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the following simplifications: it assumes that interactions between condensate particles are of the contact two-body type and also neglects anomalous contributions to self-energy. These assumptions are suitable mostly for the dilute three-dimensional condensates. If one relaxes any of these assumptions, the equation for the condensate wavefunction acquires the terms containing higher-order powers of the wavefunction. Moreover, for some physical systems the amount of such terms turns out to be infinite, therefore, the equation becomes essentially non-polynomial. The examples where this could happen are the Bose–Fermi composite condensates, effectively lower-dimensional condensates, and dense condensates and superfluid clusters and droplets. It is found that one has to go beyond the Gross-Pitaevskii equation. For example, the logarithmic term ψ ln | ψ | 2 {\displaystyle \psi \ln |\psi |^{2}} found in the Logarithmic Schrödinger equation must be added to the Gross-Pitaevskii equation along with a Ginzburg–Sobyanin contribution to correctly determine that the speed of sound scales as the cubic root of pressure for Helium-4 at very low temperatures in close agreement with experiment. ==== Other ==== However, it is clear that in a general case the behaviour of Bose–Einstein condensate can be described by coupled evolution equations for condensate density, superfluid velocity and distribution function of elementary excitations. This problem was solved in 1977 by Peletminskii et al. in microscopical approach. The Peletminskii equations are valid for any finite temperatures below the critical point. Years after, in 1985, Kirkpatrick and Dorfman obtained similar equations using another microscopical approach. The Peletminskii equations also reproduce Khalatnikov hydrodynamical equations for superfluid as a limiting case. === Superfluidity of BEC and Landau criterion === The phenomena of superfluidity of a Bose gas and superconductivity of a strongly-correlated Fermi gas (a gas of Cooper pairs) are tightly connected to Bose–Einstein condensation. Under corresponding conditions, below the temperature
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of phase transition, these phenomena were observed in helium-4 and different classes of superconductors. In this sense, the superconductivity is often called the superfluidity of Fermi gas. In the simplest form, the origin of superfluidity can be seen from the weakly interacting bosons model. == Peculiar properties == === Quantized vortices === As in many other systems, vortices can exist in BECs. Vortices can be created, for example, by "stirring" the condensate with lasers, rotating the confining trap, or by rapid cooling across the phase transition. The vortex created will be a quantum vortex with core shape determined by the interactions. Fluid circulation around any point is quantized due to the single-valued nature of the order BEC order parameter or wavefunction, that can be written in the form ψ ( r → ) = ϕ ( ρ , z ) e i ℓ θ {\displaystyle \psi ({\vec {r}})=\phi (\rho ,z)e^{i\ell \theta }} where ρ , z {\displaystyle \rho ,z} and θ {\displaystyle \theta } are as in the cylindrical coordinate system, and ℓ {\displaystyle \ell } is the angular quantum number (a.k.a. the "charge" of the vortex). Since the energy of a vortex is proportional to the square of its angular momentum, in trivial topology only ℓ = 1 {\displaystyle \ell =1} vortices can exist in the steady state; Higher-charge vortices will have a tendency to split into ℓ = 1 {\displaystyle \ell =1} vortices, if allowed by the topology of the geometry. An axially symmetric (for instance, harmonic) confining potential is commonly used for the study of vortices in BEC. To determine ϕ ( ρ , z ) {\displaystyle \phi (\rho ,z)} , the energy of ψ ( r → ) {\displaystyle \psi ({\vec {r}})} must be minimized, according to the constraint ψ ( r → ) = ϕ
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( ρ , z ) e i ℓ θ {\displaystyle \psi ({\vec {r}})=\phi (\rho ,z)e^{i\ell \theta }} . This is usually done computationally, however, in a uniform medium, the following analytic form demonstrates the correct behavior, and is a good approximation: ϕ = n x 2 + x 2 . {\displaystyle \phi ={\frac {nx}{\sqrt {2+x^{2}}}}\,.} Here, n {\displaystyle n} is the density far from the vortex and x = ρ / ( ℓ ξ ) {\displaystyle x=\rho /(\ell \xi )} , where ξ = 1 / 8 π a s n 0 {\displaystyle \xi =1/{\sqrt {8\pi a_{s}n_{0}}}} is the healing length of the condensate. A singly charged vortex ( ℓ = 1 {\displaystyle \ell =1} ) is in the ground state, with its energy ϵ v {\displaystyle \epsilon _{v}} given by ϵ v = π n ℏ 2 m ln ( 1.464 b ξ ) {\displaystyle \epsilon _{v}=\pi n{\frac {\hbar ^{2}}{m}}\ln \left(1.464{\frac {b}{\xi }}\right)} where b {\displaystyle \,b} is the farthest distance from the vortices considered.(To obtain an energy which is well defined it is necessary to include this boundary b {\displaystyle b} .) For multiply charged vortices ( ℓ > 1 {\displaystyle \ell >1} ) the energy is approximated by ϵ v ≈ ℓ 2 π n ℏ 2 m ln ( b ξ ) {\displaystyle \epsilon _{v}\approx \ell ^{2}\pi n{\frac {\hbar ^{2}}{m}}\ln \left({\frac {b}{\xi }}\right)} which is greater than that of ℓ {\displaystyle \ell } singly charged vortices, indicating that these multiply charged vortices are unstable to decay. Research has, however, indicated they are metastable states, so may have relatively long lifetimes. Closely related to the creation of vortices in BECs is the generation of so-called dark solitons in one-dimensional BECs. These topological objects feature a phase gradient across their nodal plane, which stabilizes their shape
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even in propagation and interaction. Although solitons carry no charge and are thus prone to decay, relatively long-lived dark solitons have been produced and studied extensively. === Attractive interactions === Experiments led by Randall Hulet at Rice University from 1995 through 2000 showed that lithium condensates with attractive interactions could stably exist up to a critical atom number. Quench cooling the gas, they observed the condensate to grow, then subsequently collapse as the attraction overwhelmed the zero-point energy of the confining potential, in a burst reminiscent of a supernova, with an explosion preceded by an implosion. Further work on attractive condensates was performed in 2000 by the JILA team, of Cornell, Wieman and coworkers. Their instrumentation now had better control so they used naturally attracting atoms of rubidium-85 (having negative atom–atom scattering length). Through Feshbach resonance involving a sweep of the magnetic field causing spin flip collisions, they lowered the characteristic, discrete energies at which rubidium bonds, making their Rb-85 atoms repulsive and creating a stable condensate. The reversible flip from attraction to repulsion stems from quantum interference among wave-like condensate atoms. When the JILA team raised the magnetic field strength further, the condensate suddenly reverted to attraction, imploded and shrank beyond detection, then exploded, expelling about two-thirds of its 10,000 atoms. About half of the atoms in the condensate seemed to have disappeared from the experiment altogether, not seen in the cold remnant or expanding gas cloud. Carl Wieman explained that under current atomic theory this characteristic of Bose–Einstein condensate could not be explained because the energy state of an atom near absolute zero should not be enough to cause an implosion; however, subsequent mean-field theories have been proposed to explain it. Most likely they formed molecules of two rubidium atoms; energy gained by this bond imparts velocity sufficient
|
{
"page_id": 4474,
"source": null,
"title": "Bose–Einstein condensate"
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to leave the trap without being detected. The process of creation of molecular Bose condensate during the sweep of the magnetic field throughout the Feshbach resonance, as well as the reverse process, are described by the exactly solvable model that can explain many experimental observations. == Current research == Compared to more commonly encountered states of matter, Bose–Einstein condensates are extremely fragile. The slightest interaction with the external environment can be enough to warm them past the condensation threshold, eliminating their interesting properties and forming a normal gas. Nevertheless, they have proven useful in exploring a wide range of questions in fundamental physics, and the years since the initial discoveries by the JILA and MIT groups have seen an increase in experimental and theoretical activity. Bose–Einstein condensates composed of a wide range of isotopes have been produced; see below. === Fundamental research === Examples include experiments that have demonstrated interference between condensates due to wave–particle duality, the study of superfluidity and quantized vortices, the creation of bright matter wave solitons from Bose condensates confined to one dimension, and the slowing of light pulses to very low speeds using electromagnetically induced transparency. Vortices in Bose–Einstein condensates are also currently the subject of analogue gravity research, studying the possibility of modeling black holes and their related phenomena in such environments in the laboratory. Experimenters have also realized "optical lattices", where the interference pattern from overlapping lasers provides a periodic potential. These are used to explore the transition between a superfluid and a Mott insulator. They are also useful in studying Bose–Einstein condensation in fewer than three dimensions, for example the Lieb–Liniger model (an the limit of strong interactions, the Tonks–Girardeau gas) in 1D and the Berezinskii–Kosterlitz–Thouless transition in 2D. Indeed, a deep optical lattice allows the experimentalist to freeze the motion of
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{
"page_id": 4474,
"source": null,
"title": "Bose–Einstein condensate"
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the particles along one or two directions, effectively eliminating one or two dimension from the system. Further, the sensitivity of the pinning transition of strongly interacting bosons confined in a shallow one-dimensional optical lattice originally observed by Haller has been explored via a tweaking of the primary optical lattice by a secondary weaker one. Thus for a resulting weak bichromatic optical lattice, it has been found that the pinning transition is robust against the introduction of the weaker secondary optical lattice. Studies of vortices in nonuniform Bose–Einstein condensates as well as excitations of these systems by the application of moving repulsive or attractive obstacles, have also been undertaken. Within this context, the conditions for order and chaos in the dynamics of a trapped Bose–Einstein condensate have been explored by the application of moving blue and red-detuned laser beams (hitting frequencies slightly above and below the resonance frequency, respectively) via the time-dependent Gross-Pitaevskii equation. === Applications === In 1999, Danish physicist Lene Hau led a team from Harvard University which slowed a beam of light to about 17 meters per second using a superfluid. Hau and her associates have since made a group of condensate atoms recoil from a light pulse such that they recorded the light's phase and amplitude, recovered by a second nearby condensate, in what they term "slow-light-mediated atomic matter-wave amplification" using Bose–Einstein condensates. Another current research interest is the creation of Bose–Einstein condensates in microgravity in order to use its properties for high precision atom interferometry. The first demonstration of a BEC in weightlessness was achieved in 2008 at a drop tower in Bremen, Germany by a consortium of researchers led by Ernst M. Rasel from Leibniz University Hannover. The same team demonstrated in 2017 the first creation of a Bose–Einstein condensate in space and it is
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{
"page_id": 4474,
"source": null,
"title": "Bose–Einstein condensate"
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|
also the subject of two upcoming experiments on the International Space Station. Researchers in the new field of atomtronics use the properties of Bose–Einstein condensates in the emerging quantum technology of matter-wave circuits. In 1970, BECs were proposed by Emmanuel David Tannenbaum for anti-stealth technology. === Isotopes === Bose-Einstein condensation has mainly been observed on alkaline atoms, some of which have collisional properties particularly suitable for evaporative cooling in traps, and which were the first to be laser-cooled. As of 2021, using ultra-low temperatures of 10−7 K or below, Bose–Einstein condensates had been obtained for a multitude of isotopes with more or less ease, mainly of alkali metal, alkaline earth metal, and lanthanide atoms (7Li, 23Na, 39K, 41K, 85Rb, 87Rb, 133Cs, 52Cr, 40Ca, 84Sr, 86Sr, 88Sr, 170Yb, 174Yb, 176Yb, 164Dy, 168Er, 169Tm, and metastable 4He (orthohelium)). Research was finally successful in atomic hydrogen with the aid of the newly developed method of 'evaporative cooling'. In contrast, the superfluid state of 4He below 2.17 K is differs significantly from dilute degenerate atomic gases because the interaction between the atoms is strong. Only 8% of atoms are in the condensed fraction near absolute zero, rather than near 100% of a weakly interacting BEC. The bosonic behavior of some of these alkaline gases appears odd at first sight, because their nuclei have half-integer total spin. It arises from the interplay of electronic and nuclear spins: at ultra-low temperatures and corresponding excitation energies, the half-integer total spin of the electronic shell (one outer electron) and half-integer total spin of the nucleus are coupled by a very weak hyperfine interaction. The total spin of the atom, arising from this coupling, is an integer value. Conversely, alkali isotopes which have an integer nuclear spin (such as 6Li and 40K) are fermions and can form degenerate Fermi
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{
"page_id": 4474,
"source": null,
"title": "Bose–Einstein condensate"
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gases, also called "Fermi condensates". Cooling fermions to extremely low temperatures has created degenerate gases, subject to the Pauli exclusion principle. To exhibit Bose–Einstein condensation, the fermions must "pair up" to form bosonic compound particles (e.g. molecules or Cooper pairs). The first molecular condensates were created in November 2003 by the groups of Rudolf Grimm at the University of Innsbruck, Deborah S. Jin at the University of Colorado at Boulder and Wolfgang Ketterle at MIT. Jin quickly went on to create the first fermionic condensate, working with the same system but outside the molecular regime. === Continuous Bose–Einstein condensation === Limitations of evaporative cooling have restricted atomic BECs to "pulsed" operation, involving a highly inefficient duty cycle that discards more than 99% of atoms to reach BEC. Achieving continuous BEC has been a major open problem of experimental BEC research, driven by the same motivations as continuous optical laser development: high flux, high coherence matter waves produced continuously would enable new sensing applications. Continuous BEC was achieved for the first time in 2022 with 84Sr. === In solid state physics === In 2020, researchers reported the development of superconducting BEC and that there appears to be a "smooth transition between" BEC and Bardeen–Cooper–Shrieffer regimes. === Dark matter === P. Sikivie and Q. Yang showed that cold dark matter axions would form a Bose–Einstein condensate by thermalisation because of gravitational self-interactions. Axions have not yet been confirmed to exist. However the important search for them has been greatly enhanced with the completion of upgrades to the Axion Dark Matter Experiment (ADMX) at the University of Washington in early 2018. In 2014, a potential dibaryon was detected at the Jülich Research Center at about 2380 MeV. The center claimed that the measurements confirm results from 2011, via a more replicable method. The
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{
"page_id": 4474,
"source": null,
"title": "Bose–Einstein condensate"
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particle existed for 10−23 seconds and was named d*(2380). This particle is hypothesized to consist of three up and three down quarks. It is theorized that groups of d* (d-stars) could form Bose–Einstein condensates due to prevailing low temperatures in the early universe, and that BECs made of such hexaquarks with trapped electrons could behave like dark matter. == In fiction == In the 2016 film Spectral, the US military battles mysterious enemy creatures fashioned out of Bose–Einstein condensates. In the 2003 novel Blind Lake, scientists observe sentient life on a planet 51 light-years away using telescopes powered by Bose–Einstein condensate-based quantum computers. == See also == == References == == Further reading == == External links == Bose–Einstein Condensation 2009 Conference – Frontiers in Quantum Gases BEC Homepage General introduction to Bose–Einstein condensation Nobel Prize in Physics 2001 – for the achievement of Bose–Einstein condensation in dilute gases of alkali atoms, and for early fundamental studies of the properties of the condensates Levi, Barbara G. (2001). "Cornell, Ketterle, and Wieman Share Nobel Prize for Bose–Einstein Condensates". Physics Today. 54 (12): 14–16. Bibcode:2001PhT....54l..14L. doi:10.1063/1.1445529. Bose–Einstein condensates at JILA Atomcool at Rice University Alkali Quantum Gases at MIT Atom Optics at UQ Einstein's manuscript on the Bose–Einstein condensate discovered at Leiden University Bose–Einstein condensate on arxiv.org Bosons – The Birds That Flock and Sing Together Easy BEC machine – information on constructing a Bose–Einstein condensate machine. Verging on absolute zero – Cosmos Online Archived 22 November 2008 at the Wayback Machine Lecture by W Ketterle at MIT in 2001 Bose–Einstein Condensation at NIST – NIST resource on BEC
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"page_id": 4474,
"source": null,
"title": "Bose–Einstein condensate"
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Clinical biophysics is that branch of medical science that studies the action process and the effects of non-ionising physical energies utilised for therapeutic purposes. Physical energy can be applied for diagnostic or therapeutic aims. The principle on which clinical biophysics is based are represented by the recognizability and the specificity of the physical signal applied: recognizability: the capacity of the biological target to recognise the presence of the physical energy: this aspect becomes more important with the lowering of the energy applied. specificity: the capacity of the physical agent applied to the biological target to obtain a response depending on its physical characteristics: frequency, length, energy, etc. The effects do not necessarily depend on the quantity of energy applied to the biological target. == Definition == Several papers show that the response of a biological system when exposed to non-ionizing physical stimuli is not necessarily dependent on the amount of energy applied. Specific combinations of amplitude, frequency and waveform may trigger the most intense response. For example, cell proliferation or activation of metabolic pathways. This has been demonstrated for: a) mechanical strains directly applied to the cells or tissue; b) mechanical energy applied by ultrasound; c) electromagnetic field exposure; d) electric field exposure. Several pre-clinical experiences have laid the foundation to identify exposure conditions that may be used in humans to treat diseases or to promote tissue healing. The identification of the best parameters to apply in any particular circumstance is the current goal of research activities in the field. == Medical applications == Orthopaedics PEMF LIPUS CCEF Direct current Neurology Plastic surgery Oncology == References ==
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{
"page_id": 32182651,
"source": null,
"title": "Clinical biophysics"
}
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A restriction digest is a procedure used in molecular biology to prepare DNA for analysis or other processing. It is sometimes termed DNA fragmentation, though this term is used for other procedures as well. In a restriction digest, DNA molecules are cleaved at specific restriction sites of 4-12 nucleotides in length by use of restriction enzymes which recognize these sequences. The resulting digested DNA is very often selectively amplified using polymerase chain reaction (PCR), making it more suitable for analytical techniques such as agarose gel electrophoresis, and chromatography. It is used in genetic fingerprinting, plasmid subcloning, and RFLP analysis. == Restriction site == A given restriction enzyme cuts DNA segments within a specific nucleotide sequence, at what is called a restriction site. These recognition sequences are typically four, six, eight, ten, or twelve nucleotides long and generally palindromic (i.e. the same nucleotide sequence in the 5' – 3' direction). Because there are only so many ways to arrange the four nucleotides that compose DNA (Adenine, Thymine, Guanine and Cytosine) into a four- to twelve-nucleotide sequence, recognition sequences tend to occur by chance in any long sequence. Restriction enzymes specific to hundreds of distinct sequences have been identified and synthesized for sale to laboratories, and as a result, several potential "restriction sites" appear in almost any gene or locus of interest on any chromosome. Furthermore, almost all artificial plasmids include a (often entirely synthetic) polylinker (also called "multiple cloning site") that contains dozens of restriction enzyme recognition sequences within a very short segment of DNA. This allows the insertion of almost any specific fragment of DNA into plasmid vectors, which can be efficiently "cloned" by insertion into replicating bacterial cells. After restriction digest, DNA can then be analysed using agarose gel electrophoresis. In gel electrophoresis, a sample of DNA is first
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{
"page_id": 1708412,
"source": null,
"title": "Restriction digest"
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"loaded" onto a slab of agarose gel (literally pipetted into small wells at one end of the slab). The gel is then subjected to an electric field, which draws the negatively charged DNA across it. The molecules travel at different rates (and therefore end up at different distances) depending on their net charge (more highly charged particles travel further), and size (smaller particles travel further). Since none of the four nucleotide bases carry any charge, net charge becomes insignificant and size is the main factor affecting rate of diffusion through the gel. Net charge in DNA is produced by the sugar-phosphate backbone. This is in contrast to proteins, in which there is no "backbone", and net charge is generated by different combinations and numbers of charged amino acids. == Possible uses == Restriction digest is most commonly used as part of the process of the molecular cloning of DNA fragment into a vector (such as a cloning vector or an expression vector). The vector typically contains a multiple cloning site where many restriction site may be found, and a foreign piece of DNA may be inserted into the vector by first cutting the restriction sites in the vector as well the DNA fragment, followed by ligation of the DNA fragment into the vector. Restriction digests are also necessary for performing any of the following analytical techniques: RFLP – Restriction fragment length polymorphism AFLP – Amplified fragment length polymorphism STRP – Short tandem repeat polymorphism == Various restriction enzymes == There are numerous types of restriction enzymes, each of which will cut DNA differently. Most commonly used restriction enzymes are Type II restriction endonuclease (See article on Restriction enzymes for examples). There are some that cut a three base pair sequence while others can cut four, six, and even eight. Each
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{
"page_id": 1708412,
"source": null,
"title": "Restriction digest"
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|
enzyme has distinct properties that determine how efficiently it can cut and under what conditions. Most manufacturers that produce such enzymes will often provide a specific buffer solution that contains the unique mix of cations and other components that aid the enzyme in cutting as efficiently as possible. Different restriction enzymes may also have different optimal temperatures under which they function. Note that for efficient digest of DNA, the restriction site should not be located at the very end of a DNA fragment. The restriction enzymes may require a minimum number of base pairs between the restriction site and the end of the DNA for the enzyme to work efficiently. This number may vary between enzymes, but for most commonly used restriction enzymes around 6–10 base pair is sufficient. == See also == Agarose gel electrophoresis DNA sequencing Genetic fingerprinting PCR Restriction fragment length polymorphism == References == == External links == New England Biolabs – Producer of restriction enzymes. This site contains highly detailed information on numerous enzymes, their optimal temperatures, and recognition sequences. REBASE
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{
"page_id": 1708412,
"source": null,
"title": "Restriction digest"
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The Beer–Bouguer–Lambert (BBL) extinction law is an empirical relationship describing the attenuation in intensity of a radiation beam passing through a macroscopically homogenous medium with which it interacts. Formally, it states that the intensity of radiation decays exponentially in the absorbance of the medium, and that said absorbance is proportional to the length of beam passing through the medium, the concentration of interacting matter along that path, and a constant representing said matter's propensity to interact. The extinction law's primary application is in chemical analysis, where it underlies the Beer–Lambert law, commonly called Beer's law. Beer's law states that a beam of visible light passing through a chemical solution of fixed geometry experiences absorption proportional to the solute concentration. Other applications appear in physical optics, where it quantifies astronomical extinction and the absorption of photons, neutrons, or rarefied gases. Forms of the BBL law date back to the mid-eighteenth century, but it only took its modern form during the early twentieth. == History == The first work towards the BBL law began with astronomical observations Pierre Bouguer performed in the early eighteenth century and published in 1729. Bouguer needed to compensate for the refraction of light by the earth's atmosphere, and found it necessary to measure the local height of the atmosphere. The latter, he sought to obtain through variations in the observed intensity of known stars. When calibrating this effect, Bouguer discovered that light intensity had an exponential dependence on length traveled through the atmosphere (in Bouguer's terms, a geometric progression). Bouguer's work was then popularized in Johann Heinrich Lambert's Photometria in 1760. Lambert expressed the law, which states that the loss of light intensity when it propagates in a medium is directly proportional to intensity and path length, in a mathematical form quite similar to that used in
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{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
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modern physics. Lambert began by assuming that the intensity I of light traveling into an absorbing body would be given by the differential equation − d I = μ I d x , {\displaystyle -\mathrm {d} I=\mu I\mathrm {d} x,} which is compatible with Bouguer's observations. The constant of proportionality μ was often termed the "optical density" of the body. As long as μ is constant along a distance d, the exponential attenuation law, I = I 0 e − μ d {\displaystyle I=I_{0}e^{-\mu d}} follows from integration. In 1852, August Beer noticed that colored solutions also appeared to exhibit a similar attenuation relation. In his analysis, Beer does not discuss Bouguer and Lambert's prior work, writing in his introduction that "Concerning the absolute magnitude of the absorption that a particular ray of light suffers during its propagation through an absorbing medium, there is no information available." Beer may have omitted reference to Bouguer's work because there is a subtle physical difference between color absorption in solutions and astronomical contexts. Solutions are homogeneous and do not scatter light at common analytical wavelengths (ultraviolet, visible, or infrared), except at entry and exit. Thus light within a solution is reasonably approximated as due to absorption alone. In Bouguer's context, atmospheric dust or other inhomogeneities could also scatter light away from the detector. Modern texts combine the two laws because scattering and absorption have the same effect. Thus a scattering coefficient μs and an absorption coefficient μa can be combined into a total extinction coefficient μ = μs + μa. Importantly, Beer also seems to have conceptualized his result in terms of a given thickness' opacity, writing "If λ is the coefficient (fraction) of diminution, then this coefficient (fraction) will have the value λ2 for double this thickness." Although this geometric progression is
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{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
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mathematically equivalent to the modern law, modern treatments instead emphasize the logarithm of λ, which clarifies that concentration and path length have equivalent effects on the absorption. An early, possibly the first, modern formulation was given by Robert Luther and Andreas Nikolopulos in 1913. == Mathematical formulations == There are several equivalent formulations of the BBL law, depending on the precise choice of measured quantities. All of them state that, provided that the physical state is held constant, the extinction process is linear in the intensity of radiation and amount of radiatively-active matter, a fact sometimes called the fundamental law of extinction. Many of them then connect the quantity of radiatively-active matter to a length traveled ℓ and a concentration c or number density n. For concentrations expressed as moles per volume, the latter two are related by Avogadro's number: n = NAc. A collimated beam (directed radiation) with cross-sectional area S will encounter Sℓn particles (on average) during its travel. However, not all of these particles interact with the beam. Propensity to interact is a material-dependent property, typically summarized in absorptivity ϵ or scattering cross-section σ. These almost exhibit another Avogadro-type relationship: ln(10)ε = NAσ. The factor of ln(10) appears because physicists tend to use natural logarithms and chemists decadal logarithms. Beam intensity can also be described in terms of multiple variables: the intensity I or radiant flux Φ. In the case of a collimated beam, these are related by Φ = IS, but Φ is often used in non-collimated contexts. The ratio of intensity (or flux) in to out is sometimes summarized as a transmittance coefficient T = I⁄I0. When considering an extinction law, dimensional analysis can verify the consistency of the variables, as logarithms (being nonlinear) must always be dimensionless. === Formulation === The simplest formulation of
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"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
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Beer's relates the optical attenuation of a physical material containing a single attenuating species of uniform concentration to the optical path length through the sample and absorptivity of the species. This expression is: log 10 ( I 0 / I ) = A = ε ℓ c {\displaystyle \log _{10}(I_{0}/I)=A=\varepsilon \ell c} The quantities so equated are defined to be the absorbance A, which depends on the logarithm base. The Naperian absorbance τ is then given by τ = ln(10)A and satisfies ln ( I 0 / I ) = τ = σ ℓ n . {\displaystyle \ln(I_{0}/I)=\tau =\sigma \ell n.} If multiple species in the material interact with the radiation, then their absorbances add. Thus a slightly more general formulation is that τ = ℓ ∑ i σ i n i , A = ℓ ∑ i ε i c i , {\displaystyle {\begin{aligned}\tau &=\ell \sum _{i}\sigma _{i}n_{i},\\[4pt]A&=\ell \sum _{i}\varepsilon _{i}c_{i},\end{aligned}}} where the sum is over all possible radiation-interacting ("translucent") species, and i indexes those species. In situations where length may vary significantly, absorbance is sometimes summarized in terms of an attenuation coefficient μ 10 = A l = ϵ c μ = τ l = σ n . {\displaystyle {\begin{alignedat}{3}\mu _{10}&={\frac {A}{l}}&&=\epsilon c\\\mu &={\frac {\tau }{l}}&&=\sigma n.\end{alignedat}}} In atmospheric science and radiation shielding applications, the attenuation coefficient may vary significantly through an inhomogenous material. In those situations, the most general form of the Beer–Lambert law states that the total attenuation can be obtained by integrating the attenuation coefficient over small slices dz of the beamline: A = ∫ μ 10 ( z ) d z = ∫ ∑ i ϵ i ( z ) c i ( z ) d z , τ = ∫ μ ( z ) d z = ∫ ∑ i σ
|
{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
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|
i ( z ) n i ( z ) d z . {\displaystyle {\begin{alignedat}{3}A&=\int {\mu _{10}(z)\,dz}&&=\int {\sum _{i}{\epsilon _{i}(z)c_{i}(z)}\,dz},\\\tau &=\int {\mu (z)\,dz}&&=\int {\sum _{i}{\sigma _{i}(z)n_{i}(z)}\,dz}.\end{alignedat}}} These formulations then reduce to the simpler versions when there is only one active species and the attenuation coefficients are constant. == Derivation == There are two factors that determine the degree to which a medium containing particles will attenuate a light beam: the number of particles encountered by the light beam, and the degree to which each particle extinguishes the light. Assume that a beam of light enters a material sample. Define z as an axis parallel to the direction of the beam. Divide the material sample into thin slices, perpendicular to the beam of light, with thickness dz sufficiently small that one particle in a slice cannot obscure another particle in the same slice when viewed along the z direction. The radiant flux of the light that emerges from a slice is reduced, compared to that of the light that entered, by d Φ e ( z ) = − μ ( z ) Φ e ( z ) d z , {\displaystyle \mathrm {d\Phi _{e}} (z)=-\mu (z)\Phi _{\mathrm {e} }(z)\mathrm {d} z,} where μ is the (Napierian) attenuation coefficient, which yields the following first-order linear, ordinary differential equation: d Φ e ( z ) d z = − μ ( z ) Φ e ( z ) . {\displaystyle {\frac {\mathrm {d} \Phi _{\mathrm {e} }(z)}{\mathrm {d} z}}=-\mu (z)\Phi _{\mathrm {e} }(z).} The attenuation is caused by the photons that did not make it to the other side of the slice because of scattering or absorption. The solution to this differential equation is obtained by multiplying the integrating factor exp ( ∫ 0 z μ ( z ′ ) d z
|
{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
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|
′ ) {\displaystyle \exp \left(\int _{0}^{z}\mu (z')\mathrm {d} z'\right)} throughout to obtain d Φ e ( z ) d z exp ( ∫ 0 z μ ( z ′ ) d z ′ ) + μ ( z ) Φ e ( z ) exp ( ∫ 0 z μ ( z ′ ) d z ′ ) = 0 , {\displaystyle {\frac {\mathrm {d} \Phi _{\mathrm {e} }(z)}{\mathrm {d} z}}\,\exp \left(\int _{0}^{z}\mu (z')\mathrm {d} z'\right)+\mu (z)\Phi _{\mathrm {e} }(z)\,\exp \left(\int _{0}^{z}\mu (z')\mathrm {d} z'\right)=0,} which simplifies due to the product rule (applied backwards) to d d z [ Φ e ( z ) exp ( ∫ 0 z μ ( z ′ ) d z ′ ) ] = 0. {\displaystyle {\frac {\mathrm {d} }{\mathrm {d} z}}\left[\Phi _{\mathrm {e} }(z)\exp \left(\int _{0}^{z}\mu (z')\mathrm {d} z'\right)\right]=0.} Integrating both sides and solving for Φe for a material of real thickness ℓ, with the incident radiant flux upon the slice Φ e i = Φ e ( 0 ) {\displaystyle \mathrm {\Phi _{e}^{i}} =\mathrm {\Phi _{e}} (0)} and the transmitted radiant flux Φ e t = Φ e ( ℓ ) {\displaystyle \mathrm {\Phi _{e}^{t}} =\mathrm {\Phi _{e}} (\ell )} gives Φ e t = Φ e i exp ( − ∫ 0 ℓ μ ( z ) d z ) , {\displaystyle \mathrm {\Phi _{e}^{t}} =\mathrm {\Phi _{e}^{i}} \exp \left(-\int _{0}^{\ell }\mu (z)\mathrm {d} z\right),} and finally T = Φ e t Φ e i = exp ( − ∫ 0 ℓ μ ( z ) d z ) . {\displaystyle T=\mathrm {\frac {\Phi _{e}^{t}}{\Phi _{e}^{i}}} =\exp \left(-\int _{0}^{\ell }\mu (z)\mathrm {d} z\right).} Since the decadic attenuation coefficient μ10 is related to the (Napierian) attenuation coefficient by μ 10 = μ ln 10 , {\displaystyle
|
{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
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\mu _{10}={\tfrac {\mu }{\ln 10}},} we also have T = exp ( − ∫ 0 ℓ ln ( 10 ) μ 10 ( z ) d z ) = 10 ∧ ( − ∫ 0 ℓ μ 10 ( z ) d z ) . {\displaystyle {\begin{aligned}T&=\exp \left(-\int _{0}^{\ell }\ln(10)\,\mu _{10}(z)\mathrm {d} z\right)\\[4pt]&=10^{\;\!\wedge }\!\!\left(-\int _{0}^{\ell }\mu _{10}(z)\mathrm {d} z\right).\end{aligned}}} To describe the attenuation coefficient in a way independent of the number densities ni of the N attenuating species of the material sample, one introduces the attenuation cross section σ i = μ i ( z ) n i ( z ) . {\displaystyle \sigma _{i}={\tfrac {\mu _{i}(z)}{n_{i}(z)}}.} σi has the dimension of an area; it expresses the likelihood of interaction between the particles of the beam and the particles of the species i in the material sample: T = exp ( − ∑ i = 1 N σ i ∫ 0 ℓ n i ( z ) d z ) . {\displaystyle T=\exp \left(-\sum _{i=1}^{N}\sigma _{i}\int _{0}^{\ell }n_{i}(z)\mathrm {d} z\right).} One can also use the molar attenuation coefficients ε i = N A ln 10 σ i , {\displaystyle \varepsilon _{i}={\tfrac {\mathrm {N_{A}} }{\ln 10}}\sigma _{i},} where NA is the Avogadro constant, to describe the attenuation coefficient in a way independent of the amount concentrations c i ( z ) = n i z N A {\displaystyle c_{i}(z)=n_{i}{\tfrac {z}{\mathrm {N_{A}} }}} of the attenuating species of the material sample: T = exp ( − ∑ i = 1 N ln ( 10 ) N A ε i ∫ 0 ℓ n i ( z ) d z ) = exp ( − ∑ i = 1 N ε i ∫ 0 ℓ n i ( z ) N A d z ) ln
|
{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
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|
( 10 ) = 10 ∧ ( − ∑ i = 1 N ε i ∫ 0 ℓ c i ( z ) d z ) . {\displaystyle {\begin{aligned}T&=\exp \left(-\sum _{i=1}^{N}{\frac {\ln(10)}{\mathrm {N_{A}} }}\varepsilon _{i}\int _{0}^{\ell }n_{i}(z)\mathrm {d} z\right)\\[4pt]&=\exp \left(-\sum _{i=1}^{N}\varepsilon _{i}\int _{0}^{\ell }{\frac {n_{i}(z)}{\mathrm {N_{A}} }}\mathrm {d} z\right)^{\ln(10)}\\[4pt]&=10^{\;\!\wedge }\!\!\left(-\sum _{i=1}^{N}\varepsilon _{i}\int _{0}^{\ell }c_{i}(z)\mathrm {d} z\right).\end{aligned}}} === Validity === Under certain conditions the Beer–Lambert law fails to maintain a linear relationship between attenuation and concentration of analyte. These deviations are classified into three categories: Real—fundamental deviations due to the limitations of the law itself. Chemical—deviations observed due to specific chemical species of the sample which is being analyzed. Instrument—deviations which occur due to how the attenuation measurements are made. There are at least six conditions that need to be fulfilled in order for the Beer–Lambert law to be valid. These are: The attenuators must act independently of each other. The attenuating medium must be homogeneous in the interaction volume. The attenuating medium must not scatter the radiation—no turbidity—unless this is accounted for as in DOAS. The incident radiation must consist of parallel rays, each traversing the same length in the absorbing medium. The incident radiation should preferably be monochromatic, or have at least a width that is narrower than that of the attenuating transition. Otherwise a spectrometer as detector for the power is needed instead of a photodiode which cannot discriminate between wavelengths. The incident flux must not influence the atoms or molecules; it should only act as a non-invasive probe of the species under study. In particular, this implies that the light should not cause optical saturation or optical pumping, since such effects will deplete the lower level and possibly give rise to stimulated emission. If any of these conditions are not fulfilled, there will be deviations from
|
{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
}
|
the Beer–Lambert law. The law tends to break down at very high concentrations, especially if the material is highly scattering. Absorbance within range of 0.2 to 0.5 is ideal to maintain linearity in the Beer–Lambert law. If the radiation is especially intense, nonlinear optical processes can also cause variances. The main reason, however, is that the concentration dependence is in general non-linear and Beer's law is valid only under certain conditions as shown by derivation below. For strong oscillators and at high concentrations the deviations are stronger. If the molecules are closer to each other interactions can set in. These interactions can be roughly divided into physical and chemical interactions. Physical interaction do not alter the polarizability of the molecules as long as the interaction is not so strong that light and molecular quantum state intermix (strong coupling), but cause the attenuation cross sections to be non-additive via electromagnetic coupling. Chemical interactions in contrast change the polarizability and thus absorption. In solids, attenuation is usually an addition of absorption coefficient α {\displaystyle \alpha } (creation of electron-hole pairs) or scattering (for example Rayleigh scattering if the scattering centers are much smaller than the incident wavelength). Also note that for some systems we can put 1 / λ {\displaystyle 1/\lambda } (1 over inelastic mean free path) in place of μ {\displaystyle \mu } . == Applications == === In plasma physics === The BBL extinction law also arises as a solution to the BGK equation. === Chemical analysis by spectrophotometry === The Beer–Lambert law can be applied to the analysis of a mixture by spectrophotometry, without the need for extensive pre-processing of the sample. An example is the determination of bilirubin in blood plasma samples. The spectrum of pure bilirubin is known, so the molar attenuation coefficient ε is known.
|
{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
}
|
Measurements of decadic attenuation coefficient μ10 are made at one wavelength λ that is nearly unique for bilirubin and at a second wavelength in order to correct for possible interferences. The amount concentration c is then given by c = μ 10 ( λ ) ε ( λ ) . {\displaystyle c={\frac {\mu _{10}(\lambda )}{\varepsilon (\lambda )}}.} For a more complicated example, consider a mixture in solution containing two species at amount concentrations c1 and c2. The decadic attenuation coefficient at any wavelength λ is, given by μ 10 ( λ ) = ε 1 ( λ ) c 1 + ε 2 ( λ ) c 2 . {\displaystyle \mu _{10}(\lambda )=\varepsilon _{1}(\lambda )c_{1}+\varepsilon _{2}(\lambda )c_{2}.} Therefore, measurements at two wavelengths yields two equations in two unknowns and will suffice to determine the amount concentrations c1 and c2 as long as the molar attenuation coefficients of the two components, ε1 and ε2 are known at both wavelengths. This two system equation can be solved using Cramer's rule. In practice it is better to use linear least squares to determine the two amount concentrations from measurements made at more than two wavelengths. Mixtures containing more than two components can be analyzed in the same way, using a minimum of m wavelengths for a mixture containing n components. So, in general: A λ i = ∑ j = 1 n ϵ j , λ i c j l {\displaystyle A_{\lambda _{i}}=\sum _{j=1}^{n}\epsilon _{j,\lambda _{i}}c_{j}l} where A λ i {\displaystyle A_{\lambda _{i}}} is the absorbance at wavelength λ i {\displaystyle \lambda _{i}} , ϵ j , λ i {\displaystyle \epsilon _{j,\lambda _{i}}} is the molar absorptivity of component j {\displaystyle j} at λ i {\displaystyle \lambda _{i}} , c j {\displaystyle c_{j}} is the concentration of component j {\displaystyle j} , and
|
{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
}
|
l {\displaystyle l} is the path length. The law is used widely in infra-red spectroscopy and near-infrared spectroscopy for analysis of polymer degradation and oxidation (also in biological tissue) as well as to measure the concentration of various compounds in different food samples. The carbonyl group attenuation at about 6 micrometres can be detected quite easily, and degree of oxidation of the polymer calculated. === In-atmosphere astronomy === The Bouguer–Lambert law may be applied to describe the attenuation of solar or stellar radiation as it travels through the atmosphere. In this case, there is scattering of radiation as well as absorption. The optical depth for a slant path is τ′ = mτ, where τ refers to a vertical path, m is called the relative airmass, and for a plane-parallel atmosphere it is determined as m = sec θ where θ is the zenith angle corresponding to the given path. The Bouguer-Lambert law for the atmosphere is usually written T = exp ( − m ( τ a + τ g + τ R S + τ N O 2 + τ w + τ O 3 + τ r + ⋯ ) ) , {\displaystyle T=\exp {\big (}-m(\tau _{\mathrm {a} }+\tau _{\mathrm {g} }+\tau _{\mathrm {RS} }+\tau _{\mathrm {NO_{2}} }+\tau _{\mathrm {w} }+\tau _{\mathrm {O_{3}} }+\tau _{\mathrm {r} }+\cdots ){\bigr )},} where each τx is the optical depth whose subscript identifies the source of the absorption or scattering it describes: a refers to aerosols (that absorb and scatter); g are uniformly mixed gases (mainly carbon dioxide (CO2) and molecular oxygen (O2) which only absorb); NO2 is nitrogen dioxide, mainly due to urban pollution (absorption only); RS are effects due to Raman scattering in the atmosphere; w is water vapour absorption; O3 is ozone (absorption only); r is Rayleigh scattering
|
{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
}
|
from molecular oxygen (O2) and nitrogen (N2) (responsible for the blue color of the sky); the selection of the attenuators which have to be considered depends on the wavelength range and can include various other compounds. This can include tetraoxygen, HONO, formaldehyde, glyoxal, a series of halogen radicals and others. m is the optical mass or airmass factor, a term approximately equal (for small and moderate values of θ) to 1 cos θ , {\displaystyle {\tfrac {1}{\cos \theta }},} where θ is the observed object's zenith angle (the angle measured from the direction perpendicular to the Earth's surface at the observation site). This equation can be used to retrieve τa, the aerosol optical thickness, which is necessary for the correction of satellite images and also important in accounting for the role of aerosols in climate. == See also == == References == == External links == Beer–Lambert Law Calculator Beer–Lambert Law Simpler Explanation
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{
"page_id": 4476,
"source": null,
"title": "Beer–Lambert law"
}
|
dcGO is a comprehensive ontology database for protein domains. As an ontology resource, dcGO integrates Open Biomedical Ontologies from a variety of contexts, ranging from functional information like Gene Ontology to others on enzymes and pathways, from phenotype information across major model organisms to information about human diseases and drugs. As a protein domain resource, dcGO includes annotations to both the individual domains and supra-domains (i.e., combinations of two or more successive domains). == Concepts == There are two key concepts behind dcGO. The first concept is to label protein domains with ontology, for example, with Gene Ontology. That is why it is called dcGO, domain-centric Gene Ontology. The second concept is to use ontology-labeled protein domains for, for example, protein function prediction. Put it in a simple way, the first concept is about how to create dcGO resource, and the second concept is about how to use dcGO resource. == Timelines == In 2010, the algorithm behind the dcGO was initially published as an improvement to the SUPERFAMILY database. In 2011, the 'dcGO Predictor' was ranked 10th in the 2011 CAFA competition when applied to Gene Ontology. This predictor is only domain-based method without machine learning. In 2012, the database was officially released, published in NAR database issue. In 2013, the webserver was improved to support many analyses using dcGO resource. In the early 2014, the 'dcGO Predictor' was submitted for both function and phenotype predictions, ranked top in 4th in CAFA phenotype prediction. In the late 2014, an open-source R package dcGOR was developed to help analyse ontologies and protein domain annotations. == Webserver == Recent use of dcGO is to build a domain network from a functional perspective for cross-ontology comparisons, and to combine with species tree of life (sTOL) to provide a phylogenetic context to function
|
{
"page_id": 37818751,
"source": null,
"title": "DcGO"
}
|
and phenotype. == Software == Open-source software dcGOR is developed using R programming language to analyse domain-centric ontologies and annotations. Supported analyses include: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network using random walker algorithm; high-performance parallel computing. Functionalities under active development are: algorithm and implementations for creating domain-centric ontology annotations; ontology term prediction for input protein domain architectures; reconstruction of ancestral discrete characters using maximum likelihood/parsimony. == See also == SCOP Pfam InterPro Structural domain Gene Ontology == References == == External links == SUPERFAMILY SCOP
|
{
"page_id": 37818751,
"source": null,
"title": "DcGO"
}
|
The molecular formula C20H22O7 (molar mass: 374.384 g/mol, exact mass: 374.1366 u) may refer to: Diffractaic acid Hydroxymatairesinol (HMR) Saudin Tinosporide
|
{
"page_id": 59969920,
"source": null,
"title": "C20H22O7"
}
|
Synechocystis sp. PCC6803 is a strain of unicellular, freshwater cyanobacteria. Synechocystis sp. PCC6803 is capable of both phototrophic growth by oxygenic photosynthesis during light periods and heterotrophic growth by glycolysis and oxidative phosphorylation during dark periods. Gene expression is regulated by a circadian clock and the organism can effectively anticipate transitions between the light and dark phases. == Evolutionary history == Cyanobacteria are photosynthetic prokaryotes that have existed on Earth for an estimated 2.7 billion years. The ability of cyanobacteria to produce oxygen initiated the transition from a planet consisting of high levels of carbon dioxide and little oxygen, to what has been called the Great Oxygenation Event where large amounts of oxygen gas were produced. Cyanobacteria have colonized a wide diversity of habitats, including fresh and salt water ecosystems, and most land environments. Phylogenetically, Synechocystis branches off later in the cyanobacterial evolutionary tree, further from the ancestral root (Gloeobacter violaceus). Synechocystis, which is non-diazotrophic, is related to other model cyanobacteria that can fix nitrogen. Thus, it has been proposed that Synechocystis originally possessed the ability to fix nitrogen gas into ammonia, but lost the genes required for a fully functioning nitrogen fixation (nif) gene cluster. == Growth and use as a model organism == Cyanobacteria are model microorganisms for the study of photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Synechocystis sp. PCC6803 is one of the most highly studied types of cyanobacteria as it can grow both autotrophically or heterotrophically in the absence of light. It was isolated from a freshwater lake in 1968 and grows best between 32 and 38 degrees Celsius. Synechocystis sp. PCC6803 can readily take up exogenous DNA, in addition to up taking DNA via electroporation, ultrasonic transformation and conjugation. The photosynthetic apparatus is very similar to the
|
{
"page_id": 18878850,
"source": null,
"title": "Synechocystis sp. PCC 6803"
}
|
one found in land plants. The organism also exhibits phototactic movement. Synechocystis sp. PCC6803 can be grown on either agar plates or in liquid culture. The most widely used culture medium is a BG-11 salt solution. The ideal pH is between 7 and 8.5. A light intensity of 50 μmol photons m−2 s−1 leads to best growth. Bubbling with carbon dioxide enriched air (1–2% CO2) can increase the growth rate, but may require additional buffer to maintain pH Selection is typically performed by antibiotic resistance genes. Heidorn et al. 2011 experimentally determined in Synechocystis sp. PCC6803 the ideal concentrations of kanamycin, spectinomycin, streptomycin, chloramphenicol, erythromycin, and gentamicin. Cultures can be kept on agar plates for approximately 2 weeks and re-streaked indefinitely. For long term storage, liquid cell cultures should be stored in a 15% glycerol solution at -80 degrees Celsius. == Genome == The genome of Synechocystis sp. PCC6803 is contained within approximately 12 copies of a single chromosome (3.57 megabases), three small plasmids: pCC5.2 (5.2 kb) pCA2.4 (2.4 kb), and pCB2.4 (2.4 kb) and four large plasmids: pSYSM (120 kb), pSYSX (106 kb), pSYSA (103kb), and pSYSG (44 kb). The genome of Synechocystis sp. PCC6803 is the fourth genome to be completely sequenced, and the first phototrophic organism to have its genome fully sequenced. == Additional strains == The primary strain of Synechocystis sp. is PCC6803. Further modifications of the parent PCC6803 strain have been created, such as a sub-strain lacking photosystem 1 (PSI). The other widely used sub-strain of Synechocystis sp. is a glucose tolerant strain, ATCC 27184. The parent PCC 6803 strain cannot utilize external glucose. == Light-activated heterotrophy == Synechocystis sp. PCC6803, sub-strain ATCC 27184 can live heterotrophically in the dark on the carbon source glucose, but for yet unknown reasons requires a minimum of 5
|
{
"page_id": 18878850,
"source": null,
"title": "Synechocystis sp. PCC 6803"
}
|
to 15 minutes (blue) light per day. This regulatory role of light is intact in both PSI and PSII deficient strains. Some glycolytic genes are regulated by the gene sll1330 under light and glucose-supplemented conditions. One of the most important glycolytic genes is fructose-1,6-bisphosphate aldolase (fbaA). The mRNA level of fbaA is increased under light and glucose-supplemented conditions. == Native CRISPR-Cas system == The CRISPR-Cas (Clustered Regularly Interspaced Short Palindrome Repeats – CRISPR associated proteins) system provides adaptive immunity in archaea and bacteria. Synechocystis sp. PCC6803 contains three different CRISPR-Cas systems: type I-D, and two versions of type III. All three CRISPR-Cas systems are localize on the pSYSA plasmid. All cyanobacteria are lacking the type II system, which has been widely adapted for genetic engineering purposes across many species. == RNA polymerase and sigma factors == RNA polymerase (RNAP) and sigma factors are necessary proteins for transcription of DNA into messenger RNA (mRNA). Eubacterial RNAP holoenzymes consist of a core with four major subunits α2 ββ'. In cyanobacteria, β' is formed from two smaller subunits (у and β'), which corresponds to RNAPs in plant chloroplasts. The beta subunits are responsible for binding the RNAP to the DNA, preventing premature dissociation. In Escherichia coli, the beta "clamp" first binds loosely and tightens as the RNAP approaches the start codon (AUG). In cyanobacteria, the beta clamp binds tightly at initial binding. The effect of this difference is that synthetic repressible promoters do not function as expected in Synechocystis sp. PCC6803. In E. coli, a repressor binds the DNA operon and dislodges RNAP due to the loosely bound beta clamp, whereas in Synechocystis, the RNAP is tightly bound leading the reverse phenomenon where the repressor is knocked off the DNA. Thus the gene is not effectively repressed. Synechocystis possesses the 70S sigma factor
|
{
"page_id": 18878850,
"source": null,
"title": "Synechocystis sp. PCC 6803"
}
|
(σ70), which can be divided into three groups. Group 1 sigma factors are critical for cell viability. Group 2, similar in structure to Group 1, is not essential for cell vitality. Group 3 is structurally different and involved with survival under stress conditions. Synechocystis sp. PCC6803 lacks the σN factor found in other organisms, such as Escherichia coli, which is involved with transcribing genes related to nitrogen, but is nonetheless able to metabolize nitrogen. == Natural genetic transformation == Synechocystis sp. PCC6803 is capable of natural genetic transformation. For transformation to take place, the recipient bacteria must be in a competent state. A gene, comF, was shown to be involved in competence development in Synechocystis sp. PCC6803. == Synthetic biology/genetic engineering == Synechocystis sp. PCC6803 is considered a model organism, yet there exist few synthetic parts that can be used for genetic engineering. As cyanobacteria in general have slow doubling times (4.5 to 5 h in Synechocystis sp. PCC6301 ), it is more efficient to perform as much DNA cloning as possible in a fast growing host, such as Escherichia coli. In order to create plasmids—stable, replicating circular pieces of DNA—that will function successfully in multiple species, a broad-host-range shuttle vector (see Replicative Plasmids below) is needed. Gene promoters, which control gene expression, need to also predictably work in multiple hosts (see Promoters below). === Replicative plasmids === Currently there is only one broad-host-range shuttle vector, RSF1010, that successfully replicates in Synechocystis sp. PCC6803. RSF1010 is a mobilization plasmid that facilitates conjugation between cells, allowing the horizontal gene transfer of DNA. Additionally, RSF1010 encodes its own replication machinery, so that it does not depend on its host to possess the necessary proteins and assorted factors. === Promoters === Gene promoters are responsible for recruiting RNAP and facilitating transcription of DNA.
|
{
"page_id": 18878850,
"source": null,
"title": "Synechocystis sp. PCC 6803"
}
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Type I promoters consists of a consensus -35 and -10 region (Pribnow box) upstream of the gene start site. Heidorn et al. 2011 compiled a list of native Synechocystis sp. PCC6803 promoters that have been used in synthetic constructs, although this leads to cross talk and non-orthogonal or non-specific gene expression. A handful of Anderson promoters (a group of constitutive promoters collected from a combinatorial library based on the consensus -35 (5'-TTGACA-3') and -10 (5’-TATAAT-3’) regions), represented best by BBa_J23101, have been demonstrated to function in Synechocystis sp. PCC6803. The iGem Registry hosts these promoter sequences as part of the BioBrick initiative to create interchangeable genetic parts. For synthetic biology, it is critical to have inducible promoters, or genes that can be turned on/off on demand. Several popular inducible promoters in E. coli are the pBad, pTet, and pLac promoters, all of which repress gene expression by a repressor molecule that binds the gene operator and blocks RNAP progression. Progress in engineering Synechocystis sp. PCC6803 is currently hampered by promoter issues. As noted above in RNA Polymerase and Sigma Factors, the beta clamp proteins within the RNAP complex have a higher initial binding affinity in Synechocystis sp. versus other eubacterial models. Thus promoters that turn on/off in response to small binding molecules are less effective in Synechocystis since the RNAP can knock them off the DNA strand. Camsund, Heidorn and Lindblad 2014 attempted to enhance pLac repression in Synechocystis sp. PCC6803 by engineering a promoter with multiple operons, thus facilitating DNA looping. Their attempt was too effective, as it was now too difficult to induce transcription in highly repressed variants. Huang and Lindblad 2013 created a library of modified pTet promoters with varying levels of repression and dynamic range in the glucose tolerant Synechocystis sp. ATCC 27184. Another option are
|
{
"page_id": 18878850,
"source": null,
"title": "Synechocystis sp. PCC 6803"
}
|
promoters that are inducible by heavy metals, such as: zinc, cadmium, cobalt, arsenic, nickel and chromium. Several such promoters were evaluated in Synechocystis sp. PCC6803 by Peca 2007. These promoters are not ideal, as metal ions are critical in Synechocystis’ metabolic pathways and altering concentrations can lead to compounding undesired side effects. Additionally, working with these promoters produces waste contaminated with heavy metals, increasing disposal costs === Ribosome binding site (RBS) === The ribosome binding site (RBS) is the location where a ribosome binds a strand of mRNA and begins translation. In prokaryotes, the RBS includes a Shine-Dalgarno sequence. Little is known about the translation efficiency of RBSs in Synechocystis sp. PCC6803. Heidorn et al. 2011 scanned the Synechocystis sp. PCC6803 genome and created a consensus RBS sequence (TAGTGGAGGT), which had 5 times higher output than the consensus E. coli sequence. === Terminators === Terminators are the DNA signal which halts transcription. Native Synechocystis sp. PCC6803 termination sites have been characterized. === Transcription unit (TU) === Transcription units (TUs) of Synechocystis sp. PCC6803 have been assigned using transcription start sites (TSSs) and transcript 3'-end positions (TEPs). == Biofuel production == Cyanobacteria have been used in several ways to produce renewable biofuel. The original method was to grow cyanobacteria for the biomass, which could be converted through liquefaction into liquid fuel. Current estimates suggest that biofuel production from cyanobacteria is unfeasible, as the energy return on energy invested (EROEI) is unfavorable. The EROEI is not advantageous as numerous large, closed loop bioreactors with ideal growth conditions (sunlight, fertilizers, concentrated carbon dioxide, oxygen) need to be constructed and operated, which consumes fossil fuels. Additionally, further post processing of cyanobacterial products is necessary, which requires additional fossil fuels. Synechocystis sp. PCC6803 has been used as a model to increase cyanobacterial energy yields through
|
{
"page_id": 18878850,
"source": null,
"title": "Synechocystis sp. PCC 6803"
}
|
genetic engineering by the following manipulations: broadening the range of photosynthetic light absorption, altering antenna size in photosystem II, increasing bicarbonate uptake, modifying the Rubisco enzyme to increase carbon fixation, and introduction of biofuel producing metabolic pathways. It is not yet clear whether cyanobacterial biofuels will be a viable future alternative to non-renewable fossil fuels. == Databases == SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. SynechoNET is a specialized cyanobacterial protein-protein interaction database. It shows feasible cyanobacterial domain-domain interactions, as well as their protein level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. Additionally, SynechoNET provides transmembrane topology and domain information, as well as interaction networks in graphical web interfaces. CyanoBase: Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on Earth. This organism is also interesting from an evolutionary viewpoint, for it arose in a very ancient age and has survived in various environments. The algal and land plant chloroplast evolved from cyanobacterial ancestors which developed an endosymbiotic relationship with a eukaryotic host cell. CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. This database was originally developed by Makoto Hirosawa, Takakazu Kaneko and Satoshi Tabata, and the current version of CyanoBase has been developed and maintained by Yasukazu Nakamura, Takakazu Kaneko, and Satoshi Tabata at Kazusa DNA Research Institute. STRING: STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context, High-throughput Experiments, (Conserved) Coexpression, and Previous Knowledge. The database currently contains 1,513,782 proteins in 373 species. Especially, the database provides interactions for Synechocystis sp. PCC 6803. cTFbase: cTFbase contains 1288 putative transcription factors (TFs) identified
|
{
"page_id": 18878850,
"source": null,
"title": "Synechocystis sp. PCC 6803"
}
|
from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase also provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding domain and ortholog identification from any selected genomes. == See also == == References ==
|
{
"page_id": 18878850,
"source": null,
"title": "Synechocystis sp. PCC 6803"
}
|
MEGARes is a hand-curated antibiotic resistance database which incorporates previously published resistance sequences for antimicrobial drugs, while also expanding to include published sequences for metal and biocide resistance determinants. In MEGARes 3.0, the nodes of the acyclic hierarchical ontology include four antimicrobial compound types, 59 classes, 223 mechanisms of resistance, and 1,448 gene groups that classify the 8,733 gene accessions. This works in conjunction with the AMR++ bioinformatics pipelin (version 3.0) to classify resistome sequences directly from FASTA. The database focuses on the analysis of large-scale, ecological sequence datasets with an annotation structure that allows for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes annotation consists of three hierarchical levels when looking at AMR genes: drug class, mechanism, and group. The comprehensive MEGARes content was compiled from all published sequences included various other databases: Resfinder, ARG-ANNOT, Comprehensive Antibiotic Resistance Database (CARD), and the National Center for Biotechnology Information (NCBI) Lahey Clinic beta-lactamase archive. MEGARes allows users to analyze antimicrobial resistance on a population-level, similar to a microbiome analysis, from a FASTA sequence. Furthermore, users can access AMR++, a bioiinformatics pipeline for resistome analysis of metagenomic datasets that can be integrated with the MEGARes database. == See also == Antimicrobial Resistance databases == References ==
|
{
"page_id": 61084034,
"source": null,
"title": "MEGARes"
}
|
The breasts are two prominences located on the upper ventral region of the torso among humans and other primates. Both sexes develop breasts from the same embryological tissues. The relative size and development of the breasts is a major secondary sex distinction between females and males. There is also considerable variation in size between individuals. Permanent breast growth during puberty is caused by estrogens in conjunction with the growth hormone. Female humans are the only mammals that permanently develop breasts at puberty; all other mammals develop their mammary tissue during the latter period of pregnancy. In females, the breast serves as the mammary gland, which produces and secretes milk to feed infants. Subcutaneous fat covers and envelops a network of ducts that converge on the nipple, and these tissues give the breast its distinct size and globular shape. At the ends of the ducts are lobules, or clusters of alveoli, where milk is produced and stored in response to hormonal signals. During pregnancy, the breast responds to a complex interaction of hormones, including estrogens, progesterone, and prolactin, that mediate the completion of its development, namely lobuloalveolar maturation, in preparation of lactation and breastfeeding. Along with their major function in providing nutrition for infants, several cultures ascribe social and sexual characteristics to female breasts, and may regard bare breasts in public as immodest or indecent. Breasts have been featured in ancient and modern sculpture, art, and photography. Breasts can represent fertility, femininity, or abundance. They can figure prominently in the perception of a woman's body and sexual attractiveness. Breasts, especially the nipples, can be an erogenous zone. == Etymology and terminology == The English word breast derives from the Old English word brēost 'breast, bosom' from Proto-Germanic *breustam 'breast', from the Proto-Indo-European base *bhreus– 'to swell, to sprout'. The breast spelling
|
{
"page_id": 4489,
"source": null,
"title": "Breast"
}
|
conforms to the Scottish and North English dialectal pronunciations. The Merriam-Webster Dictionary states that "Middle English brest, [comes] from Old English brēost; akin to Old High German brust..., Old Irish brú [belly], [and] Russian bryukho"; the first known usage of the term was before the 12th century. Breasts is often used to refer to female breasts in particular, though the stricter anatomical term refers to the same region on members of either sex. Male breasts are sometimes referred to in the singular to mean the collective upper chest area, whereas female breasts are referred to in the plural unless speaking of a specific left or right breast. A large number of colloquial terms for female breasts are used in English, ranging from fairly polite terms to vulgar or slang. Some vulgar slang expressions may be considered to be derogatory or sexist to women. == Evolutionary development == Humans are the only mammals whose breasts become permanently enlarged after sexual maturity (known in humans as puberty). The reason for this evolutionary change is unknown. Several hypotheses have been put forward: A link has been proposed to processes for synthesizing the endogenous steroid hormone precursor dehydroepiandrosterone which takes place in fat rich regions of the body like the buttocks and breasts. These contributed to human brain development and played a part in increasing brain size. Breast enlargement may for this purpose have occurred as early as Homo ergaster (1.7–1.4 MYA). Other breast formation hypotheses may have then taken over as principal drivers. It has been suggested by zoologists Avishag and Amotz Zahavi that the size of the human breasts can be explained by the handicap theory of sexual dimorphism. This would see the explanation for larger breasts as them being an honest display of the women's health and ability to grow and
|
{
"page_id": 4489,
"source": null,
"title": "Breast"
}
|
carry them in her life. Prospective mates can then evaluate the genes of a potential mate for their ability to sustain her health even with the additional energy demanding burden she is carrying. The zoologist Desmond Morris describes a sociobiological approach in his science book The Naked Ape. He suggests, by making comparisons with the other primates, that breasts evolved to replace swelling buttocks as a sex signal of ovulation. He notes how humans have, relatively speaking, large penises as well as large breasts. Furthermore, early humans adopted bipedalism and face-to-face coitus. He therefore suggested enlarged sexual signals helped maintain the bond between a mated male and female even though they performed different duties and therefore were separated for lengths of time. A 2001 study proposed that the rounded shape of a woman's breast evolved to prevent the sucking infant offspring from suffocating while feeding at the teat; that is, because of the human infant's small jaw, which did not project from the face to reach the nipple, they might block the nostrils against the mother's breast if it were of a flatter form (compare with the common chimpanzee). Theoretically, as the human jaw receded into the face, the woman's body compensated with round breasts. Ashley Montague (1965) proposed that breasts came about as an adaptation for infant feeding for a different reason, as early human ancestors adopted bipedalism and the loss of body hair. Human upright stance meant infants must be carried at the hip or shoulder instead of on the back as in the apes. This gives the infant less opportunity to find the nipple or the purchase to cling on to the mother's body hair. The mobility of the nipple on a large breast in most human females gives the infant more ability to find it, grasp
|
{
"page_id": 4489,
"source": null,
"title": "Breast"
}
|
it and feed. Other suggestions include simply that permanent breasts attracted mates, that "pendulous" breasts gave infants something to cling to, or that permanent breasts shared the function of a camel's hump, to store fat as an energy reserve. == Structure == In women, the breasts overlie the pectoralis major muscles and extend on average from the level of the second rib to the level of the sixth rib in the front of the rib cage; thus, the breasts cover much of the chest area and the chest walls. At the front of the chest, the breast tissue can extend from the clavicle (collarbone) to the middle of the sternum (breastbone). At the sides of the chest, the breast tissue can extend into the axilla (armpit), and can reach as far to the back as the latissimus dorsi muscle, extending from the lower back to the humerus bone (the bone of the upper arm). As a mammary gland, the breast is composed of differing layers of tissue, predominantly two types: adipose tissue; and glandular tissue, which affects the lactation functions of the breasts.: 115 The natural resonant frequency of the human breast is about 2 hertz. Morphologically, the breast is tear-shaped. The superficial tissue layer (superficial fascia) is separated from the skin by 0.5–2.5 cm of subcutaneous fat (adipose tissue). The suspensory Cooper's ligaments are fibrous-tissue prolongations that radiate from the superficial fascia to the skin envelope. The female adult breast contains 14–18 irregular lactiferous lobes that converge at the nipple. The 2.0–4.5 mm milk ducts are immediately surrounded with dense connective tissue that support the glands. Milk exits the breast through the nipple, which is surrounded by a pigmented area of skin called the areola. The size of the areola can vary widely among women. The areola contains modified
|
{
"page_id": 4489,
"source": null,
"title": "Breast"
}
|
sweat glands known as Montgomery's glands. These glands secrete oily fluid that lubricate and protect the nipple during breastfeeding. Volatile compounds in these secretions may also serve as an olfactory stimulus for the newborn's appetite. The dimensions and weight of the breast vary widely among women. A small-to-medium-sized breast weighs 500 grams (1.1 pounds) or less, and a large breast can weigh approximately 750 to 1,000 grams (1.7 to 2.2 pounds) or more. In terms of composition, the breasts are about 80 to 90% stromal tissue (fat and connective tissue), while epithelial or glandular tissue only accounts for about 10 to 20% of the volume of the breasts. The tissue composition ratios of the breast also vary among women. Some women's breasts have a higher proportion of glandular tissue than of adipose or connective tissues. The fat-to-connective-tissue ratio determines the density or firmness of the breast. During a woman's life, her breasts change size, shape, and weight due to hormonal changes during puberty, the menstrual cycle, pregnancy, breastfeeding, and menopause. === Glandular structure === The breast is an apocrine gland that produces the milk used to feed an infant. The nipple of the breast is surrounded by the areola (nipple-areola complex). The areola has many sebaceous glands, and the skin color varies from pink to dark brown. The basic units of the breast are the terminal duct lobular units (TDLUs), which produce the fatty breast milk. They give the breast its offspring-feeding functions as a mammary gland. They are distributed throughout the body of the breast. Approximately two-thirds of the lactiferous tissue is within 30 mm of the base of the nipple. The terminal lactiferous ducts drain the milk from TDLUs into 4–18 lactiferous ducts, which drain to the nipple. The milk-glands-to-fat ratio is 2:1 in a lactating woman, and
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{
"page_id": 4489,
"source": null,
"title": "Breast"
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|
1:1 in a non-lactating woman. In addition to the milk glands, the breast is also composed of connective tissues (collagen, elastin), white fat, and the suspensory Cooper's ligaments. Sensation in the breast is provided by the peripheral nervous system innervation by means of the front (anterior) and side (lateral) cutaneous branches of the fourth-, fifth-, and sixth intercostal nerves. The T-4 nerve (Thoracic spinal nerve 4), which innervates the dermatomic area, supplies sensation to the nipple-areola complex. === Lymphatic drainage === Approximately 75% of the lymph from the breast travels to the axillary lymph nodes on the same side of the body, while 25% of the lymph travels to the parasternal nodes (beside the sternum bone).: 116 A small amount of remaining lymph travels to the other breast and to the abdominal lymph nodes. The subareolar region has a lymphatic plexus known as the "subareolar plexus of Sappey". The axillary lymph nodes include the pectoral (chest), subscapular (under the scapula), and humeral (humerus-bone area) lymph-node groups, which drain to the central axillary lymph nodes and to the apical axillary lymph nodes. The lymphatic drainage of the breasts is especially relevant to oncology because breast cancer is common to the mammary gland, and cancer cells can metastasize (break away) from a tumor and be dispersed to other parts of the body by means of the lymphatic system. === Morphology === The morphologic variations in the size, shape, volume, tissue density, pectoral locale, and spacing of the breasts determine their natural shape, appearance, and position on a woman's chest. Breast size and other characteristics do not predict the fat-to-milk-gland ratio or the potential for the woman to nurse an infant. The size and the shape of the breasts are influenced by normal-life hormonal changes (thelarche, menstruation, pregnancy, menopause) and medical conditions (e.g.
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{
"page_id": 4489,
"source": null,
"title": "Breast"
}
|
virginal breast hypertrophy). The shape of the breasts is naturally determined by the support of the suspensory Cooper's ligaments, the underlying muscle and bone structures of the chest, and by the skin envelope. The suspensory ligaments sustain the breast from the clavicle (collarbone) and the clavico-pectoral fascia (collarbone and chest) by traversing and encompassing the fat and milk-gland tissues. The breast is positioned, affixed to, and supported upon the chest wall, while its shape is established and maintained by the skin envelope. In most women, one breast is slightly larger than the other. More obvious and persistent asymmetry in breast size occurs in up to 25% of women. The base of each breast is attached to the chest by the deep fascia over the pectoralis major muscles. The base of the breast is semi-circular, however the shape and position of the breast above the surface is variable. The space between the breast and the pectoralis major muscle, called retromammary space, gives mobility to the breast. The chest (thoracic cavity) progressively slopes outwards from the thoracic inlet (atop the breastbone) and above to the lowest ribs that support the breasts. The inframammary fold (IMF), where the lower portion of the breast meets the chest, is an anatomic feature created by the adherence of the breast skin and the underlying connective tissues of the chest; the IMF is the lower-most extent of the anatomic breast. Normal breast tissue has a texture that feels nodular or granular, with considerable variation from woman to woman. Breasts have been categorized into four general morphological groups: "flat, spheric, protruded, and drooped", or "small/flat, large/inward, upward, and droopy". ==== Support ==== While it is a common belief that breastfeeding causes breasts to sag, researchers have found that a woman's breasts sag due to four key factors: cigarette
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{
"page_id": 4489,
"source": null,
"title": "Breast"
}
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smoking, number of pregnancies, gravity, and weight loss or gain. Women sometimes wear bras because they mistakenly believe they prevent breasts from sagging as they get older. Physicians, lingerie retailers, teenagers, and adult women used to believe that bras were medically required to support breasts. In a 1952 article in Parents' Magazine, Frank H. Crowell erroneously reported that it was important for teen girls to begin wearing bras early. According to Crowell, this would prevent sagging breasts, stretched blood vessels, and poor circulation later on. This belief was based on the false idea that breasts cannot anatomically support themselves. Sports bras are sometimes used for cardiovascular exercise, sports bras are designed to secure the breasts closely to the body to prevent movement during high-motion activity such as running. Studies have indicated sports bras which are overly tight may restrict respiratory function. == Development == The breasts are principally composed of adipose, glandular, and connective tissues. Because these tissues have hormone receptors, their sizes and volumes fluctuate according to the hormonal changes particular to thelarche (sprouting of breasts), menstruation (egg production), pregnancy (reproduction), lactation (feeding of offspring), and menopause (end of menstruation). === Puberty === The morphological structure of the human breast is identical in males and females until puberty. For pubescent girls in thelarche (the breast-development stage), the female sex hormones (principally estrogens) in conjunction with growth hormone promote the sprouting, growth, and development of the breasts. During this time, the mammary glands grow in size and volume and begin resting on the chest. These development stages of secondary sex characteristics (breasts, pubic hair, etc.) are illustrated in the five-stage Tanner scale. During thelarche, the developing breasts are sometimes of unequal size, and usually the left breast is slightly larger. This condition of asymmetry is transitory and statistically normal in
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{
"page_id": 4489,
"source": null,
"title": "Breast"
}
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female physical and sexual development. Medical conditions can cause overdevelopment (e.g., virginal breast hypertrophy, macromastia) or underdevelopment (e.g., tuberous breast deformity, micromastia) in girls and women. Approximately two years after the onset of puberty (a girl's first menstrual cycle), estrogen and growth hormone stimulate the development and growth of the glandular fat and suspensory tissues that compose the breast. This continues for approximately four years until the final shape of the breast (size, volume, density) is established at about the age of 21. Mammoplasia (breast enlargement) in girls begins at puberty, unlike all other primates, in which breasts enlarge only during lactation. === Hormone replacement therapy === Hormone replacement therapy, including gender-affirming hormone therapy, stimulates the growth of glandular and adipose tissue through estrogen supplementation. In menopausal women, HRT helps restore breast volume and skin elasticity diminished by declining estrogen levels, typically using oral or transdermal estradiol. In gender-affirming hormone therapy, breast development is induced through feminizing HRT, often combining estrogen with anti-androgens to suppress testosterone. Maximum growth is usually achieved after 2–3 years. Factors such as age, genetics, and hormone dosage influence outcomes. === Changes during the menstrual cycle === During the menstrual cycle, the breasts are enlarged by premenstrual water retention and temporary growth as influenced by changing hormone levels. === Pregnancy and breastfeeding === The breasts reach full maturity only when a woman's first pregnancy occurs. Changes to the breasts are among the first signs of pregnancy. The breasts become larger, the nipple-areola complex becomes larger and darker, the Montgomery's glands enlarge, and veins sometimes become more visible. Breast tenderness during pregnancy is common, especially during the first trimester. By mid-pregnancy, the breast is physiologically capable of lactation and some women can express colostrum, a form of breast milk. Pregnancy causes elevated levels of the hormone prolactin,
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{
"page_id": 4489,
"source": null,
"title": "Breast"
}
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which has a key role in the production of milk. However, milk production is blocked by the hormones progesterone and estrogen until after delivery, when progesterone and estrogen levels plummet. === Menopause === At menopause, breast atrophy occurs. The breasts can decrease in size when the levels of circulating estrogen decline. The adipose tissue and milk glands also begin to wither. The breasts can also become enlarged from adverse side effects of combined oral contraceptive pills. The size of the breasts can also increase and decrease in response to weight fluctuations. Physical changes to the breasts are often recorded in the stretch marks of the skin envelope; they can serve as historical indicators of the increments and the decrements of the size and volume of a woman's breasts throughout the course of her life. Breast changes during menopause are sometimes treated with hormone replacement therapy. === Cancer === Breast cancer is a cancer that develops from breast tissue. Signs of breast cancer may include a lump in the breast, a change in breast shape, dimpling of the skin, milk rejection, fluid coming from the nipple, a newly inverted nipple, or a red or scaly patch of skin. In those with distant spread of the disease, there may be bone pain, swollen lymph nodes, shortness of breath, or yellow skin. Risk factors for developing breast cancer include obesity, a lack of physical exercise, alcohol consumption, hormone replacement therapy during menopause, ionizing radiation, an early age at first menstruation, having children late in life (or not at all), older age, having a prior history of breast cancer, and a family history of breast cancer. About five to ten percent of cases are the result of an inherited genetic predisposition, including BRCA mutations among others. Breast cancer most commonly develops in cells from
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{
"page_id": 4489,
"source": null,
"title": "Breast"
}
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