Thursday, May 11, 2023

05-11-2023-0415 - List of Rock Types

The following is a list of rock types recognized by geologists. There is no agreed number of specific types of rocks. Any unique combination of chemical composition, mineralogy, grain size, texture, or other distinguishing characteristics can describe a rock type. Additionally, different classification systems exist for each major type of rock.^[1] There are three major types of rock: igneous rock, metamorphic rock, and sedimentary rock.

Igneous rocks

A sample of andesite (dark groundmass) with amygdaloidal vesicles filled with zeolite. Diameter of view is 8 cm.

Adakite – Volcanic rock type
Andesite – Type of volcanic rock
Alkali feldspar granite – Type of igneous rock rich in alkali feldspar
Anorthosite – Mafic intrusive igneous rock composed predominantly of plagioclase
Aplite – Fine-grained intrusive igneous rock type similar to granite
Basalt – Magnesium- and iron-rich extrusive igneous rock
- ʻAʻā – Molten rock expelled by a volcano during an eruption – Basaltic lava with a crumpled appearance
- Pāhoehoe – Molten rock expelled by a volcano during an eruption – Basaltic lava with a flowing, often ropy appearance
Basaltic trachyandesite – Naming system for volcanic rocks
- Mugearite – Volcanic rock type
- Shoshonite – Potassium-rich variety of basaltic trachyandesite
Basanite – A silica-undersaturated basalt
Blairmorite – Rare porphyritic volcanic rock
Boninite – Ultramafic extrusive rock high in both magnesium and silica
Carbonatite – Igneous rock with more than 50% carbonate minerals
Charnockite – Type of granite containing orthopyroxene
- Enderbite – Igneous rock of the charnockite series
Dacite – Volcanic rock intermediate in composition between andesite and rhyolite
Diabase, also known as dolerite – Type of igneous rock
Diorite – Igneous rock type
- Napoleonite, also known as corsite – Variety of diorite with orbicular structure
Dunite – Ultramafic and ultrabasic rock from Earth's mantle which is made of the mineral olivine
Essexite – Igneous rock type
Foidolite – Igneous rock rich in feldspathoid minerals
Gabbro – Coarse-grained mafic intrusive rock
Granite – Common type of intrusive, felsic, igneous rock with granular structure
Granodiorite – Type of coarse grained intrusive igneous rock
Granophyre – Subvolcanic rock that contains quartz and alkali feldspar in characteristic angular intergrowths
Harzburgite – Ultramafic mantle rock
Hornblendite – Plutonic rock consisting mainly of the amphibole hornblende
Hyaloclastite – Volcaniclastic accumulation or breccia
Icelandite – Igneous rock type
Ignimbrite – Type of volcanic rock
Ijolite – Igneous rock consisting essentially of nepheline and augite
Kimberlite – Igneous rock which sometimes contains diamonds
Komatiite – Ultramafic mantle-derived volcanic rock
Lamproite – Ultrapotassic mantle-derived volcanic or subvolcanic rock
Lamprophyre – Ultrapotassic igneous rocks – An ultramafic, ultrapotassic intrusive rock dominated by mafic phenocrysts in a feldspar groundmass
Latite – Type of volcanic rock – A silica-undersaturated form of andesite
Lherzolite – an ultramafic and ultrabasic rock that is composed of olivine and pyroxene – An ultramafic rock, essentially a peridotite
Monzogranite – A silica-undersaturated granite with <5% normative quartz
Monzonite – Igneous intrusive rock with low quartz and equal plagioclase and alkali feldspar – a plutonic rock with <5% normative quartz
Nepheline syenite – Holocrystalline plutonic rock – A silica-undersaturated plutonic rock of nepheline and alkali feldspar
Nephelinite – Igneous rock made up almost entirely of nepheline and clinopyroxene – A silica-undersaturated plutonic rock with >90% nepheline
Norite – igneous rock – A hypersthene-bearing gabbro
Obsidian – Naturally occurring volcanic glass
Pegmatite – Igneous rock with very large interlocked crystals
Peridotite – Coarse-grained ultramafic igneous rock type
Phonolite – Uncommon extrusive rock – A silica-undersaturated volcanic rock; essentially similar to nepheline syenite
Phonotephrite – strongly alkaline volcanic rock with a composition between phonolite and tephrite – A volcanic rock with a composition between phonolite and tephrite
Picrite – Variety of high-magnesium basalt that is very rich in the mineral olivine – An olivine-bearing basalt
Porphyry – Textural form of igneous rock with large grained crystals in a fine matrix
Pumice – Light colored highly vesicular volcanic rock
Pyroxenite – Igneous rock - a coarse grained plutonic rock composed of >90% pyroxene
Quartz diorite – Igneous, plutonic rock – A diorite with >5% modal quartz
Quartz monzonite – Type of igneous rock – An intermediate plutonic rock, essentially a monzonite with 5–10% modal quartz
Quartzolite – Extremely rare igneous rock made mostly of quartz – An intrusive rock composed mostly of quartz
Rhyodacite – Volcanic rock rich in silica and low in alkali metal oxides – A felsic volcanic rock which is intermediate between a rhyolite and a dacite
Rhyolite – Igneous, volcanic rock, of felsic (silica-rich) composition
- Comendite – Hard, peralkaline igneous rock, a type of light blue grey rhyolite
- Pantellerite – Peralkaline rhyolite type of volcanic rock
Scoria – Dark vesicular volcanic rock
Shonkinite – Intrusive igneous rock – a plutonic rock
Sovite – igneous rock – A coarse-grained carbonatite rock
Syenite – Intrusive igneous rock – A plutonic rock dominated by orthoclase feldspar; a type of granitoid
Tachylyte – Form of basaltic volcanic glass – Essentially a basaltic glass
Tephriphonolite – A volcanic rock with a composition between phonotephrite and phonolite
Tephrite – Igneous, volcanic rock – A silica-undersaturated volcanic rock
Tonalite – igneous rock – A plagioclase-dominant granitoid
Trachyandesite – Extrusive igneous rock – An alkaline intermediate volcanic rock
- Benmoreite – Volcanic rock type - sodic trachyandesite
Trachybasalt – A volcanic rock with a composition between basalt and trachyte
- Hawaiite – Volcanic rock – a sodic type of trachybasalt, typically formed by ocean island (hot spot) volcanism
Trachyte – Extrusive igneous rock – A silica-undersaturated volcanic rock; essentially a feldspathoid-bearing rhyolite
Troctolite – Igneous rock – A plutonic ultramafic rock containing olivine, pyroxene and plagioclase
Trondhjemite – Light-colored intrusive igneous rock – A form of tonalite where plagioclase-group feldspar is oligoclase
Tuff – Rock consolidated from volcanic ash
Websterite – ultramafic and ultrabasic rock – A type of pyroxenite, composed of clinoproxene and orthopyroxene
Wehrlite – Ultramafic rock - An ultramafic plutonic or cumulate rock, a type of peridotite, composed of olivine and clinopyroxene

Sedimentary rocks

Bituminous coal seam in West Virginia

Limey shale overlaid by limestone. Cumberland Plateau, Tennessee

Dolomite crystals from Touissite, Morocco

Turbidite (Gorgoglione Flysch), Miocene, South Italy

Argillite – Sedimentary rock, mostly of indurated clay particles
Arkose – Type of sandstone containing at least 25% feldspar
Banded iron formation – Distinctive layered units of iron-rich sedimentary rock that are almost always of Precambrian age
Breccia – Rock composed of broken fragments cemented by a matrix
Calcarenite – Type of limestone that is composed predominantly of sand-size grains
Chalk – Soft, white, porous sedimentary rock made of calcium carbonate
Chert – Hard, fine-grained sedimentary rock composed of cryptocrystalline silica
Claystone – Clastic sedimentary rock composed primarily of clay-sized particles
Coal – Combustible sedimentary rock composed primarily of carbon
Conglomerate – Coarse-grained sedimentary rock composed mostly of rounded to sub-angular fragments
Coquina – Sedimentary rock that is composed mostly of fragments of shells
Diamictite – Type of sedimentary rock
Diatomite – Soft, siliceous sedimentary rock that is easily crumbled
Dolomite (rock), also known as Dolostone – Sedimentary carbonate rock that contains a high percentage of the mineral dolomite
Evaporite – Water-soluble mineral deposit formed by evaporation from an aqueous solution
Flint – Cryptocrystalline form of the mineral quartz
Geyserite – Form of opaline silica that is often found around hot springs and geysers
Greywacke – Hard, dark sandstone with poorly sorted angular grains in a compact, clay-fine matrix
Gritstone – Hard, coarse-grained, siliceous sandstone
Itacolumite – Porous sandstone known for flexibility
Jaspillite – Banded mixture of hematite and quartz
Laterite – Product of rock weathering in wet tropical climate rich in iron and aluminium
Lignite – Soft, brown, combustible, sedimentary rock
Limestone – Sedimentary rocks made of calcium carbonate
Marl – Lime-rich mud or mudstone which contains variable amounts of clays and silt
Mudstone – Fine grained sedimentary rock whose original constituents were clays or muds
Oil shale – Organic-rich fine-grained sedimentary rock containing kerogen
Oolite – Sedimentary rock formed from ooids
Phosphorite – Sedimentary rock containing large amounts of phosphate minerals – A non-detrital sedimentary rock that contains high amounts of phosphate minerals
Sandstone – Type of sedimentary rock
Shale – Fine-grained, clastic sedimentary rock
Siltstone – Sedimentary rock which has a grain size in the silt range
Sylvinite – A sedimentary rock made of a mechanical mixture of sylvite and halite
Tillite – Till which has been indurated or lithified by burial
Travertine – Form of limestone deposited by mineral springs
Tufa – Porous limestone rock formed when carbonate minerals precipitate out of ambient temperature water
Turbidite – Geologic deposit of a turbidity current
Wackestone – Mud-supported carbonate rock that contains greater than 10% grains

Metamorphic rocks

Phyllite

Banded gneiss with a dike of granite orthogneiss

Marble

Quartzite

Manhattan Schist, from Southeastern New York

Slate

Anthracite – Hard, compact variety of coal
Amphibolite – A metamorphic rock containing mainly amphibole and plagioclase
Blueschist – Type of metavolcanic rock
Cataclasite – Rock found at geological faults – A rock formed by faulting
Eclogite – A dense metamorphic rock formed under high pressure
Gneiss – Common high-grade metamorphic rock
Granulite – Class of high-grade medium to coarse grained metamorphic rocks
Greenschist – Metamorphic rocks – A mafic metamorphic rock dominated by green amphiboles
Hornfels – series of contact metamorphic rocks that have been baked and indurated by the heat of intrusive igneous masses
- Calcflinta – A type of hornfels found in the Scottish Highlands
Litchfieldite – Nepheline syenite gneiss
Marble – Type of rock – a metamorphosed limestone
Migmatite – Mixture of metamorphic rock and igneous rock
Mylonite – Metamorphic rock – A metamorphic rock formed by shearing
Metapelite – Metamorphic rock – A metamorphic rock with a protolith of clay-rich (siltstone) sedimentary rock
Metapsammite – A metamorphic rock with a protolith of quartz-rich (sandstone) sedimentary rock
Phyllite – Type of foliated metamorphic rock – A low grade metamorphic rock composed mostly of micaceous minerals
Pseudotachylite – Glassy, or very fine-grained, rock type – A glass formed by melting within a fault via friction
Quartzite – Hard, non-foliated metamorphic rock which was originally pure quartz sandstone – A metamorphosed sandstone typically composed of >95% quartz
Schist – Easily split medium-grained metamorphic rock
Serpentinite – Rock formed by hydration and metamorphic transformation of olivine
Skarn – Hard, coarse-grained, hydrothermally altered metamorphic rocks
Slate – Metamorphic rock - A low grade metamorphic rock formed from shale or silts
Suevite – Rock consisting partly of melted material formed during an impact event – A rock formed by partial melting during a meteorite impact
Talc carbonate – A metamorphosed ultramafic rock with talc as an essential constituent; similar to a serpentinite
- Soapstone – Talc-bearing metamorphic rock – Essentially a talc schist
Tectonite – rock type – A rock whose fabric reflects the history of its deformation
Whiteschist – A high pressure metamorphic rock containing talc and kyanite

Specific varieties

The following are terms for rocks that are not petrographically or genetically distinct but are defined according to various other criteria; most are specific classes of other rocks, or altered versions of existing rocks. Some archaic and vernacular terms for rocks are also included.

Adamellite – Type of igneous rock – A variety of quartz monzonite
Appinite – A group of varieties of lamprophyre, mostly rich in hornblende
Aphanite – Igneous rock composed of very small crystals invisible to the naked eye
Borolanite – Variety of nepheline syenite from Loch Borralan, Scotland – A variety of nepheline syenite from Loch Borralan, Scotland
Blue Granite – Variety of monzonite, an igneous rock
Epidosite – Hydrothermally altered epidote- and quartz-bearing rock
Felsite – Very fine-grained volcanic rock that sometimes contains larger crystals
Flint – Cryptocrystalline form of the mineral quartz
Ganister – Hard, fine-grained quartzose sandstone, or orthoquartzite
Gossan – Intensely oxidized, weathered or decomposed rock
Hyaloclastite – Volcaniclastic accumulation or breccia
Ijolite – Igneous rock consisting essentially of nepheline and augite
Jadeitite – Metamorphic rock found in blueschist-grade metamorphic terranes
Jasperoid – A hematite-silica metasomatite analogous to a skarn
Kenyte – Type of igneous rock - A variety of phonolite, first found on Mount Kenya
Lapis lazuli – Metamorphic rock containing lazurite, prized for its intense blue color - A rock composed of lazurite and other minerals
Larvikite – Variety of monzonite, an igneous rock
Litchfieldite – A metamorphosed nepheline syenite occurrence near Litchfield, Maine
Llanite – Type of mineral – A hypabyssal rhyolite with microcline and blue quartz phenocrysts from the Llano Uplift in Texas
Luxullianite – Rare type of granite
Mangerite – Plutonic intrusive igneous rock, that is essentially a hypersthene-bearing monzonite
Minette – A variety of lamprophyre
Novaculite – A type of chert found in Oklahoma, Arkansas, and Texas
Pietersite – Breccia rock of hawk's eyes and tiger's eyes
Pyrolite – theoretical rock making up the earth's upper mantle – A chemical analogue considered to theoretically represent the earth's upper mantle
Rapakivi granite – Type of igneous rock
Rhomb porphyry – Textural form of igneous rock with large grained crystals in a fine matrix – A type of latite with euhedral rhombic phenocrysts of feldspar
Rodingite – metamorphic rock – A mafic rock metasomatized by serpentinization fluids
Shonkinite – Intrusive igneous rock – melitilic and kalsititic rocks
Taconite – Variety of iron-bearing sedimentary rock
Tachylite – Form of basaltic volcanic glass
Teschenite – A silica undersaturated, analcime bearing gabbro
Theralite – igneous rock – A nepheline gabbro
Unakite – metamorphic rock – An altered granite
Variolite – Igneous rocks which contain varioles
Vogesite – Ultrapotassic igneous rocks – A variety of lamprophyre
Wad – Porous secondary manganese oxyhydroxide – A rock rich in manganese oxide or manganese hydroxide

References

"BGS Rock Classification Scheme - Igneous - Metamorphic - Sedimentary - Superficial". British Geological Survey (BGS). Retrieved 2019-05-28.

External links

Categories:

https://en.wikipedia.org/wiki/List_of_rock_types

Category:Geology-related lists

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Geology-related lists.

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Geology-related lists by country‎ (13 C)

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Outline of geology

*

Index of geology articles

0–9

List of 21st century sinkholes

A

C

D

List of deserts by area

E

List of places on land with elevations below sea level

F

G

I

List of ice cores

K

List of karst areas

L

M

N

List of new islands

O

P

R

S

T

V

List of large volcanic eruptions

Categories:

https://en.wikipedia.org/wiki/Category:Geology-related_lists

The world's longest above-water mountain range is the Andes,^[1]^[2] about 7,000 km (4,300 mi) long. The range stretches from north to south through seven countries in South America, along the west coast of the continent: Venezuela, Colombia, Ecuador, Peru, Bolivia, Chile, and Argentina. Aconcagua is the highest peak, at about 6,962 m (22,841 ft).

This list does not include submarine mountain ranges. If submarine mountains are included, the longest is the global mid-ocean ridge system which extends for about 65,000 km (40,000 mi).^[3]

https://en.wikipedia.org/wiki/List_of_longest_mountain_chains_on_Earth

https://en.wikipedia.org/wiki/List_of_mountain_ranges

https://en.wikipedia.org/wiki/Himalayas

https://en.wikipedia.org/wiki/Great_Dividing_Range

https://en.wikipedia.org/wiki/Transantarctic_Mountains

https://en.wikipedia.org/wiki/Category:Industrial_gases

Gas blending is the process of mixing gases for a specific purpose where the composition of the resulting mixture is specified and controlled. A wide range of applications include scientific and industrial processes, food production and storage and breathing gases.

Gas mixtures are usually specified in terms of molar gas fraction (which is closely approximated by volumetric gas fraction for many permanent gases): by percentage, parts per thousand or parts per million. Volumetric gas fraction converts trivially to partial pressure ratio, following Dalton's law of partial pressures. Partial pressure blending at constant temperature is computationally simple, and pressure measurement is relatively inexpensive, but maintaining constant temperature during pressure changes requires significant delays for temperature equalization. Blending by mass fraction is unaffected by temperature variation during the process, but requires accurate measurement of mass or weight, and calculation of constituent masses from the specified molar ratio. Both partial pressure and mass fraction blending are used in practice.

https://en.wikipedia.org/wiki/Gas_blending

https://en.wikipedia.org/wiki/Dalton%27s_law

https://en.wikipedia.org/wiki/Gas_laws

Gas mixtures for brewing

Sparging: An inert gas such as nitrogen is bubbled through the wine, which removes the dissolved oxygen. Carbon dioxide is also removed and to ensure that an appropriate amount of carbon dioxide remains, a mixture of nitrogen and carbon dioxide may be used for the sparging gas.^[3]
Purging and blanketing: The removal of oxygen from the headspace above the wine in a container by flushing with a similar gas mixture to that used for sparging is called purging, and if it is left there it is called blanketing or inerting.^[3]

https://en.wikipedia.org/wiki/Gas_blending

The anesthetic machine is used to blend breathing gas for patients under anesthesia during surgery. The gas mixing and delivery system lets the anesthetist control oxygen fraction, nitrous oxide concentration and the concentration of volatile anesthetic agents.^[5] The machine is usually supplied with oxygen (O₂) and nitrous oxide (N₂O) from low pressure lines and high pressure reserve cylinders, and the metered gas is mixed at ambient pressure, after which additional anesthetic agents may be added by a vaporizer, and the gas may be humidified. Air is used as a diluent to decrease oxygen concentration. In special cases other gases may also be added to the mixture. These may include carbon dioxide (CO₂), used to stimulate respiration, and helium (He) to reduce resistance to flow or to enhance heat transfer.^[6]

Gas mixing systems may be mechanical, using conventional rotameter banks, or electronic, using proportional solenoids or pulsed injectors, and control may be manual or automatic.^[5]

Controlled atmosphere manufacture and storage

Protective gas mixtures may be used to exclude air or other gases from the surface of sensitive materials during processing. Examples include melting of reactive metals such as magnesium, and heat treatment of steels.

Customized gas mixtures for analytical applications

Calibration gases:

Span gases are used for testing and calibrating gas detection equipment by exposing the sensor to a known concentration of a contaminant. The gases are used as a reference point to ensure correct readings after calibration and have very accurate composition, with a content of the gas to be detected close to the set value for the detector.
Zero gas is normally a gas free of the component to be measured, and as similar as practicable to the composition of the gas to be monitored, used to calibrate the zero point of the sensor.

Calibration gas mixtures are generally produced in batches by gravimetric or volumetric methods.

The gravimetric method uses sensitive and accurately calibrated scales to weigh the amounts of gases added into the cylinder. Precise measurement is required as inaccuracy or impurities can result in incorrect calibration. The container for calibration gas must be as close to perfectly clean as practicable. The cylinders may be cleaned by purging with high purity nitrogen, the vacuumed. For particularly critical mixtures the cylinder may be heated while being vacuumed to facilitate removal of any impurities adhering to the walls.^[7]

After filling, the gas mixture must be thoroughly mixed to ensure that all components are evenly distributed throughout the container to prevent possible variations on composition within the container. This is commonly done by rolling the container horizontally for 2 to 4 hours.^[7]

Oxygen content is relatively simple to monitor using electro-galvanic cells and these are routinely used in the underwater diving industry for this purpose, though other methods may be more accurate and reliable.

https://en.wikipedia.org/wiki/Gas_blending

Underwater acoustic communication is a technique of sending and receiving messages below water.^[1] There are several ways of employing such communication but the most common is by using hydrophones. Underwater communication is difficult due to factors such as multi-path propagation, time variations of the channel, small available bandwidth and strong signal attenuation, especially over long ranges. Compared to terrestrial communication, underwater communication has low data rates because it uses acoustic waves instead of electromagnetic waves.

At the beginning of the 20th century some ships communicated by underwater bells as well as using the system for navigation. Submarine signals were at the time competitive with the primitive maritime radionavigation.^[2] The later Fessenden oscillator allowed communication with submarines.

https://en.wikipedia.org/wiki/Underwater_acoustic_communication

Radio navigation or radionavigation is the application of radio frequencies to determine a position of an object on the Earth, either the vessel or an obstruction.^[1]^[2] Like radiolocation, it is a type of radiodetermination.

The basic principles are measurements from/to electric beacons, especially

Angular directions, e.g. by bearing, radio phases or interferometry,
Distances, e.g. ranging by measurement of time of flight between one transmitter and multiple receivers or vice versa,
Distance differences by measurement of times of arrival of signals from one transmitter to multiple receivers or vice versa
Partly also velocity, e.g. by means of radio Doppler shift.^{[citation needed]}

Combinations of these measurement principles also are important—e.g., many radars measure range and azimuth of a target.^{[citation needed]}

https://en.wikipedia.org/wiki/Radio_navigation

Reverse RDF

The Orfordness Beacon as it appears today.

The main problem with RDF is that it required a special antenna on the vehicle, which may not be easy to mount on smaller vehicles or single-crew aircraft. A smaller problem is that the accuracy of the system is based to a degree on the size of the antenna, but larger antennas would likewise make the installation more difficult.^{[citation needed]}

During the era between World War I and World War II, a number of systems were introduced that placed the rotating antenna on the ground. As the antenna rotated through a fixed position, typically due north, the antenna was keyed with the morse code signal of the station's identification letters so the receiver could ensure they were listening to the right station. Then they waited for the signal to either peak or disappear as the antenna briefly pointed in their direction. By timing the delay between the morse signal and the peak/null, then dividing by the known rotational rate of the station, the bearing of the station could be calculated.^{[citation needed]}

The first such system was the German Telefunken Kompass Sender, which began operations in 1907 and was used operationally by the Zeppelin fleet until 1918.^[4] An improved version was introduced by the UK as the Orfordness Beacon in 1929 and used until the mid-1930s. A number of improved versions followed, replacing the mechanical motion of the antennas with phasing techniques that produced the same output pattern with no moving parts. One of the longest lasting examples was Sonne, which went into operation just before World War II and was used operationally under the name Consol until 1991. The modern VOR system is based on the same principles (see below).^{[citation needed]}

ADF and NDB

A great advance in the RDF technique was introduced in the form of phase comparisons of a signal as measured on two or more small antennas, or a single highly directional solenoid. These receivers were smaller, more accurate, and simpler to operate. Combined with the introduction of the transistor and integrated circuit, RDF systems were so reduced in size and complexity that they once again became quite common during the 1960s, and were known by the new name, automatic direction finder, or ADF.^{[citation needed]}

This also led to a revival in the operation of simple radio beacons for use with these RDF systems, now referred to as non-directional beacons (NDB). As the LF/MF signals used by NDBs can follow the curvature of earth, NDB has a much greater range than VOR which travels only in line of sight. NDB can be categorized as long range or short range depending on their power. The frequency band allotted to non-directional beacons is 190–1750 kHz, but the same system can be used with any common AM-band commercial station.^{[citation needed]}

VOR

VOR transmitter station

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VHF omnidirectional range, or VOR, is an implementation of the reverse-RDF system, but one that is more accurate and able to be completely automated.^{[citation needed]}

The VOR station transmits two audio signals on a VHF carrier – one is Morse code at 1020 Hz to identify the station, the other is a continuous 9960 Hz audio modulated at 30 Hz, with the 0-degree referenced to magnetic north. This signal is rotated mechanically or electrically at 30 Hz, which appears as a 30 Hz AM signal added to the previous two signals, the phasing of which is dependent on the position of the aircraft relative to the VOR station.^{[citation needed]}

The VOR signal is a single RF carrier that is demodulated into a composite audio signal composed of a 9960 Hz reference signal frequency modulated at 30 Hz, a 30 Hz AM reference signal, and a 1020 Hz 'marker' signal for station identification. Conversion from this audio signal into a usable navigation aid is done by a navigation converter, which takes the reference signal and compares the phasing with the variable signal. The phase difference in degrees is provided to navigational displays. Station identification is by listening to the audio directly, as the 9960 Hz and 30 Hz signals are filtered out of the aircraft internal communication system, leaving only the 1020 Hz Morse-code station identification.^{[citation needed]}

The system may be used with a compatible glideslope and marker beacon receiver, making the aircraft ILS-capable (Instrument Landing System)}. Once the aircraft's approach is accurate (the aircraft is in the "right place"), the VOR receiver will be used on a different frequency to determine if the aircraft is pointed in the "right direction." Some aircraft will usually employ two VOR receiver systems, one in VOR-only mode to determine "right place" and another in ILS mode in conjunction with a glideslope receiver to determine "right direction." }The combination of both allows for a precision approach in foul weather.^[5]

Beam systems

Beam systems broadcast narrow signals in the sky, and navigation is accomplished by keeping the aircraft centred in the beam. A number of stations are used to create an airway, with the navigator tuning in different stations along the direction of travel. These systems were common in the era when electronics were large and expensive, as they placed minimum requirements on the receivers – they were simply voice radio sets tuned to the selected frequencies. However, they did not provide navigation outside of the beams, and were thus less flexible in use. The rapid miniaturization of electronics during and after World War II made systems like VOR practical, and most beam systems rapidly disappeared.^{[citation needed]}

Lorenz

In the post-World War I era, the Lorenz company of Germany developed a means of projecting two narrow radio signals with a slight overlap in the center. By broadcasting different audio signals in the two beams, the receiver could position themselves very accurately down the centreline by listening to the signal in their headphones. The system was accurate to less than a degree in some forms.^{[citation needed]}

Originally known as "Ultrakurzwellen-Landefunkfeuer" (LFF), or simply "Leitstrahl" (guiding beam), little money was available to develop a network of stations. The first widespread radio navigation network, using Low and Medium Frequencies, was instead led by the US (see LFF, below). Development was restarted in Germany in the 1930s as a short-range system deployed at airports as a blind landing aid. Although there was some interest in deploying a medium-range system like the US LFF, deployment had not yet started when the beam system was combined with the Orfordness timing concepts to produce the highly accurate Sonne system. In all of these roles, the system was generically known simply as a "Lorenz beam". Lorenz was an early predecessor to the modern Instrument Landing System.^{[citation needed]}

In the immediate pre-World War II era the same concept was also developed as a blind-bombing system. This used very large antennas to provide the required accuracy at long distances (over England), and very powerful transmitters. Two such beams were used, crossing over the target to triangulate it. Bombers would enter one of the beams and use it for guidance until they heard the second one in a second radio receiver, using that signal to time the dropping of their bombs. The system was highly accurate, and the 'Battle of the Beams' broke out when United Kingdom intelligence services attempted, and then succeeded, in rendering the system useless through electronic warfare.^{[citation needed]}

Low-frequency radio range

LFR ground station

The low-frequency radio range (LFR, also "Four Course Radio Range" among other names) was the main navigation system used by aircraft for instrument flying in the 1930s and 1940s in the U.S. and other countries, until the advent of the VOR in the late 1940s. It was used for both en route navigation as well as instrument approaches.^{[citation needed]}

The ground stations consisted of a set of four antennas that projected two overlapping directional figure-eight signal patterns at a 90 degree angle to each other. One of these patterns was "keyed" with the Morse code signal "A", dit-dah, and the second pattern "N", dah-dit. This created two opposed "A" quadrants and two opposed "N" quadrants around the station. The borders between these quadrants created four course legs or "beams" and if the pilot flew down these lines, the "A" and "N" signal merged into a steady "on course" tone and the pilot was "on the beam". If the pilot deviated to either side the "A" or "N" tone would become louder and the pilot knew to make a correction. The beams were typically aligned with other stations to produce a set of airways, allowing an aircraft to travel from airport to airport by following a selected set of stations. Effective course accuracy was about three degrees, which near the station provided sufficient safety margins for instrument approaches down to low minimums. At its peak deployment, there were over 400 LFR stations in the US.^[6]

Glide path and the localizer of ILS

The remaining widely used beam systems are glide path and the localizer of the instrument landing system (ILS). ILS uses a localizer to provide horizontal position and glide path to provide vertical positioning. ILS can provide enough accuracy and redundancy to allow automated landings.

For more information see also:

Transponder systems

Positions can be determined with any two measures of angle or distance. The introduction of radar in the 1930s provided a way to directly determine the distance to an object even at long distances. Navigation systems based on these concepts soon appeared, and remained in widespread use until recently. Today they are used primarily for aviation, although GPS has largely supplanted this role.^{[citation needed]}

Radar and transponders

Early radar systems, like the UK's Chain Home, consisted of large transmitters and separate receivers. The transmitter periodically sends out a short pulse of a powerful radio signal, which is sent into space through broadcast antennas. When the signal reflects off a target, some of that signal is reflected back in the direction of the station, where it is received. The received signal is a tiny fraction of the broadcast power, and has to be powerfully amplified in order to be used.^{[citation needed]}

The same signals are also sent over local electrical wiring to the operator's station, which is equipped with an oscilloscope. Electronics attached to the oscilloscope provides a signal that increases in voltage over a short period of time, a few microseconds. When sent to the X input of the oscilloscope, this causes a horizontal line to be displayed on the scope. This "sweep" is triggered by a signal tapped off the broadcaster, so the sweep begins when the pulse is sent. Amplified signals from the receiver are then sent to the Y input, where any received reflection causes the beam to move upward on the display. This causes a series of "blips" to appear along the horizontal axis, indicating reflected signals. By measuring the distance from the start of the sweep to the blip, which corresponds to the time between broadcast and reception, the distance to the object can be determined.^{[citation needed]}

Soon after the introduction of radar, the radio transponder appeared. Transponders are a combination of receiver and transmitter whose operation is automated – upon reception of a particular signal, normally a pulse on a particular frequency, the transponder sends out a pulse in response, typically delayed by some very short time. Transponders were initially used as the basis for early IFF systems; aircraft with the proper transponder would appear on the display as part of the normal radar operation, but then the signal from the transponder would cause a second blip to appear a short time later. Single blips were enemies, double blips friendly.^{[citation needed]}

Transponder-based distance-distance navigation systems have a significant advantage in terms of positional accuracy. Any radio signal spreads out over distance, forming the fan-like beams of the Lorenz signal, for instance. As the distance between the broadcaster and receiver grows, the area covered by the fan increases, decreasing the accuracy of location within it. In comparison, transponder-based systems measure the timing between two signals, and the accuracy of that measure is largely a function of the equipment and nothing else. This allows these systems to remain accurate over very long range.^{[citation needed]}

The latest transponder systems (mode S) can also provide position information, possibly derived from GNSS, allowing for even more precise positioning of targets.^{[citation needed]}

Bombing systems

The first distance-based navigation system was the German Y-Gerät blind-bombing system. This used a Lorenz beam for horizontal positioning, and a transponder for ranging. A ground-based system periodically sent out pulses which the airborne transponder returned. By measuring the total round-trip time on a radar's oscilloscope, the aircraft's range could be accurately determined even at very long ranges. An operator then relayed this information to the bomber crew over voice channels, and indicated when to drop the bombs.^{[citation needed]}

The British introduced similar systems, notably the Oboe system. This used two stations in England that operated on different frequencies and allowed the aircraft to be triangulated in space. To ease pilot workload only one of these was used for navigation – prior to the mission a circle was drawn over the target from one of the stations, and the aircraft was directed to fly along this circle on instructions from the ground operator. The second station was used, as in Y-Gerät, to time the bomb drop. Unlike Y-Gerät, Oboe was deliberately built to offer very high accuracy, as good as 35 m, much better than even the best optical bombsights.^{[citation needed]}

One problem with Oboe was that it allowed only one aircraft to be guided at a time. This was addressed in the later Gee-H system by placing the transponder on the ground and broadcaster in the aircraft. The signals were then examined on existing Gee display units in the aircraft (see below). Gee-H did not offer the accuracy of Oboe, but could be used by as many as 90 aircraft at once. This basic concept has formed the basis of most distance measuring navigation systems to this day.^{[citation needed]}

Beacons

The key to the transponder concept is that it can be used with existing radar systems. The ASV radar introduced by RAF Coastal Command was designed to track down submarines and ships by displaying the signal from two antennas side by side and allowing the operator to compare their relative strength. Adding a ground-based transponder immediately turned the same display into a system able to guide the aircraft towards a transponder, or "beacon" in this role, with high accuracy.^{[citation needed]}

The British put this concept to use in their Rebecca/Eureka system, where battery-powered "Eureka" transponders were triggered by airborne "Rebecca" radios and then displayed on ASV Mk. II radar sets. Eureka's were provided to French resistance fighters, who used them to call in supply drops with high accuracy. The US quickly adopted the system for paratroop operations, dropping the Eureka with pathfinder forces or partisans, and then homing in on those signals to mark the drop zones.^{[citation needed]}

The beacon system was widely used in the post-war era for blind bombing systems. Of particular note were systems used by the US Marines that allowed the signal to be delayed in such a way to offset the drop point. These systems allowed the troops at the front line to direct the aircraft to points in front of them, directing fire on the enemy. Beacons were widely used for temporary or mobile navigation as well, as the transponder systems were generally small and low-powered, able to be man portable or mounted on a Jeep.^{[citation needed]}

DME

In the post-war era, a general navigation system using transponder-based systems was deployed as the distance measuring equipment (DME) system.^{[citation needed]}

DME was identical to Gee-H in concept, but used new electronics to automatically measure the time delay and display it as a number, rather than having the operator time the signals manually on an oscilloscope. This led to the possibility that DME interrogation pulses from different aircraft might be confused, but this was solved by having each aircraft send out a different series of pulses which the ground-based transponder repeated back.

DME is almost always used in conjunction with VOR, and is normally co-located at a VOR station. This combination allows a single VOR/DME station to provide both angle and distance, and thereby provide a single-station fix. DME is also used as the distance-measuring basis for the military TACAN system, and their DME signals can be used by civilian receivers.^{[citation needed]}

Hyperbolic systems

Hyperbolic navigation systems are a modified form of transponder systems which eliminate the need for an airborne transponder. The name refers to the fact that they do not produce a single distance or angle, but instead indicate a location along any number of hyperbolic lines in space. Two such measurements produces a fix. As these systems are almost always used with a specific navigational chart with the hyperbolic lines plotted on it, they generally reveal the receiver's location directly, eliminating the need for manual triangulation. As these charts were digitized, they became the first true location-indication navigational systems, outputting the location of the receiver as latitude and longitude. Hyperbolic systems were introduced during World War II and remained the main long-range advanced navigation systems until GPS replaced them in the 1990s.^{[citation needed]}

Gee

The first hyperbolic system to be developed was the British Gee system, developed during World War II. Gee used a series of transmitters sending out precisely timed signals, with the signals leaving the stations at fixed delays. An aircraft using Gee, RAF Bomber Command's heavy bombers, examined the time of arrival on an oscilloscope at the navigator's station. If the signal from two stations arrived at the same time, the aircraft must be an equal distance from both transmitters, allowing the navigator to determine a line of position on his chart of all the positions at that distance from both stations. More typically, the signal from one station would be received earlier than the other. The difference in timing between the two signals would reveal them to be along a curve of possible locations. By making similar measurements with other stations, additional lines of position can be produced, leading to a fix. Gee was accurate to about 165 yards (150 m) at short ranges, and up to a mile (1.6 km) at longer ranges over Germany. Gee remained in use long after World War II, and equipped RAF aircraft as late as the 1960s (approx freq was by then 68 MHz).^{[citation needed]}

LORAN

With Gee entering operation in 1942, similar US efforts were seen to be superfluous. They turned their development efforts towards a much longer-ranged system based on the same principles, using much lower frequencies that allowed coverage across the Atlantic Ocean. The result was LORAN, for "LOng-range Aid to Navigation". The downside to the long-wavelength approach was that accuracy was greatly reduced compared to the high-frequency Gee. LORAN was widely used during convoy operations in the late war period.^[7]

Decca

Another British system from the same era was Decca Navigator. This differed from Gee primarily in that the signals were not pulses delayed in time, but continuous signals delayed in phase. By comparing the phase of the two signals, the time difference information as Gee was returned. However, this was far easier to display; the system could output the phase angle to a pointer on a dial removing any need for visual interpretation. As the circuitry for driving this display was quite small, Decca systems normally used three such displays, allowing quick and accurate reading of multiple fixes. Decca found its greatest use post-war on ships, and remained in use into the 1990s.^{[citation needed]}

LORAN-C

Almost immediately after the introduction of LORAN, in 1952 work started on a greatly improved version. LORAN-C (the original retroactively became LORAN-A) combined the techniques of pulse timing in Gee with the phase comparison of Decca.^{[citation needed]}

The resulting system (operating in the low frequency (LF) radio spectrum from 90 to 110 kHz) that was both long-ranged (for 60 kW stations, up to 3400 miles) and accurate. To do this, LORAN-C sent a pulsed signal, but modulated the pulses with an AM signal within it. Gross positioning was determined using the same methods as Gee, locating the receiver within a wide area. Finer accuracy was then provided by measuring the phase difference of the signals, overlaying that second measure on the first. By 1962, high-power LORAN-C was in place in at least 15 countries.^[8]

LORAN-C was fairly complex to use, requiring a room of equipment to pull out the different signals. However, with the introduction of integrated circuits, this was quickly reduced further and further. By the late 1970s, LORAN-C units were the size of a stereo amplifier and were commonly found on almost all commercial ships as well as some larger aircraft. By the 1980s, this had been further reduced to the size of a conventional radio, and it became common even on pleasure boats and personal aircraft. It was the most popular navigation system in use through the 1980s and 90s, and its popularity led to many older systems being shut down, like Gee and Decca. However, like the beam systems before it, civilian use of LORAN-C was short-lived when GPS technology drove it from the market.^{[citation needed]}

Other hyperbolic systems

Similar hyperbolic systems included the US global-wide VLF/Omega Navigation System, and the similar Alpha deployed by the USSR. These systems determined pulse timing not by comparison of two signals, but by comparison of a single signal with a local atomic clock. The expensive-to-maintain Omega system was shut down in 1997 as the US military migrated to using GPS. Alpha is still in use.^{[citation needed]}

Satellite navigation

Cessna 182 with GPS-based "glass cockpit" avionics

Since the 1960s, navigation has increasingly moved to satellite navigation systems. These are essentially hyperbolic^[9]^[10] systems whose transmitters are in orbits. That the satellites move with respect to the receiver requires that the calculation of the positions of the satellites must be taken into account, which can only be handled effectively with a computer.^{[citation needed]}

Satellite navigation systems send several signals that are used to decode the satellite's position, distance between the user satellite, and the user's precise time. One signal encodes the satellite's ephemeris data, which is used to accurately calculate the satellite's location at any time. Space weather and other effects causes the orbit to change over time so the ephemeris has to be updated periodically. Other signals send out the time as measured by the satellite's onboard atomic clock. By measuring signal times of arrival (TOAs) from at least four satellites, the user's receiver can re-build an accurate clock signal of its own and allows hyperbolic navigation to be carried out.^{[citation needed]}

Satellite navigation systems offer better accuracy than any land-based system, are available at almost all locations on the Earth, can be implemented (receiver-side) a modest cost and complexity, with modern electronics, and require only a few dozen satellites to provide worldwide coverage^{[citation needed]}. As a result of these advantages, satellite navigation has led to almost all previous systems falling from use^{[citation needed]}. LORAN, Omega, Decca, Consol and many other systems disappeared during the 1990s and 2000s^{[citation needed]}. The only other systems still in use are aviation aids, which are also being turned off^{[citation needed]} for long-range navigation while new differential GPS systems are being deployed to provide the local accuracy needed for blind landings.^{[citation needed]}

International regulation

Radionavigation service (short: RNS) is – according to Article 1.42 of the International Telecommunication Union's (ITU) Radio Regulations (RR)^[11] – defined asA radiodetermination service for the purpose of radionavigation, including obstruction warning.'

This service is a so-called safety-of-life service, must be protected for Interferences, and is essential part of Navigation.^{[citation needed]}

This radiocommunication service is classified in accordance with ITU Radio Regulations (article 1) as follows:
Radiodetermination service (article 1.40)

Radiodetermination-satellite service (article 1.41)
Radionavigation service (article 1.42)
- Radionavigation-satellite service (article 1.43)
- Maritime radionavigation service (article 1.44)
  - Maritime radionavigation-satellite service (article 1.45)
- Aeronautical radionavigation service (article 1.46)
  - Aeronautical radionavigation-satellite service (article 1.47)

Aeronautical

ILS-antenna on Hannover Airport

VHF direction finder antenna of the ARNS on Deister nearby Hanover

Aeronautical radionavigation service (short: ARNS) is – according to Article 1.46 of the International Telecommunication Union's (ITU) Radio Regulations (RR)^[12] – defined as "A radionavigation service intended for the benefit and for the safe operation of aircraft."

This service is a so-called safety-of-life service, must be protected against interference, and is an essential part of navigation.

Maritime

Radionavigation land station (LORAN-C-transmitter Rantum)

Radionavigation mobile station (RDF) 1930

Maritime radionavigation service (short: MRNS) is – according to Article 1.44 of the International Telecommunication Union's (ITU) Radio Regulations (RR)^[13] – defined as "A radionavigation service intended for the benefit and for the safe operation of ships."

This service is a so-called safety-of-life service, must be protected for interferences, and is essential part of navigation.

Stations

Land station

1 DME; 2 VOR Radionavigation land stations

A radionavigation land station is – according to article 1.88 of the International Telecommunication Union´s (ITU) ITU Radio Regulations (RR)^[14] – defined as "A radio station in the radionavigation service not intended to be used while in motion."

Each radio station shall be classified by the radiocommunication service in which it operates permanently or temporarily. This station operates in a safety-of-life service and must be protected for Interferences.^{[citation needed]}

In accordance with ITU Radio Regulations (article 1) this type of radio station might be classified as follows:
Radiodetermination station (article 1.86) of the radiodetermination service (article 1.40 )

Radionavigation mobile station (article 1.87) of the radionavigation service (article 1.42)
Radionavigation land station

Selection radionavigation land stations

Mobile station

A radionavigation mobile station is – according to article 1.87 of the International Telecommunication Union's (ITU) ITU Radio Regulations (RR)^[15] – defined as "A radio station in the radionavigation service intended to be used while in motion or during halts at unspecified points."

Radionavigation mobile station

Selection radionavigation mobile stations

Mobile TACAN-station in Alaska
TACAN sea borne
ILS receiver indicator onboard
ILS indicator onboard aircraft
Antenna DME / VOR

References

Dutton, Benjamin (2004). "15 – Basic Radio Navigation". Dutton's Nautical Navigation (15 ed.). Naval Institute Press. pp. 154–163. ISBN 155750248X.

Kayton, Myron; Walter R. Fried (1997). "4 – Terrestrial Radio-Navigation Systems". Avionics Navigation Systems. John Wiley & Sons. pp. 99–177.

Kayton, Fried 1977, p.116

Bauer, Arthur O. (Dec 26, 2004). "Some historical and technical aspects of radio navigation, in Germany, over the period 1907 to 1945" (PDF). Retrieved 25 July 2013.

VOR/ILS Testing with Signal Generator SMT

"Low Frequency Radio Range, Flying the Beam". Archived from the original on 2021-01-16. Retrieved 2021-02-01.

"The Loran-C System of Navigation" (PDF). Jansky & Bailey. February 1962. pp. 18–23. Archived from the original (PDF) on 22 July 2013. Retrieved 25 July 2013.

Jansky & Baily 1962, pp.23–37.

"Existence and uniqueness of GPS solutions", J.S. Abel and J.W. Chaffee, IEEE Transactions on Aerospace and Electronic Systems, vol. 26, no. 6, pp. 748–53, Sept. 1991.

"Comments on "Existence and uniqueness of GPS solutions" by J.S. Abel and J.W. Chaffee", B.T. Fang, IEEE Transactions on Aerospace and Electronic Systems, vol. 28, no. 4, Oct. 1992.

ITU Radio Regulations, Section IV. Radio Stations and Systems – Article 1.42, definition: radionavigation service

ITU Radio Regulations, Section IV. Radio Stations and Systems – Article 1.46, definition: aeronautical radionavigation service

ITU Radio Regulations, Section IV. Radio Stations and Systems – Article 1.44, definition: maritime radionavigation service

ITU Radio Regulations, Section IV. Radio Stations and Systems – Article 1.88, definition: radionavigation land station

ITU Radio Regulations, Section IV. Radio Stations and Systems – Article 1.87, definition: radionavigation mobile station

External links

Department of Transportation and Department of Defense (March 25, 2002). "2001 Federal Radionavigation Systems" (PDF). Retrieved November 27, 2005.
UK Navaids Gallery with detailed Technical Descriptions of their operation
U.S. Federal Radionavigation Plan

Categories:

https://en.wikipedia.org/wiki/Radio_navigation

Category:Wireless locating

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Subcategories

This category has the following 8 subcategories, out of 8 total.

G

Global Positioning System‎ (5 C, 133 P)

GLONASS‎ (1 C, 7 P)

I

Indoor positioning system‎ (14 P)

P

Phased arrays‎ (2 P)

R

Radio geopositioning‎ (2 C, 8 P)

S

Satellite navigation systems‎ (7 C, 6 P)

T

Telematics‎ (4 C, 6 P)

Tracking‎ (4 C, 47 P)

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https://en.wikipedia.org/wiki/Electro-galvanic_oxygen_sensor

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https://en.wikipedia.org/wiki/Cryptand

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https://en.wikipedia.org/wiki/Phase-transfer_catalyst

https://en.wikipedia.org/wiki/Ion_exchange

https://en.wikipedia.org/wiki/Ion-exchange_resin

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https://en.wikipedia.org/wiki/Ionomer

An ionomer (/ˌaɪˈɑːnəmər/) (iono- + -mer) is a polymer composed of repeat units of both electrically neutral repeating units and ionized units covalently bonded to the polymer backbone as pendant group moieties. Usually no more than 15 mole percent are ionized. The ionized units are often carboxylic acid groups.

The classification of a polymer as an ionomer depends on the level of substitution of ionic groups as well as how the ionic groups are incorporated into the polymer structure. For example, polyelectrolytes also have ionic groups covalently bonded to the polymer backbone, but have a much higher ionic group molar substitution level (usually greater than 80%); ionenes are polymers where ionic groups are part of the actual polymer backbone. These two classes of ionic-group-containing polymers have vastly different morphological and physical properties and are therefore not considered ionomers.

Ionomers have unique physical properties including electrical conductivity and viscosity—increase in ionomer solution viscosity with increasing temperatures (see conducting polymer). Ionomers also have unique morphological properties as the non-polar polymer backbone is energetically incompatible with the polar ionic groups. As a result, the ionic groups in most ionomers will undergo microphase separation to form ionic-rich domains.

Commercial applications for ionomers include golf ball covers, semipermeable membranes, sealing tape and thermoplastic elastomers. Common examples of ionomers include polystyrene sulfonate, Nafion and Hycar.

https://en.wikipedia.org/wiki/Ionomer

https://en.wikipedia.org/wiki/pattern

Atom transfer radical polymerization (ATRP) is an example of a reversible-deactivation radical polymerization. Like its counterpart, ATRA, or atom transfer radical addition, ATRP is a means of forming a carbon-carbon bond with a transition metal catalyst. Polymerization from this method is called atom transfer radical addition polymerization (ATRAP). As the name implies, the atom transfer step is crucial in the reaction responsible for uniform polymer chain growth. ATRP (or transition metal-mediated living radical polymerization) was independently discovered by Mitsuo Sawamoto^[1] and by Krzysztof Matyjaszewski and Jin-Shan Wang in 1995.^[2]^[3]

The following scheme presents a typical ATRP reaction:

General ATRP reaction. A. Initiation. B. Equilibrium with dormant species. C. Propagation

IUPAC definition for ATRP

Controlled reversible-deactivation radical polymerization in which the deactivation
of the radicals involves reversible atom transfer or reversible group transfer catalyzed usually,
though not exclusively, by transition-metal complexes.^[4]

https://en.wikipedia.org/wiki/Atom_transfer_radical_polymerization

Number average molar mass

The number average molar mass is a way of determining the molecular mass of a polymer. Polymer molecules, even ones of the same type, come in different sizes (chain lengths, for linear polymers), so the average molecular mass will depend on the method of averaging. The number average molecular mass is the ordinary arithmetic mean or average of the molecular masses of the individual macromolecules. It is determined by measuring the molecular mass of $n$ polymer molecules, summing the masses, and dividing by $n$ .

${\bar{M}}_{n} = \frac{\sum_{i} N_{i} M_{i}}{\sum_{i} N_{i}}$

The number average molecular mass of a polymer can be determined by gel permeation chromatography, viscometry via the (Mark–Houwink equation), colligative methods such as vapor pressure osmometry, end-group determination or proton NMR.^[4]

High number-average molecular mass polymers may be obtained only with a high fractional monomer conversion in the case of step-growth polymerization, as per the Carothers' equation.

https://en.wikipedia.org/wiki/Molar_mass_distribution#Number_average_molar_mass

Chemical uses

Polystyrene sulfonates are useful because of their ion exchange properties.^[15] Linear ionic polymers are generally water-soluble, whereas cross-linked materials (called resins) do not dissolve in water. These polymers are classified as polysalts and ionomers.^[15]

Water softening

Water softening is achieved by percolating hard water through a bed of the sodium form of cross-linked polystyrene sulfonate. The hard ions such as calcium (Ca²⁺) and magnesium (Mg²⁺) adhere to the sulfonate groups, displacing sodium ions. The resulting solution of sodium ions is softened.

Idealized image of water softening process involving replacement of calcium ions in water with sodium ions donated by a cation exchange resin.

Other uses

Sodium polystyrene sulfonate is used as a superplastifier in cement, as a dye improving agent for cotton, and as proton exchange membranes in fuel cell applications. In its acid form, the resin is used as a solid acid catalyst in organic synthesis.^[16]

^{https://en.wikipedia.org/wiki/Polystyrene_sulfonate}

The surface area of a solid object is a measure of the total area that the surface of the object occupies.^[1] The mathematical definition of surface area in the presence of curved surfaces is considerably more involved than the definition of arc length of one-dimensional curves, or of the surface area for polyhedra (i.e., objects with flat polygonal faces), for which the surface area is the sum of the areas of its faces. Smooth surfaces, such as a sphere, are assigned surface area using their representation as parametric surfaces. This definition of surface area is based on methods of infinitesimal calculus and involves partial derivatives and double integration.

A general definition of surface area was sought by Henri Lebesgue and Hermann Minkowski at the turn of the twentieth century. Their work led to the development of geometric measure theory, which studies various notions of surface area for irregular objects of any dimension. An important example is the Minkowski content of a surface.

https://en.wikipedia.org/wiki/Surface_area

In mathematics (specifically multivariable calculus), a multiple integral is a definite integral of a function of several real variables, for instance, $f (x, y)$ or $f (x, y, z)$ . Integrals of a function of two variables over a region in $R^{2}$ (the real-number plane) are called double integrals, and integrals of a function of three variables over a region in $R^{3}$ (real-number 3D space) are called triple integrals.^[1] For multiple integrals of a single-variable function, see the Cauchy formula for repeated integration.

https://en.wikipedia.org/wiki/Multiple_integral

Divinylbenzene (DVB) is an organic compound with the chemical formula C₆H₄(CH=CH₂)₂ and structure H₂C=CH−C₆H₄−HC=CH₂ (a benzene ring with two vinyl groups as substituents). It is related to styrene (vinylbenzene, C₆H₅−CH=CH₂) by the addition of a second vinyl group.^[2] It is a colorless liquid manufactured by the thermal dehydrogenation of isomeric diethylbenzenes. Under synthesis conditions, o-divinylbenzene converts to naphthalene and thus is not a component of the usual mixtures of DVB.^[3]

Yellow Divinylbenzene (DVB) is not acceptable for national security products.

https://en.wikipedia.org/wiki/Divinylbenzene

Anion resins

Anion resins may be either strongly or weakly basic. Strongly basic anion resins maintain their negative charge across a wide pH range, whereas weakly basic anion resins are neutralized at higher pH levels.^[3] Weakly basic resins do not maintain their charge at a high pH because they undergo deprotonation.^[3] They do, however, offer excellent mechanical and chemical stability. This, combined with a high rate of ion exchange, make weakly base anion resins well suited for the organic salts.

For anion resins, regeneration typically involves treatment of the resin with a strongly basic solution, e.g. aqueous sodium hydroxide. During regeneration, the regenerant chemical is passed through the resin, and trapped negative ions are flushed out, renewing the resin exchange capacity.

Cation-exchange resin

Formula: R−H acidic

The cation exchange method removes the hardness of water but induces acidity in it, which is further removed in the next stage of treatment of water by passing this acidic water through an anion exchange process.^[4]

Reaction:

R−H + M⁺ = R−M + H⁺.

Anion-exchange resin

Formula: –NR₄⁺OH⁻

Often these are styrene–divinylbenzene copolymer resins that have quaternary ammonium cations as an integral part of the resin matrix.^[4]

Reaction:

–NR₄⁺OH⁻ + HCl = –NR₄⁺Cl⁻ + H₂O.

Anion-exchange chromatography makes use of this principle to extract and purify materials from mixtures or solutions.

https://en.wikipedia.org/wiki/Ion-exchange_resin

https://en.wikipedia.org/wiki/Iminodiacetic_acid

https://en.wikipedia.org/wiki/Chelating_resin

https://en.wikipedia.org/wiki/Hydraulic_head#Head_loss

https://en.wikipedia.org/wiki/Polystyrene

https://en.wikipedia.org/wiki/Ion-exchange_membrane

https://en.wikipedia.org/wiki/Electrodialysis

https://en.wikipedia.org/wiki/Activated_carbon

Ion exchange in metal separation

A drum of yellowcake

Ion-exchange processes are used to separate and purify metals, including separating uranium from plutonium and other actinides, including thorium; and lanthanum, neodymium, ytterbium, samarium, lutetium, from each other and the other lanthanides. There are two series of rare-earth metals, the lanthanides and the actinides. Members of each family have very similar chemical and physical properties. Ion exchange was for many years the only practical way to separate the rare earths in large quantities. This application was developed in the 1940s by Frank Spedding. Subsequently, solvent extraction has mostly supplanted use of ion-exchange resins except for the highest-purity products.

A very important case is the PUREX process (plutonium-uranium extraction process), which is used to separate the plutonium and the uranium from the spent fuel products from a nuclear reactor, and to be able to dispose of the waste products. Then, the plutonium and uranium are available for making nuclear-energy materials, such as new reactor fuel and nuclear weapons.

Ion-exchange beads are also an essential component in in-situ leach uranium mining. In-situ recovery involves the extraction of uranium-bearing water (grading as low as 0.05% U₃O₈) through boreholes. The extracted uranium solution is then filtered through the resin beads. Through an ion-exchange process, the resin beads attract uranium from the solution. Uranium-loaded resins are then transported to a processing plant, where U₃O₈ is separated from the resin beads, and yellowcake is produced. The resin beads can then be returned to the ion-exchange facility, where they are reused.

The ion-exchange process is also used to separate other sets of very similar chemical elements, such as zirconium and hafnium, which incidentally is also very important for the nuclear industry. Zirconium is practically transparent to free neutrons, used in building reactors, but hafnium is a very strong absorber of neutrons, used in reactor control rods.

https://en.wikipedia.org/wiki/Ion-exchange_resin

https://en.wikipedia.org/wiki/Control_rod

https://en.wikipedia.org/wiki/Yellowcake

https://en.wikipedia.org/wiki/Triuranium_octoxide

https://en.wikipedia.org/wiki/PUREX

https://en.wikipedia.org/wiki/Liquid%E2%80%93liquid_extraction

https://en.wikipedia.org/wiki/Quaternary_ammonium_cation

https://en.wikipedia.org/wiki/Acid_catalysis#Solid_acid_catalysts

https://en.wikipedia.org/wiki/Polyelectrolyte

https://en.wikipedia.org/wiki/Direct_air_capture

https://en.wikipedia.org/wiki/Colestipol

https://en.wikipedia.org/wiki/Chelation_therapy

https://en.wikipedia.org/wiki/Excipient

https://en.wikipedia.org/wiki/Category:Synthetic_resins

https://en.wikipedia.org/wiki/Category:Phenol_formaldehyde_resins

https://en.wikipedia.org/wiki/Ebonite

https://en.wikipedia.org/wiki/Novolak

https://en.wikipedia.org/wiki/Silicone_resin

https://en.wikipedia.org/wiki/Prepolymer

https://en.wikipedia.org/wiki/Polyvinyl_butyral

https://en.wikipedia.org/wiki/Polyol

https://en.wikipedia.org/wiki/Polyester_resin

https://en.wikipedia.org/wiki/Polyester

https://en.wikipedia.org/wiki/Polybenzoxazine

https://en.wikipedia.org/wiki/Epoxy

https://en.wikipedia.org/wiki/Synthetic_resin

https://en.wikipedia.org/wiki/Waterborne_resins

https://en.wikipedia.org/wiki/Cyanoacrylate

https://en.wikipedia.org/wiki/Hybtonite

https://en.wikipedia.org/wiki/Carbon_nanotube

https://en.wikipedia.org/wiki/Hexagonal_tiling

https://en.wikipedia.org/wiki/Truncation_(geometry)

https://en.wikipedia.org/wiki/Nanotechnology

https://en.wikipedia.org/wiki/Molecular_nanotechnology

https://en.wikipedia.org/wiki/Self-replicating_machine

https://en.wikipedia.org/wiki/Von_Neumann_universal_constructor

https://en.wikipedia.org/wiki/Fullerene

The discovery of fullerenes greatly expanded the number of known allotropes of carbon, which had previously been limited to graphite, diamond, and amorphous carbon such as soot and charcoal.

https://en.wikipedia.org/wiki/Fullerene

https://en.wikipedia.org/wiki/Nanomaterials

https://en.wikipedia.org/wiki/Microfabrication

The major concepts and principles of microfabrication are microlithography, doping, thin films, etching, bonding, and polishing.

Simplified illustration of the process of fabrication of a CMOS inverter on p-type substrate in semiconductor microfabrication. Each etch step is detailed in the following image. Note: Gate, source and drain contacts are not normally located in the same plane in real devices, and th

https://en.wikipedia.org/wiki/Microfabrication

Origins

Microfabrication technologies originate from the microelectronics industry, and the devices are usually made on silicon wafers even though glass, plastics and many other substrate are in use. Micromachining, semiconductor processing, microelectronic fabrication, semiconductor fabrication, MEMS fabrication and integrated circuit technology are terms used instead of microfabrication, but microfabrication is the broad general term.

Traditional machining techniques such as electro-discharge machining, spark erosion machining, and laser drilling have been scaled from the millimeter size range to micrometer range, but they do not share the main idea of microelectronics-originated microfabrication: replication and parallel fabrication of hundreds or millions of identical structures. This parallelism is present in various imprint, casting and moulding techniques which have successfully been applied in the microregime. For example, injection moulding of DVDs involves fabrication of submicrometer-sized spots on the disc.

https://en.wikipedia.org/wiki/Microfabrication

Electroplating is also a 19th-century technique adapted to produce micrometre scale structures, as are various stamping and embossing techniques.

https://en.wikipedia.org/wiki/Microfabrication

https://en.wikipedia.org/wiki/Optical_engineering

https://en.wikipedia.org/wiki/Microfluidics

https://en.wikipedia.org/wiki/Nanosensor

https://en.wikipedia.org/wiki/Thin-film_transistor

https://en.wikipedia.org/wiki/Microoptoelectromechanical_systems

Modern microprocessors are made with 30 masks while a few masks suffice for a microfluidic device or a laser diode. Microfabrication resembles multiple exposure photography, with many patterns aligned to each other to create the final structure.

https://en.wikipedia.org/wiki/Microfabrication

To fabricate a microdevice, many processes must be performed, one after the other, many times repeatedly. These processes typically include depositing a film, patterning the film with the desired micro features, and removing (or etching) portions of the film. Thin film metrology is used typically during each of these individual process steps, to ensure the film structure has the desired characteristics in terms of thickness (t), refractive index (n) and extinction coefficient (k),^[2] for suitable device behavior. For example, in memory chip fabrication there are some 30 lithography steps, 10 oxidation steps, 20 etching steps, 10 doping steps, and many others are performed. The complexity of microfabrication processes can be described by their mask count. This is the number of different pattern layers that constitute the final device.

https://en.wikipedia.org/wiki/Microfabrication

Microfabricated devices are not generally freestanding devices but are usually formed over or in a thicker support substrate. For electronic applications, semiconducting substrates such as silicon wafers can be used. For optical devices or flat panel displays, transparent substrates such as glass or quartz are common. The substrate enables easy handling of the micro device through the many fabrication steps. Often many individual devices are made together on one substrate and then singulated into separated devices toward the end of fabrication.

https://en.wikipedia.org/wiki/Microfabrication

Microfabricated devices are typically constructed using one or more thin films (see Thin film deposition). The purpose of these thin films depends upon the type of device. Electronic devices may have thin films which are conductors (metals), insulators (dielectrics) or semiconductors. Optical devices may have films which are reflective, transparent, light guiding or scattering. Films may also have a chemical or mechanical purpose as well as for MEMS applications. Examples of deposition techniques include:

Patterning

It is often desirable to pattern a film into distinct features or to form openings (or vias) in some of the layers. These features are on the micrometer or nanometer scale and the patterning technology is what defines microfabrication. This patterning technique typically uses a 'mask' to define portions of the film which will be removed. Examples of patterning techniques include:

Photolithography
Shadow masking

Etching

Etching is the removal of some portion of the thin film or substrate. The substrate is exposed to an etching (such as an acid or plasma) which chemically or physically attacks the film until it is removed. Etching techniques include:

Dry etching (plasma etching) such as reactive-ion etching (RIE) or deep reactive-ion etching (DRIE)
Wet etching or chemical etching

Microforming

Microforming is a microfabrication process of microsystem or microelectromechanical system (MEMS) "parts or structures with at least two dimensions in the submillimeter range."^[3]^[4]^[5] It includes techniques such as microextrusion,^[4] microstamping,^[6] and microcutting.^[7] These and other microforming processes have been envisioned and researched since at least 1990,^[3] leading to the development of industrial- and experimental-grade manufacturing tools. However, as Fu and Chan pointed out in a 2013 state-of-the-art technology review, several issues must still be resolved before the technology can be implemented more widely, including deformation load and defects, forming system stability, mechanical properties, and other size-related effects on the crystallite (grain) structure and boundaries:^[4]^[5]^[8]

In microforming, the ratio of the total surface area of grain boundaries to the material volume decreases with the decrease of specimen size and the increase of grain size. This leads to the decrease of grain boundary strengthening effect. Surface grains have lesser constraints compared to internal grains. The change of flow stress with part geometry size is partly attributed to the change of volume fraction of surface grains. In addition, the anisotropic properties of each grain become significant with the decrease of workpiece size, which results in the inhomogeneous deformation, irregular formed geometry and the variation of deformation load. There is a critical need to establish the systematic knowledge of microforming to support the design of part, process, and tooling with the consideration of size effects.^[8]

Other

a wide variety of other processes for cleaning, planarizing, or modifying the chemical properties of microfabricated devices can also be performed. Some examples include:

Doping by either thermal diffusion or ion implantation
Chemical-mechanical planarization (CMP)
Wafer cleaning, also known as "surface preparation" (see below)
Wire bonding

Cleanliness in wafer fabrication

Microfabrication is carried out in cleanrooms, where air has been filtered of particle contamination and temperature, humidity, vibrations and electrical disturbances are under stringent control. Smoke, dust, bacteria and cells are micrometers in size, and their presence will destroy the functionality of a microfabricated device.

Cleanrooms provide passive cleanliness but the wafers are also actively cleaned before every critical step. RCA-1 clean in ammonia-peroxide solution removes organic contamination and particles; RCA-2 cleaning in hydrogen chloride-peroxide mixture removes metallic impurities. Sulfuric acid-peroxide mixture (a.k.a. Piranha) removes organics. Hydrogen fluoride removes native oxide from silicon surface. These are all wet cleaning steps in solutions. Dry cleaning methods include oxygen and argon plasma treatments to remove unwanted surface layers, or hydrogen bake at elevated temperature to remove native oxide before epitaxy. Pre-gate cleaning is the most critical cleaning step in CMOS fabrication: it ensures that the ca. 2 nm thick oxide of a MOS transistor can be grown in an orderly fashion. Oxidation, and all high temperature steps are very sensitive to contamination, and cleaning steps must precede high temperature steps.

Surface preparation is just a different viewpoint, all the steps are the same as described above: it is about leaving the wafer surface in a controlled and well known state before you start processing. Wafers are contaminated by previous process steps (e.g. metals bombarded from chamber walls by energetic ions during ion implantation), or they may have gathered polymers from wafer boxes, and this might be different depending on wait time.

Wafer cleaning and surface preparation work similarly to the machines in a bowling alley: first they remove all unwanted bits and pieces, and then they reconstruct the desired pattern so that the game can go on.

Rapid prototyping

Much like their macroscopic analog, microstructures can be produced using rapid prototyping methods. These techniques generally involve the layering of some resin, with each layer being much thinner than that used for conventional processes in order to produce higher resolution microscopic components. Layers in processes such as electrochemical fabrication can be as thin as 5 to 10 μm.^[2] The creation of microscopic structures is similar to conventional additive manufacturing techniques in that a computer aided design model is sliced into an appropriate number of two-dimensional layers in order to create a toolpath. This toolpath is then followed by a mechanical system to produce the desired geometry.

A popular application is stereolithography (SLA), which involves the use of a UV light or laser beam on a surface to create a layer, which are then lowered into a tank so that a new layer can be formed on top. Another commonly used method is fused deposition modeling (FDM), in which a moving head creates a layer by melting the model material (usually a polymer) and extrudes the melted material onto a surface. Other methods such as selective laser sintering (SLS) are also used in the additive manufacturing of 3D microstructures.^[1]

3D laser microfabrication

Setup of a typical laser microfabrication

Laser-based techniques are the most common approach for producing microstructures. Typical techniques involve the use of lasers to add or subtract material from a bulk sample. Recent applications of lasers involve the use of ultrashort pulses of lasers focused to a small area in order to create a pattern that is layered to create a structure. The use of lasers in such a manner is known as laser direct-writing (LDW). Microscopic mechanical elements such as micromotors, micropumps, and other microfluidic devices can be produced using direct-write concepts. In addition to additive and subtractive processes, LDW allows for the modification of the properties of a material. Mechanisms that allow for these modifications include sintering, microstereolithography, and multiphoton processes. These use a series of laser pulses to deliver a precise amount of energy to induce a physical or chemical change that can result in annealing and surface structuring of a material.^[3]

Microstereolithography

Microstereolithography is a common technique based on stereolithography principles. 3D components are fabricated by repeatedly layering photopolymerizable resin and curing under an ultraviolet laser. Earlier systems that employ this technique use a scanning principle in which a focused light beam is fixed onto one location and the translation stage moves to fabricate each layer vector by vector. A faster alternate involves using a projection principle in which the image is projected onto the surface of the resin so that the irradiation of a layer is done in one step only. The high-resolution results allow for the fabrication of complex shapes that would otherwise be difficult to produce at such small scales.^[1]

Multiphoton lithography

Multiphoton lithography can be used to 3D print structures with sub-micrometer resolution. The process uses the focal point of a laser to photopolymerize the resin or glass at a specific point. By moving the focal point around in three dimensional space and solidifying the medium at different points, the desired geometry can be built. There are currently limits to the resolution of the features in geometries built through this method. The limits relate to the medium that the geometry is being constructed from as well as the precision of the focal point of the laser.^[3]

Other additive processes

Additive processes involve the layering of materials in a certain pattern. These include laser chemical vapor deposition (LCVD), which use organic precursors to write patterns on a structure or bulk material. This application can be found in the field of electronics, particularly in the repair of transistor arrays for displays. Another additive process is laser-induced forward transfer (LIFT), which uses pulsed lasers aimed at a coated substrate to transfer material in the direction of the laser flow.^[1] LIFT has been used to produce transfer thermo-electric materials, polymers^[4] and has been used to print copper wires. ^[5]

With inclined/rotated UV lithography

Focus on the 3D microstructures now, it have been focused in a lot of microsystems like electronic, mechanical, micro-optical and analysis systems. And when this technology is developing, we found that the traditional and conventional micro machining technologies like surface micromachining, bulk micromachining and GIGA process are not sufficient to fabricate or produce oblique and curved 3D microstructures.^[6]

Fabrication

The basic setup of inclined UV exposure has conventional UV source, a contact stage, and a tilting stage. Plus, we place a photomask and a photoresist coated substrate between the upper and lower plates of the contact stage, and it is fixed by pushing up the lower plate with a screw. Then, we can expose the photoresist to the inclined UV.

An example of the fabrication process: Su-8 is a negative thick photoresist, which used in novel 3D micro fabrication method with inclined/rotated UV lithography. During the process, we coat SU-8 50 on a silicon wafer with a thickness of about 100ųm. Then, soft bake the resist on a 65 °C hot plate for 10 minutes and on a 95 °C plate for 30 minutes. It is contacted with a photomask using the contact stage. This stage, is leaned against the tilting stage and the resist is exposed to the UV. The dose of 365 nm UV is 500mJ/cm². After the exposure, the resist is post-exposure baked on a 65 °C hot plate for 3 minutes and on a 95 °C plate for 10 minutes. In the end, the resist is developed in the SU-8 for about 10 to 15 minutes at the room temperature with mild agitation and then, rinsed with isopropyl alcohol. Besides that, there can be a lot of other procedures. For example, inclined UV lithography, inclined and rotated UV lithography and lithography using reflected UV.

When the trace of the incident UV with a right angle is on a straight line, so the patterns of a photomask are transcribed to the resist. When talking about inclined UV exposure processes, the UV is refracted and reflected, this makes it possible to fabricate various of 3D structures. The microstructures fabricated by the 3D micro fabrication technology can be allied to a lot of microsystems directly. Also, it can be used as the molds for electroplating. As a result, these technology can be applied to a variety of fields like filters, mixers, jets, micro channels, light guide panels of LCD monitor and more.

Self-folding materials

Design of complicated 3D microstructure can be highly challenging task for development of novel materials for optics, biotechnology and micro/nano electronics. 3D materials can be fabricated using a lot of methods like two-photon photolithography, interference lithography and molding. But 3D structuring using these techniques is very complicated, experimentally. This can limit their upscaling and broad applicability.

Nature offers a large number of ideas for the design of novel materials with superior properties. Self-assembly and self-organization being the main principle of structure formation in nature attract significant interest as promising concepts for the design of intelligent materials.

Stimuli-responsive hydrogels mimic swelling/shrinking behavior of plant cells and produce macroscopic actuation in response to a small variation of environmental conditions. Mostly, homogenous expansion or contraction in all directions can result a change of conditions. Also, inhomogeneous expansion and shrinkage can result more complex behavior like bending, twisting and folding and they can happen with different magnitudes in different directions. Utilization of these phenomena for the design of structured materials can be highly attractive because they allow simple, template-free fabrication of very complex repetitive 2D and 3D patterns. However, they cannot be prepared by using sophisticated fabrication methods like two-photon and interference photolithography as mentioned before. There is an advantage of the self-folding approach, is the possibility of quick, reversible, and reproducible fabrication of 3D hollow objects with controlled chemical properties and morphology of both the exterior and the interior.

One experimental application of self-folding materials is pasta that ships flat but folds into the desired shape on contact with boiling water.^[7]

Outlook

One factor that limit broad applicability of self-folding polymer films is the manufacturing cost. Actually, polymer can be deposited by spinning and dipping coating at ambient conditions, the fabrication of polymer self-folding films is substantially cheaper than fabrication of inorganic ones, which are produced by vacuum deposition. In another word, there is no method, which is cheap and large-scale production of self-folding polymer films that substantially limits their application.

To solve these issues, the future research must be focused on deeper investigation of folding to allow design of complex 3D structures using just 2D shapes. On the other hand, searching a way, which is cheap and fast manufacturing of large quantity of self-folding films can be greatly helpful.^[8]

References

Baldacchini, Tommasso, ed. (2016). Three-Dimensional Microfabrication Using Two-Photon Polymerization: Fundamentals, Technology, and Applications. Elsevier. ISBN 978-0-323-35321-2.

Groover, Mikell (2012). Fundamentals of Modern Manufacturing: Materials, Processes, and Systems (5 ed.). Wiley. p. 846. ISBN 978-1118231463.

Misawa, Hiroaki, ed. (2006). 3D Laser Microfabrication: Principles and Applications. Germany: Wiley. ISBN 978-3-527-31055-5.

Heath, Daniel J; Feinaeugle, Matthias; Grant-Jacob, James A; Mills, Ben; Eason, Robert W (2015-05-01). "Dynamic spatial pulse shaping via a digital micromirror device for patterned laser-induced forward transfer of solid polymer films". Optical Materials Express. 5 (5): 1129. doi:10.1364/OME.5.001129. ISSN 2159-3930.

Grant-Jacob, James A.; Mills, Benjamin; Feinaeugle, Matthias; Sones, Collin L.; Oosterhuis, Gerrit; Hoppenbrouwers, Marc B.; Eason, Robert W. (2013-06-01). "Micron-scale copper wires printed using femtosecond laser-induced forward transfer with automated donor replenishment". Optical Materials Express. 3 (6): 747–754. doi:10.1364/OME.3.000747. ISSN 2159-3930.

Han, Manhee (2004). Sensors and Actuators A: Physical.

Nanos, Janelle (June 5, 2017), "MIT researchers develop a shape-shifting pasta", The Boston Globe

Ionov, Leonid (2013). Polymer Reviews, 2013, Vol.53(1). Germany: Taylor & Francis Group. pp. 92–107.

Categories:

https://en.wikipedia.org/wiki/3D_microfabrication

https://en.wikipedia.org/wiki/Integrated_circuit

https://en.wikipedia.org/wiki/Epitaxy

https://en.wikipedia.org/wiki/Evaporation_(deposition)

https://en.wikipedia.org/wiki/Sputter_deposition

https://en.wikipedia.org/wiki/Chemical_vapor_deposition

https://en.wikipedia.org/wiki/LOCOS

https://en.wikipedia.org/wiki/Polymerization

https://en.wikipedia.org/wiki/Multiphoton_lithography

https://en.wikipedia.org/wiki/Selective_laser_sintering

https://en.wikipedia.org/wiki/Fused_filament_fabrication#Fused_deposition_modeling

https://en.wikipedia.org/wiki/Stereolithography

Because of the large surface area to volume ratio of MEMS, forces produced by ambient electromagnetism (e.g., electrostatic charges and magnetic moments), and fluid dynamics (e.g., surface tension and viscosity) are more important design considerations than with larger scale mechanical devices. MEMS technology is distinguished from molecular nanotechnology or molecular electronics in that the latter two must also consider surface chemistry.

https://en.wikipedia.org/wiki/MEMS

The digital micromirror device, or DMD, is the microoptoelectromechanical system (MOEMS) that is the core of the trademarked DLP projection technology from Texas Instruments (TI). Texas Instrument's DMD was created by solid-state physicist and TI Fellow Emeritus Dr. Larry Hornbeck in 1987.^[1] However, the technology goes back to 1973 with Harvey C. Nathanson's (inventor of MEMS c. 1965) use of millions of microscopically small moving mirrors to create a video display of the type now found in digital projectors.^[2]

^{https://en.wikipedia.org/wiki/Digital_micromirror_device}

History

The DMD project began as the deformable mirror device in 1977 using micromechanical analog light modulators. The first analog DMD product was the TI DMD2000 airline ticket printer that used a DMD instead of a laser scanner.^[3]

Construction and use

A DMD chip has on its surface several hundred thousand microscopic mirrors arranged in a rectangular array which correspond to the pixels in the image to be displayed. The mirrors can be individually rotated ±10-12°, to an on or off state. In the on state, light from the projector bulb is reflected into the lens making the pixel appear bright on the screen. In the off state, the light is directed elsewhere (usually onto a heatsink), making the pixel appear dark. To produce greyscales, the mirror is toggled on and off very quickly, and the ratio of on time to off time determines the shade produced (binary pulse-width modulation).^[4] Contemporary DMD chips can produce up to 1024 shades of gray (10 bits).^[5] See Digital Light Processing for discussion of how color images are produced in DMD-based systems.

Diagram of a digital micromirror showing the mirror mounted on the suspended yoke with the torsion spring running bottom left to top right (light grey), with the electrostatic pads of the memory cells below (top left and bottom right)

The mirrors themselves are made of aluminum and are around 16 micrometers across. Each mirror is mounted on a yoke which in turn is connected to two support posts by compliant torsion hinges. In this type of hinge, the axle is fixed at both ends and twists in the middle. Because of the small scale, hinge fatigue is not a problem, and tests have shown that even 1 trillion (10¹²) operations do not cause noticeable damage. Tests have also shown that the hinges cannot be damaged by normal shock and vibration, since it is absorbed by the DMD superstructure.^[6]

Two pairs of electrodes control the position of the mirror by electrostatic attraction. Each pair has one electrode on each side of the hinge, with one of the pairs positioned to act on the yoke and the other acting directly on the mirror. The majority of the time, equal bias charges are applied to both sides simultaneously. Instead of flipping to a central position as one might expect, this actually holds the mirror in its current position. This is because the attraction force on the side the mirror is already tilted towards is greater since that side is closer to the electrodes.^[7]

To move the mirrors, the required state is first loaded into an SRAM cell located beneath each pixel, which is also connected to the electrodes. Once all the SRAM cells have been loaded, the bias voltage is removed, allowing the charges from the SRAM cell to prevail, moving the mirror. When the bias is restored, the mirror is once again held in position, and the next required movement can be loaded into the memory cell.

The bias system is used because it reduces the voltage levels required to address the pixels such that they can be driven directly from the SRAM cell, and also because the bias voltage can be removed at the same time for the whole chip, so every mirror moves at the same instant. The advantages of the latter are more accurate timing and a more cinematic moving image.

A broken DMD chip showing the "white dots" appearing on screen as "white pixels".

The described failure mode on these is caused by internal contamination usually due to seal failure corroding the mirror supports. A related failure was the glue used between 2007 and 2013, under which heat and light degrades and outgasses: this normally causes fogging inside the glass and eventually white/black pixels. This cannot usually be repaired, but defective DMD chips can sometimes be used for less critical projects not needing rapidly changing patterns if the existing bad pixels can be made part of the projected image or otherwise mapped out, including 3D scanning. ^[8]

Applications

https://en.wikipedia.org/wiki/Digital_micromirror_device

Technique

Three primary components in the application of optogenetics are as follows (A) Identification or synthesis of a light-sensitive protein (opsin) such as channelrhodopsin-2 (ChR2), halorhodopsin (NpHR), etc… (B) The design of a system to introduce the genetic material containing the opsin into cells for protein expression such as application of Cre recombinase or an adeno-associated-virus (C) application of light emitting instruments.^[79]

The technique of using optogenetics is flexible and adaptable to the experimenter's needs. Cation-selective channelrhodopsins (e.g. ChR2) are used to excite neurons, anion-conducting channelrhodopsins (e.g. GtACR2) inhibit neuronal activity. Combining these tools into a single construct (e.g. BiPOLES) allows for both inhibition and excitation, depending on the wavelength of illumination.^[80]

Introducing the microbial opsin into a specific subset of cells is challenging. A popular approach is to introduce an engineered viral vector that contains the optogenetic actuator gene attached to a specific promoter such as CAMKIIα, which is active in excitatory neurons. This allows for some level of specificity, preventing e.g. expression in glia cells.^[81]

A more specific approach is based on transgenic "driver" mice which express Cre recombinase, an enzyme that catalyzes recombination between two lox-P sites, in a specific subset of cells, e.g. parvalbumin-expressing interneurons. By introducing an engineered viral vector containing the optogenetic actuator gene in between two lox-P sites, only the cells producing Cre recombinase will express the microbial opsin. This technique has allowed for multiple modified optogenetic actuators to be used without the need to create a whole line of transgenic animals every time a new microbial opsin is needed.^[82]

After the introduction and expression of the microbial opsin, a computer-controlled light source has to be optically coupled to the brain region in question. Light-emitting diodes (LEDs) or fiber-coupled diode-pumped solid-state lasers (DPSS) are frequently used. Recent advances include the advent of wireless head-mounted devices that apply LEDs to the targeted areas and as a result, give the animals more freedom to move.^[83]^[84]

Fiber-based approaches can also be used to combine optical stimulation and calcium imaging.^[77] This enables researchers to visualize and manipulate the activity of single neurons in awake behaving animals.^[85] It is also possible to record from multiple deep brain regions at the same using GRIN lenses connected via optical fiber to an externally positioned photodetector and photostimulator.^[86]^[87]

https://en.wikipedia.org/wiki/Optogenetics#Technique

Optogenetics is a biological technique to control the activity of neurons or other cell types with light. This is achieved by expression of light-sensitive ion channels, pumps or enzymes specifically in the target cells. On the level of individual cells, light-activated enzymes and transcription factors allow precise control of biochemical signaling pathways.^[1] In systems neuroscience, the ability to control the activity of a genetically defined set of neurons has been used to understand their contribution to decision making,^[2] learning,^[3] fear memory,^[4] mating,^[5] addiction,^[6] feeding,^[7] and locomotion.^[8] In a first medical application of optogenetic technology, vision was partially restored in a blind patient.^[9]

Optogenetic techniques have also been introduced to map the functional connectivity of the brain.^[10]^[11] By altering the activity of genetically labelled neurons with light and using imaging and electrophysiology techniques to record the activity of other cells, researchers can identify the statistical dependencies between cells and brain regions.^[12]^[13]

In a broader sense, optogenetics also includes methods to record cellular activity with genetically encoded indicators.

In 2010, optogenetics was chosen as the "Method of the Year" across all fields of science and engineering by the interdisciplinary research journal Nature Methods.^[14] At the same time, optogenetics was highlighted in the article on "Breakthroughs of the Decade" in the academic research journal Science.^[15]^[16]^[17]

Description

Fig 1. Channelrhodopsin-2 (ChR2) induces temporally precise blue light-driven activity in rat prelimbic prefrontal cortical neurons. a) In vitro schematic (left) showing blue light delivery and whole-cell patch-clamp recording of light-evoked activity from a fluorescent CaMKllα::ChR2-EYFP expressing pyramidal neuron (right) in an acute brain slice. b) In vivo schematic (left) showing blue light (473 nm) delivery and single-unit recording. (bottom left) Coronal brain slice showing expression of CaMKllα::ChR2-EYFP in the prelimbic region. Light blue arrow shows tip of the optical fiber; black arrow shows tip of the recording electrode (left). White bar, 100 µm. (bottom right) In vivo light recording of prefrontal cortical neuron in a transduced CaMKllα::ChR2-EYFP rat showing light-evoked spiking to 20 Hz delivery of blue light pulses (right). Inset, representative light-evoked single-unit response.^[56]

Fig 2. Halorhodopsin (NpHR) rapidly and reversibly silences spontaneous activity in vivo in rat prelimbic prefrontal cortex. (Top left) Schematic showing in vivo green (532 nm) light delivery and single- unit recording of a spontaneously active CaMKllα::eNpHR3.0- EYFP expressing pyramidal neuron. (Right) Example trace showing that continuous 532 nm illumination inhibits single-unit activity in vivo. Inset, representative single unit event; Green bar, 10 seconds.^[56]

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A nematode expressing the light-sensitive ion channel Mac. Mac is a proton pump originally isolated in the fungus Leptosphaeria maculans and now expressed in the muscle cells of C. elegans that opens in response to green light and causes hyperpolarizing inhibition. Of note is the extension in body length that the worm undergoes each time it is exposed to green light, which is presumably caused by Mac's muscle-relaxant effects.^[57]

A nematode expressing ChR2 in its gubernacular-oblique muscle group responding to stimulation by blue light. Blue light stimulation causes the gubernacular-oblique muscles to repeatedly contract, causing repetitive thrusts of the spicule, as would be seen naturally during copulation.^[58]

Optogenetics provides millisecond-scale temporal precision which allows the experimenter to keep pace with fast biological information processing (for example, in probing the causal role of specific action potential patterns in defined neurons). Indeed, to probe the neural code, optogenetics by definition must operate on the millisecond timescale to allow addition or deletion of precise activity patterns within specific cells in the brains of intact animals, including mammals (see Figure 1). By comparison, the temporal precision of traditional genetic manipulations (employed to probe the causal role of specific genes within cells, via "loss-of-function" or "gain of function" changes in these genes) is rather slow, from hours or days to months. It is important to also have fast readouts in optogenetics that can keep pace with the optical control. This can be done with electrical recordings ("optrodes") or with reporter proteins that are biosensors, where scientists have fused fluorescent proteins to detector proteins. Additionally, beyond its scientific impact optogenetics represents an important case study in the value of both ecological conservation (as many of the key tools of optogenetics arise from microbial organisms occupying specialized environmental niches), and in the importance of pure basic science as these opsins were studied over decades for their own sake by biophysicists and microbiologists, without involving consideration of their potential value in delivering insights into neuroscience and neuropsychiatric disease.^[59]

Light-activated proteins: channels, pumps and enzymes

The hallmark of optogenetics therefore is introduction of fast light-activated channels, pumps, and enzymes that allow temporally precise manipulation of electrical and biochemical events while maintaining cell-type resolution through the use of specific targeting mechanisms. Among the microbial opsins which can be used to investigate the function of neural systems are the channelrhodopsins (ChR2, ChR1, VChR1, and SFOs) to excite neurons and anion-conducting channelrhodopsins for light-induced inhibition. Indirectly light-controlled potassium channels have recently been engineered to prevent action potential generation in neurons during blue light illumination.^[60]^[61] Light-driven ion pumps are also used to inhibit neuronal activity, e.g. halorhodopsin (NpHR),^[62] enhanced halorhodopsins (eNpHR2.0 and eNpHR3.0, see Figure 2),^[63] archaerhodopsin (Arch), fungal opsins (Mac) and enhanced bacteriorhodopsin (eBR).^[64]

Optogenetic control of well-defined biochemical events within behaving mammals is now also possible. Building on prior work fusing vertebrate opsins to specific G-protein coupled receptors^[65] a family of chimeric single-component optogenetic tools was created that allowed researchers to manipulate within behaving mammals the concentration of defined intracellular messengers such as cAMP and IP3 in targeted cells.^[66] Other biochemical approaches to optogenetics (crucially, with tools that displayed low activity in the dark) followed soon thereafter, when optical control over small GTPases and adenylyl cyclase was achieved in cultured cells using novel strategies from several different laboratories.^[67]^[68]^[69] Photoactivated adenylyl cyclases have been discovered in fungi and successfully used to control cAMP levels in mammalian neurons.^[70]^[71] This emerging repertoire of optogenetic actuators now allows cell-type-specific and temporally precise control of multiple axes of cellular function within intact animals.^[72]

Hardware for light application

Another necessary factor is hardware (e.g. integrated fiberoptic and solid-state light sources) to allow specific cell types, even deep within the brain, to be controlled in freely behaving animals. Most commonly, the latter is now achieved using the fiberoptic-coupled diode technology introduced in 2007,^[73]^[74]^[75] though to avoid use of implanted electrodes, researchers have engineered ways to inscribe a "window" made of zirconia that has been modified to be transparent and implanted in mice skulls, to allow optical waves to penetrate more deeply to stimulate or inhibit individual neurons.^[76] To stimulate superficial brain areas such as the cerebral cortex, optical fibers or LEDs can be directly mounted to the skull of the animal. More deeply implanted optical fibers have been used to deliver light to deeper brain areas.^[77] Complementary to fiber-tethered approaches, completely wireless techniques have been developed utilizing wirelessly delivered power to headborne LEDs for unhindered study of complex behaviors in freely behaving organisms.^[78]

Expression of optogenetic actuators

Optogenetics also necessarily includes the development of genetic targeting strategies such as cell-specific promoters or other customized conditionally-active viruses, to deliver the light-sensitive probes to specific populations of neurons in the brain of living animals (e.g. worms, fruit flies, mice, rats, and monkeys). In invertebrates such as worms and fruit flies some amount of all-trans-retinal (ATR) is supplemented with food. A key advantage of microbial opsins as noted above is that they are fully functional without the addition of exogenous co-factors in vertebrates.^[75]

Technique

Technical challenges

Selective expression

One of the main problems of optogenetics is that not all the cells in question may express the microbial opsin gene at the same level. Thus, even illumination with a defined light intensity will have variable effects on individual cells. Optogenetic stimulation of neurons in the brain is even less controlled as the light intensity drops exponentially from the light source (e.g. implanted optical fiber).

It remains difficult to target opsin to defined subcellular compartments, e.g. the plasma membrane, synaptic vesicles, or mitochondria.^[63]^[88] Restricting the opsin to specific regions of the plasma membrane such as dendrites, somata or axon terminals provides a more robust understanding of neuronal circuitry.^[88]

Mathematical modelling shows that selective expression of opsin in specific cell types can dramatically alter the dynamical behavior of the neural circuitry. In particular, optogenetic stimulation that preferentially targets inhibitory cells can transform the excitability of the neural tissue, affecting non-transfected neurons as well.^[89]

Kinetics and synchronization

The original channelrhodopsin-2 was slower closing than typical cation channels of cortical neurons, leading to prolonged depolarization and calcium influx.^[90] Many channelrhodopsin variants with more favorable kinetics have since been engineered.^[55][56]

A difference between natural spike patterns and optogenetic activation is that pulsed light stimulation produces synchronous activation of expressing neurons, which removes the possibility of sequential activity in the stimulated population. Therefore, it is difficult to understand how the cells in the population affected communicate with one another or how their phasic properties of activation relate to circuit function.

Optogenetic activation has been combined with functional magnetic resonance imaging (ofMRI) to elucidate the connectome, a thorough map of the brain's neural connections.^[88]^[91] Precisely timed optogenetic activation is used to calibrate the delayed hemodynamic signal (BOLD) fMRI is based on.

Light absorption spectrum

The opsin proteins currently in use have absorption peaks across the visual spectrum, but remain considerably sensitive to blue light.^[88] This spectral overlap makes it very difficult to combine opsin activation with genetically encoded indicators (GEVIs, GECIs, GluSnFR, synapto-pHluorin), most of which need blue light excitation. Opsins with infrared activation would, at a standard irradiance value, increase light penetration and augment resolution through reduction of light scattering.

Spatial response

Due to scattering, a narrow light beam to stimulate neurons in a patch of neural tissue can evoke a response profile that is much broader than the stimulation beam.^[92] In this case, neurons may be activated (or inhibited) unintentionally. Computational simulation tools^[93]^[94] are used to estimate the volume of stimulated tissue for different wavelengths of light.

Applications

The field of optogenetics has furthered the fundamental scientific understanding of how specific cell types contribute to the function of biological tissues such as neural circuits in vivo. On the clinical side, optogenetics-driven research has led to insights into Parkinson's disease^[95]^[96] and other neurological and psychiatric disorders such as autism, Schizophrenia, drug abuse, anxiety, and depression.^[64]^[97]^[98]^[99] An experimental treatment for blindness involves a channel rhodopsin expressed in ganglion cells, stimulated with light patterns from engineered goggles.^[100]^[9]

Identification of particular neurons and networks

Amygdala

Optogenetic approaches have been used to map neural circuits in the amygdala that contribute to fear conditioning.^[101]^[102]^[103]^[104] One such example of a neural circuit is the connection made from the basolateral amygdala to the dorsal-medial prefrontal cortex where neuronal oscillations of 4 Hz have been observed in correlation to fear induced freezing behaviors in mice. Transgenic mice were introduced with channelrhodoposin-2 attached with a parvalbumin-Cre promoter that selectively infected interneurons located both in the basolateral amygdala and the dorsal-medial prefrontal cortex responsible for the 4 Hz oscillations. The interneurons were optically stimulated generating a freezing behavior and as a result provided evidence that these 4 Hz oscillations may be responsible for the basic fear response produced by the neuronal populations along the dorsal-medial prefrontal cortex and basolateral amygdala.^[105]

Olfactory bulb

Optogenetic activation of olfactory sensory neurons was critical for demonstrating timing in odor processing^[106] and for mechanism of neuromodulatory mediated olfactory guided behaviors (e.g. aggression, mating)^[107] In addition, with the aid of optogenetics, evidence has been reproduced to show that the "afterimage" of odors is concentrated more centrally around the olfactory bulb rather than on the periphery where the olfactory receptor neurons would be located. Transgenic mice infected with channel-rhodopsin Thy1-ChR2, were stimulated with a 473 nm laser transcranially positioned over the dorsal section of the olfactory bulb. Longer photostimulation of mitral cells in the olfactory bulb led to observations of longer lasting neuronal activity in the region after the photostimulation had ceased, meaning the olfactory sensory system is able to undergo long term changes and recognize differences between old and new odors.^[108]

Nucleus accumbens

Optogenetics, freely moving mammalian behavior, in vivo electrophysiology, and slice physiology have been integrated to probe the cholinergic interneurons of the nucleus accumbens by direct excitation or inhibition. Despite representing less than 1% of the total population of accumbal neurons, these cholinergic cells are able to control the activity of the dopaminergic terminals that innervate medium spiny neurons (MSNs) in the nucleus accumbens.^[109] These accumbal MSNs are known to be involved in the neural pathway through which cocaine exerts its effects, because decreasing cocaine-induced changes in the activity of these neurons has been shown to inhibit cocaine conditioning. The few cholinergic neurons present in the nucleus accumbens may prove viable targets for pharmacotherapy in the treatment of cocaine dependence^[64]

Prefrontal cortex

Cages for rat equipped with optogenetic led commutators which permit in vivo study of animal behavior during optogenetic stimulations.

In vivo and in vitro recordings from the University of Colorado, Boulder Optophysiology Laboratory of Donald C. Cooper Ph.D. showing individual CAMKII AAV-ChR2 expressing pyramidal neurons within the prefrontal cortex that demonstrated high fidelity action potential output with short pulses of blue light at 20 Hz (Figure 1).^[56]

Motor cortex

In vivo repeated optogenetic stimulation in healthy animals was able to eventually induce seizures.^[110] This model has been termed optokindling.

Piriform cortex

In vivo repeated optogenetic stimulation of pyramidal cells of the piriform cortex in healthy animals was able to eventually induce seizures.^[111] In vitro studies have revealed a loss of feedback inhibition in the piriform circuit due to impaired GABA synthesis.^[111]

Heart

Optogenetics was applied on atrial cardiomyocytes to end spiral wave arrhythmias, found to occur in atrial fibrillation, with light.^[112] This method is still in the development stage. A recent study explored the possibilities of optogenetics as a method to correct for arrythmias and resynchronize cardiac pacing. The study introduced channelrhodopsin-2 into cardiomyocytes in ventricular areas of hearts of transgenic mice and performed in vitro studies of photostimulation on both open-cavity and closed-cavity mice. Photostimulation led to increased activation of cells and thus increased ventricular contractions resulting in increasing heart rates. In addition, this approach has been applied in cardiac resynchronization therapy (CRT) as a new biological pacemaker as a substitute for electrode based-CRT.^[113] Lately, optogenetics has been used in the heart to defibrillate ventricular arrhythmias with local epicardial illumination,^[114] a generalized whole heart illumination^[115] or with customized stimulation patterns based on arrhythmogenic mechanisms in order to lower defibrillation energy.^[116]

Spiral ganglion

Optogenetic stimulation of the spiral ganglion in deaf mice restored auditory activity.^[117] Optogenetic application onto the cochlear region allows for the stimulation or inhibition of the spiral ganglion cells (SGN). In addition, due to the characteristics of the resting potentials of SGN's, different variants of the protein channelrhodopsin-2 have been employed such as Chronos,^[118] CatCh and f-Chrimson.^[119] Chronos and CatCh variants are particularly useful in that they have less time spent in their deactivated states, which allow for more activity with less bursts of blue light emitted. Additionally, using engineered red-shifted channels as f-Chrimson allow for stimulation using longer wavelengths, which decreases the potential risks of phototoxicity in the long term without compromising gating speed.^[120] The result being that the LED producing the light would require less energy and the idea of cochlear prosthetics in association with photo-stimulation, would be more feasible.^[121]

Brainstem

Optogenetic stimulation of a modified red-light excitable channelrhodopsin (ReaChR) expressed in the facial motor nucleus enabled minimally invasive activation of motoneurons effective in driving whisker movements in mice.^[122] One novel study employed optogenetics on the Dorsal Raphe Nucleus to both activate and inhibit dopaminergic release onto the ventral tegmental area. To produce activation transgenic mice were infected with channelrhodopsin-2 with a TH-Cre promoter and to produce inhibition the hyperpolarizing opsin NpHR was added onto the TH-Cre promoter. Results showed that optically activating dopaminergic neurons led to an increase in social interactions, and their inhibition decreased the need to socialize only after a period of isolation.^[123]

Visual system

Studying the visual system using optogenetics can be challenging. Indeed, the light used for optogenetic control may lead to the activation of photoreceptors, as a result of the proximity between primary visual circuits and these photoreceptors. In this case, spatial selectivity is difficult to achieve (particularly in the case of the fly optic lobe). Thus, the study of the visual system requires spectral separation, using channels that are activated by different wavelengths of light than rhodopsins within the photoreceptors (peak activation at 480 nm for Rhodopsin 1 in Drosophila). Red-shifted CsChrimson^[124] or bistable Channelrhodopsin^[125] are used for optogenetic activation of neurons (i.e. depolarization), as both allow spectral separation. In order to achieve neuronal silencing (i.e. hyperpolarization), an anion channelrhodopsin discovered in the cryptophyte algae species Guillardia theta (named GtACR1).^[126] can be used. GtACR1 is more light sensitive than other inhibitory channels such as the Halorhodopsin class of chlorid pumps and imparts a strong conductance. As its activation peak (515 nm) is close to that of Rhodopsin 1, it is necessary to carefully calibrate the optogenetic illumination as well as the visual stimulus. The factors to take into account are the wavelength of the optogenetic illumination (possibly higher than the activation peak of GtACR1), the size of the stimulus (in order to avoid the activation of the channels by the stimulus light) and the intensity of the optogenetic illumination. It has been shown that GtACR1 can be a useful inhibitory tool in optogenetic study of Drosophila's visual system by silencing T4/T5 neurons expression.^[127] These studies can also be led on intact behaving animals, for instance to probe optomotor response.

Sensorimotor system

Optogenetically inhibiting or activating neurons tests their necessity and sufficiency, respectively, in generating a behavior.^[128] Using this approach, researchers can dissect the neural circuitry controlling motor output. By perturbing neurons at various places in the sensorimotor system, researchers have learned about the role of descending neurons in eliciting stereotyped behaviors,^[129] how localized tactile sensory input^[130] and activity of interneurons^[131] alters locomotion, and the role of Purkinje cells in generating and modulating movement.^[132] This is a powerful technique for understanding the neural underpinnings of animal locomotion and movement more broadly.

Precise temporal control of interventions

The currently available optogenetic actuators allow for the accurate temporal control of the required intervention (i.e. inhibition or excitation of the target neurons) with precision routinely going down to the millisecond level.^[133] The temporal precision varies, however, across optogenetic actuators,^[134] and depends on the frequency and intensity of the stimulation.^[92]

Experiments can now be devised where the light used for the intervention is triggered by a particular element of behavior (to inhibit the behavior), a particular unconditioned stimulus (to associate something to that stimulus) or a particular oscillatory event in the brain (to inhibit the event).^[135]^[136] This kind of approach has already been used in several brain regions:

Hippocampus

Sharp waves and ripple complexes (SWRs) are distinct high frequency oscillatory events in the hippocampus thought to play a role in memory formation and consolidation. These events can be readily detected by following the oscillatory cycles of the on-line recorded local field potential. In this way the onset of the event can be used as a trigger signal for a light flash that is guided back into the hippocampus to inhibit neurons specifically during the SWRs and also to optogenetically inhibit the oscillation itself.^[137] These kinds of "closed-loop" experiments are useful to study SWR complexes and their role in memory.

Cellular biology/cell signaling pathways

0:10

Optogenetic control of cellular forces and induction of mechanotransduction.^[138] Pictured cells receive an hour of imaging concurrent with blue light that pulses every 60 seconds. This is also indicated when the blue point flashes onto the image. The cell relaxes for an hour without light activation and then this cycle repeats again. The square inset magnifies the cell's nucleus.

Analogously to how natural light-gated ion channels such as channelrhodopsin-2 allows optical control of ion flux, which is especially useful in neuroscience, natural light-controlled signal transduction proteins also allow optical control of biochemical pathways, including both second-messenger generation and protein-protein interactions, which is especially useful in studying cell and developmental biology.^[139] In 2002, the first example of using photoproteins from another organism for controlling a biochemical pathway was demonstrated using the light-induced interaction between plant phytochrome and phytochrome-interacting factor (PIF) to control gene transcription in yeast.^[1] By fusing phytochrome to a DNA-binding domain and PIF to a transcriptional activation domain, transcriptional activation of genes recognized by the DNA-binding domain could be induced by light.^[1] This study anticipated aspects of the later development of optogenetics in the brain, for example, by suggesting that "Directed light delivery by fiber optics has the potential to target selected cells or tissues, even within larger, more-opaque organisms."^[1] The literature has been inconsistent as to whether control of cellular biochemistry with photoproteins should be subsumed within the definition of optogenetics, as optogenetics in common usage refers specifically to the control of neuronal firing with opsins,^[140]^[141]^[17]^[142] and as control of neuronal firing with opsins postdates and utilizes distinct mechanisms from control of cellular biochemistry with photoproteins.^[139]

Photosensitive proteins utilized in various cell signaling pathways

In addition to phytochromes, which are found in plants and cyanobacteria, LOV domains(Light-oxygen-voltage-sensing domain) from plants and yeast and cryptochrome domains from plants are other natural photosensory domains that have been used for optical control of biochemical pathways in cells.^[143]^[139] In addition, a synthetic photosensory domain has been engineered from the fluorescent protein Dronpa for optical control of biochemical pathways.^[139] In photosensory domains, light absorption is either coupled to a change in protein-protein interactions (in the case of phytochromes, some LOV domains, cryptochromes, and Dronpa mutants) or a conformational change that exposes a linked protein segment or alters the activity of a linked protein domain (in the case of phytochromes and some LOV domains).^[139] Light-regulated protein-protein interactions can then be used to recruit proteins to DNA, for example to induce gene transcription or DNA modifications, or to the plasma membrane, for example to activate resident signaling proteins.^[138]^[144]^[145]^[146]^[147]^[148] CRY2 also clusters when active, so has been fused with signaling domains and subsequently photoactivated to allow for clustering-based activation.^[149] The LOV2 domain of Avena sativa(common oat) has been used to expose short peptides or an active protein domain in a light-dependent manner.^[150]^[151]^[152] Introduction of this LOV domain into another protein can regulate function through light induced peptide disorder.^[153] The asLOV2 protein, which optogenetically exposes a peptide, has also been used as a scaffold for several synthetic light induced dimerization and light induced dissociation systems (iLID and LOVTRAP, respectively).^[154]^[155] The systems can be used to control proteins through a protein splitting strategy.^[156] Photodissociable Dronpa domains have also been used to cage a protein active site in the dark, uncage it after cyan light illumination, and recage it after violet light illumination.^[157]

Temporal control of signal transduction with light

The ability to optically control signals for various time durations is being explored to elucidate how cell signaling pathways convert signal duration and response to different outputs.^[158] Natural signaling cascades are capable of responding with different outputs to differences in stimulus timing duration and dynamics.^[159] For example, treating PC12 cells with epidermal growth factor (EGF, inducing a transient profile of ERK activity) leads to cellular proliferation whereas introduction of nerve growth factor (NGF, inducing a sustained profile of ERK activity) leads to differentiation into neuron-like cells.^[160] This behavior was initially characterized using EGF and NGF application, but the finding has been partially replicated with optical inputs.^[161] In addition, a rapid negative feedback loop in the RAF-MEK-ERK pathway was discovered using pulsatile activation of a photoswitchable RAF engineered with photodissociable Dronpa domains.^[157]

Optogenetic noise-photostimulation

Professor Elias Manjarrez´s research group introduced the Optogenetic noise-photostimulation.^[162]^[163]^[164] This is a technique that uses random noisy light to activate neurons expressing ChR2. An optimal level of optogenetic-noise photostimulation on the brain can increase the somatosensory evoked field potentials, the firing frequency response of pyramidal neurons to somatosensory stimulation, and the sodium current amplitude.

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External links

"Optogenetics: shedding light on the brain's secrets". Scientifica.
"Optogenetics: Integrated Calcium Imaging and Optogenetics". Inscopix.

Categories:

https://en.wikipedia.org/wiki/Optogenetics#Technique

^{https://en.wikipedia.org/wiki/Neuroscience}

^{https://en.wikipedia.org/wiki/Optogenetic_methods_to_record_cellular_activity}

^{https://en.wikipedia.org/wiki/Channelrhodopsin}

^{https://en.wikipedia.org/wiki/Retinylidene_protein}

^{https://en.wikipedia.org/wiki/Brain_connectivity_estimators}

^{https://en.wikipedia.org/wiki/Transmembrane_domain}

^{https://en.wikipedia.org/wiki/Visual_phototransduction}

^{https://en.wikipedia.org/wiki/Rhodopsin}

^{https://en.wikipedia.org/wiki/Chromophore}

^{https://en.wikipedia.org/wiki/Flagellate}

^{https://en.wikipedia.org/wiki/Phototaxis}

^{https://en.wikipedia.org/wiki/Channelrhodopsin}

^{https://en.wikipedia.org/wiki/Light-gated_ion_channel}

^{https://en.wikipedia.org/wiki/Eyespot_apparatus}

^{https://en.wikipedia.org/wiki/Molecular_cloning}

^{https://en.wikipedia.org/wiki/Glossary_of_biology#intracellular}

^{https://en.wikipedia.org/wiki/Electromagnetic_radiation}

^{https://en.wikipedia.org/wiki/Microwave}

Structure

Crystal structure of channelrhodopsin. PDB 3ug9^[13]

In terms of structure, channelrhodopsins are retinylidene proteins. They are seven-transmembrane proteins like rhodopsin, and contain the light-isomerizable chromophore all-trans-retinal (an aldehyde derivative of vitamin A). The retinal chromophore is covalently linked to the rest of the protein through a protonated Schiff base. Whereas most 7-transmembrane proteins are G protein-coupled receptors that open other ion channels indirectly via second messengers (i.e., they are metabotropic), channelrhodopsins directly form ion channels (i.e., they are ionotropic).^[11] This makes cellular depolarization extremely fast, robust, and useful for bioengineering and neuroscience applications, including photostimulation.

^{https://en.wikipedia.org/wiki/Channelrhodopsin}

^{https://en.wikipedia.org/wiki/G_protein-coupled_receptor}

^{https://en.wikipedia.org/wiki/Second_messenger_system}

^{https://en.wikipedia.org/wiki/Photostimulation}

^{https://en.wikipedia.org/wiki/tissues}

Function

Scheme of ChR2-RFP fusion construct

The natural ("wild-type") ChR2 absorbs blue light with an absorption and action spectrum maximum at 480 nm.^[14] When the all-trans-retinal complex absorbs a photon, it induces a conformational change from all-trans to 13-cis-retinal. This change introduces a further one in the transmembrane protein, opening the pore to at least 6 Å. Within milliseconds, the retinal relaxes back to the all-trans form, closing the pore and stopping the flow of ions.^[11] Most natural channelrhodopsins are nonspecific cation channels (CCRs), conducting H⁺, Na⁺, K⁺, and Ca²⁺ ions. Recently discovered anion-conducting channelrhodopsins (ACRs)^[15] and potassium-selective channelrhodpsins (HcKCR1, HcKCR2) ^[16] were structurally analyzed to understand their ion selectivity.^[17]^[18] ACRs and KCRs have been used to inhibit neuronal activity.

Development as a molecular tool

In 2005, three groups sequentially established ChR2 as a tool for genetically targeted optical remote control (optogenetics) of neurons, neural circuits and behavior.

At first, Karl Deisseroth's lab demonstrated that ChR2 could be deployed to control mammalian neurons in vitro, achieving temporal precision on the order of milliseconds (both in terms of delay to spiking and in terms of temporal jitter).^[19] Because all opsins require retinal as the light-sensing co-factor and it was unclear whether central mammalian nerve cells would contain sufficient retinal levels, but they do. It also showed, despite the small single-channel conductance, sufficient potency to drive mammalian neurons above action potential threshold. From this, channelrhodopsin became the first optogenetic tool, with which neural activity could be controlled with the temporal precision at which neurons operate (milliseconds). A second study was published later confirming the ability of ChR2 to control the activity of vertebrate neurons, at this time in the chick spinal cord.^[20] This study was the first wherein ChR2 was expressed alongside an optical silencer, vertebrate rhodopsin-4 in this case, demonstrating for the first time that excitable cells could be activated and silenced using these two tools simultaneously, illuminating the tissue at different wavelengths.

It was demonstrated that ChR2, if expressed in specific neurons or muscle cells, can evoke predictable behaviors, i.e. can control the nervous system of an intact animal, in this case the invertebrate C. elegans.^[21] This was the first using ChR2 to steer the behavior of an animal in an optogenetic experiment, rendering a genetically specified cell type subject to optical remote control. Although both aspects had been illustrated earlier that year by the group of Gero Miesenböck, deploying the indirectly light-gated ion channel P2X2,^[22] it was henceforth microbial opsins like channelrhodopsin that dominated the field of genetically targeted remote control of excitable cells, due to the power, speed, targetability, ease of use, and temporal precision of direct optical activation, not requiring any external chemical compound such as caged ligands.^[23]

To overcome its principal downsides — the small single-channel conductance (especially in steady-state), the limitation to one optimal excitation wavelength (~470 nm, blue) as well as the relatively long recovery time, not permitting controlled firing of neurons above 20–40 Hz — ChR2 has been optimized using genetic engineering. A point mutation H134R (exchanging the amino acid Histidine in position 134 of the native protein for an Arginine) resulted in increased steady-state conductance, as described in a 2005 paper that also established ChR2 as an optogenetic tool in C. elegans.^[21] In 2009, Roger Tsien's lab optimized ChR2 for further increases in steady-state conductance and dramatically reduced desensitization by creating chimeras of ChR1 and ChR2 and mutating specific amino acids, yielding ChEF and ChIEF, which allowed the driving of trains of action potentials up to 100 Hz.^[24]^[25] In 2010, the groups of Hegemann and Deisseroth introduced an E123T mutation into native ChR2, yielding ChETA, which has faster on- and off-kinetics, permitting the control of individual action potentials at frequencies up to 200 Hz (in appropriate cell types).^[26]^[24]

The groups of Hegemann and Deisseroth also discovered that the introduction of the point mutation C128S makes the resulting ChR2-derivative a step-function tool: Once "switched on" by blue light, ChR2(C128S) stays in the open state until it is switched off by yellow light – a modification that deteriorates temporal precision, but increases light sensitivity by two orders of magnitude.^[27] They also discovered and characterized VChR1 in the multicellular algae Volvox carteri. VChR1 produces only tiny photocurrents, but with an absorption spectrum that is red-shifted relative to ChR2.^[28] Using parts of the ChR1 sequence, photocurrent amplitude was later improved to allow excitation of two neuronal populations at two distinct wavelengths.^[29]

Deisseroth's group has pioneered many applications in live animals such as genetically targeted remote control in rodents in vivo,^[30] the optogenetic induction of learning in rodents,^[31] the experimental treatment of Parkinson's disease in rats,^[32]^[33] and the combination with fMRI (opto-fMRI).^[34] Other labs have pioneered the combination of ChR2 stimulation with calcium imaging for all-optical experiments,^[35] mapping of long-range^[36] and local^[37] neural circuits, ChR2 expression from a transgenic locus – directly^[38] or in the Cre-lox conditional paradigm^[37] – as well as the two-photon excitation of ChR2, permitting the activation of individual cells.^[39]^[40]^[41]

In March 2013, the Brain Prize (Grete Lundbeck European Brain Research Prize) was jointly awarded to Bamberg, Boyden, Deisseroth, Hegemann, Miesenböck, and Nagel for "their invention and refinement of optogenetics".^[42] The same year, Hegemann and Nagel received the Louis-Jeantet Prize for Medicine for "the discovery of channelrhodopsin". In 2015, Boyden and Deisseroth received the Breakthrough Prize in Life Sciences and in 2020, Miesenböck, Hegemann and Nagel received the Shaw prize in Life Science and Medicine for the development of optogenetics.

Designer-channelrhodopsins

Channelrhodopsins are key tools in optogenetics. The C-terminal end of Channelrhodopsin-2 extends into the intracellular space and can be replaced by fluorescent proteins without affecting channel function. This kind of fusion construct can be useful to visualize the morphology of ChR2 expressing cells, i.e. simultaneously indicate which cells are tagged with FP and allow the activity to be controlled by the channelrhodopsin.^[19]^[35] Point mutations close to the retinal binding pocket have been shown to affect the biophysical properties of the channelrhodopsin, resulting in a variety of different tools.

Kinetics

Closing of the channel after optical activation can be substantially delayed by mutating the protein residues C128 or D156. This modification results in super-sensitive channelrhodopsins that can be opened by a blue light pulse and closed by a green or yellow light pulse (Step-function opsins).^[27]^[43]^[29] Mutating the E123 residue accelerates channel kinetics (ChETA), and the resulting ChR2 mutants have been used to spike neurons at up to 200 Hz.^[26] In general, channelrhodopsins with slow kinetics are more light-sensitive on the population level, as open channels accumulate over time even at low light levels.

Photocurrent amplitude

H134R and T159C mutants display increased photocurrents, and a combination of T159 and E123 (ET/TC) has slightly larger photocurrents and slightly faster kinetics than wild-type ChR2.^[44] ChIEF, a chimera and point mutant of ChR1 and ChR2, demonstrates large photocurrents, little desensitization and kinetics similar to wild-type ChR2.^[24] Variants with extended open time (ChR2-XXL) produce extremely large photocurrents and are very light sensitive on the population level.^[45]

Wavelength

Chimeric channelrhodopsins have been developed by combining transmembrane helices from ChR1 and VChR1, leading to the development of ChRs with red spectral shifts (such as C1V1 and ReaChR).^[29]^[46] ReaChR has improved membrane trafficking and strong expression in mammalian cells, and has been used for minimally invasive, transcranial activation of brainstem motoneurons. Searches for homologous sequences in other organisms has yielded spectrally improved and stronger red-shifted channelrhodpsins (Chrimson).^[47] In combination with ChR2, these yellow/red light-sensitive channelrhodopsins allow controlling two populations of neurons independently with light pulses of different colors.^[48]^[49]

A blue-shifted channelrhodopsin has been discovered in the alga Scherffelia dubia. After some engineering to improve membrane trafficking and speed, the resulting tool (CheRiff) produced large photocurrents at 460 nm excitation.^[50] It has been combined with the Genetically Encoded Calcium Indicator jRCaMP1b ^[51] in an all-optical system called the OptoCaMP.^[52]

Ion selectivity

Most channelrhodopsins are unspecific cation channels. When expressed in neurons, they conduct mostly Na⁺ ions and are therefore depolarizing (excitatory). Variants with moderate to high calcium permeability have been engineered (CatCh, CapChRs).^[53]^[54] K⁺-specific channelrhodopsins (KCRs, WiChR) were recently discovered in various protists.^[55]^[56] When expressed in neurons, potassium-selective channelrhodopsins hyperpolarize the membrane upon illumination, preventing spike generation (inhibitory).

Mutating E90 to the positively charged amino acid arginine turns channelrhodopsin from an unspecific cation channel into a chloride-conducting channel (ChloC).^[57] The selectivity for Cl- was further improved by replacing negatively charged residues in the channel pore, making the reversal potential more negative.^[58]^[59] Anion-conducting channelrhodopsins (iChloC, iC++, GtACR) inhibit neuronal spiking in cell culture and in intact animals when illuminated with blue light.

Applications

Channelrhodopsins can be readily expressed in excitable cells such as neurons using a variety of transfection techniques (viral transfection, electroporation, gene gun) or transgenic animals. The light-absorbing pigment retinal is present in most cells (of vertebrates) as Vitamin A, making it possible to photostimulate neurons without adding any chemical compounds. Before the discovery of channelrhodopsins, neuroscientists were limited to recording the activity of neurons in the brain and correlate this activity with behavior. This is not sufficient to prove that the recorded neural activity actually caused that behavior. Controlling networks of genetically modified cells with light, an emerging field known as Optogenetics., allows researchers now to explore the causal link between activity in a specific group of neurons and mental events, e.g. decision making. Optical control of behavior has been demonstrated in nematodes, fruit flies, zebrafish, and mice.^[60]^[61] Recently, chloride-conducting channelrhodopsins have been engineered and were also found in nature.^[15]^[57] These tools can be used to silence neurons in cell culture and in live animals by shunting inhibition.^[58]^[59]

Using multiple colors of light expands the possibilities of optogenetic experiments. The blue-light sensitive ChR2 and the yellow light-activated chloride pump halorhodopsin together enable multiple-color optical activation and silencing of neural activity.^[62]^[63] Another interesting pair is the blue-light sensitive chloride channel GtACR2^[64] and the red-light sensitive cation channel Chrimson^[65] which have been combined in a single protein (BiPOLES) for bidirectional control of membrane potential.^[66]

Using fluorescently labeled ChR2, light-stimulated axons and synapses can be identified.^[35] This is useful to study the molecular events during the induction of synaptic plasticity.^[67]^[68] Transfected cultured neuronal networks can be stimulated to perform some desired behaviors for applications in robotics and control.^[69] ChR2 has also been used to map long-range connections from one side of the brain to the other, and to map the spatial location of inputs on the dendritic tree of individual neurons.^[36]^[70]

In 2006, it was reported that transfection with Channelrhodopsin could restore eyesight to blind mice.^[71]

Neurons can tolerate ChR expression for a long time, and several laboratories are testing optogenetic stimulation to solve medical needs. In blind mice, visual function can be partially restored by expressing ChR2 in inner retinal cells.^[72]^[73] In 2021, the red-light sensitive ChR ChrimsonR was virally delivered to the eyes of a human patient suffering from retinal degeneration (Retinitis pigmentosa), leading to partial recovery of his vision.^[74]^[75] Optical cochlear implants have been shown to work well in animal experiments and are currently undergoing clinical trials.^[76]^[77]^[78] In the future, ChRs may find even more medical applications, e.g. for deep-brain stimulation of Parkinson patients or to control certain forms of Epilepsy.

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External links

v t e Optogenetics
Optogenetic actuators	Channelrhodopsin (Anion-conducting) Halorhodopsin Archaerhodopsin Bacteriorhodopsin Proteorhodopsin
Optogenetic sensors	Calcium Voltage Glutamate Vesicle
Related techniques	Voltage-sensitive dye
Commons

Categories:

^{https://en.wikipedia.org/wiki/Channelrhodopsin}

Classes of genetically encoded indicators

The calcium indicator GCaMP in its calcium-bound (top) and calcium-free form (bottom). When Ca-calmodulin (cyan) binds to M13, the conformation changes and the cpGFP barrel closes, enabling green fluorescence.

Indicators have been designed to measure ion concentrations, membrane potential, neurotransmitters, and various intracellular signaling molecules. The following list provides only examples for each class; many more have been published.

Intracellular signaling:

Genetically encoded calcium indicators (GECI): A large class of tools, based on natural calcium binding proteins (calmodulin, troponin). Different affinities, kinetics, and colors (green, red) available. Read-out via fluorescence intensity (single wavelength indicators), FRET or BRET. Have been targeted to various organelles. Current version: JGCaMP8^[12]
Genetically encoded chloride indicators: Clomeleon^[13]
Genetically encoded potassium indicators: GINKO2^[14]
Genetically encoded indicators for intracellular pH (GEPhI): CypHer^[15]
Genetically encoded voltage indicators (GEVI): ArcLight^[16]
Genetically encoded vesicle fusion sensors: Synapto-pHluorin, Synaptophysin-pHluorin^[17]
Genetically encoded cAMP sensors: EPAC^[18]
Genetically encoded ATP sensors: QUEEN-37C^[19]
Genetically encoded kinase activity sensors: CaMui,^[20] SmURFP
Genetically encoded Small G-protein sensors: FRas^[21]

Neurotransmitters and other extracellular signals:

Genetically encoded glutamate sensors: GluSnFR^[22]
Genetically encoded GABA sensors: iGABASnFR^[23]
Genetically encoded dopamine sensors: dLight1,^[24] GRAB-DA^[25]
Genetically encoded serotonin sensors: GRAB_5-HT,^[26] sDarken^[27]
Genetically encoded norepinephrine sensors: GRAB_NE^[28]
Genetically encoded sensor for endocannabinoid activity: GRAB_eCB2.0^[29]
Genetically encoded sensor for orexin/hypocretin neuropeptides: OxLight1^[30]
Genetically encoded sensor for lactate: eLACCO1.1^[31]

External links

Fluorescent Biosensor Database, a fairly complete searchable list of published sensors and their basic properties, maintained by Jin Zhang's lab at UCSD.^[32]
Fluorescent Biosensors available on Addgene, a nonprofit plasmid repository.

References

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Duffet L, Kosar S, Panniello M, Viberti B, Bracey E, Zych AD, et al. (February 2022). "A genetically encoded sensor for in vivo imaging of orexin neuropeptides". Nature Methods. 19 (2): 231–241. doi:10.1038/s41592-021-01390-2. PMC 8831244. PMID 35145320.

Nasu, Yusuke; Murphy-Royal, Ciaran; Wen, Yurong; Haidey, Jordan N.; Molina, Rosana S.; Aggarwal, Abhi; Zhang, Shuce; Kamijo, Yuki; Paquet, Marie-Eve; Podgorski, Kaspar; Drobizhev, Mikhail; Bains, Jaideep S.; Lemieux, M. Joanne; Gordon, Grant R.; Campbell, Robert E. (2021-12-06). "A genetically encoded fluorescent biosensor for extracellular l-lactate". Nature Communications. 12 (1): 7058. doi:10.1038/s41467-021-27332-2. ISSN 2041-1723. PMC 8648760. PMID 34873165.

Greenwald EC, Mehta S, Zhang J (December 2018). "Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks". Chemical Reviews. 118 (24): 11707–11794. doi:10.1021/acs.chemrev.8b00333. PMC 7462118. PMID 30550275.

v t e Optogenetics
Optogenetic actuators	Channelrhodopsin (Anion-conducting) Halorhodopsin Archaerhodopsin Bacteriorhodopsin Proteorhodopsin
Optogenetic sensors	Calcium Voltage Glutamate Vesicle
Related techniques	Voltage-sensitive dye
Commons

Categories:

https://en.wikipedia.org/wiki/Optogenetic_methods_to_record_cellular_activity

https://en.wikipedia.org/wiki/Troponin

https://en.wikipedia.org/wiki/Multiplexing

https://en.wikipedia.org/wiki/Confocal_microscopy

https://en.wikipedia.org/wiki/Viral_vector

https://en.wikipedia.org/wiki/Nematode

https://en.wikipedia.org/wiki/Cell_culture

https://en.wikipedia.org/wiki/Organelle

https://en.wikipedia.org/wiki/Intrabody_(protein)

https://en.wikipedia.org/wiki/Pyramidal_cell

https://en.wikipedia.org/wiki/Astrocyte

https://en.wikipedia.org/wiki/Photometry_(optics)

https://en.wikipedia.org/wiki/Radiant_energy

https://en.wikipedia.org/wiki/Radiant_flux

https://en.wikipedia.org/wiki/Joule

https://en.wikipedia.org/wiki/Energy

https://en.wikipedia.org/wiki/Measurement

https://en.wikipedia.org/wiki/Gravitational_wave

Visible light such as sunlight carries radiant energy, which is used in solar power generation.

In physics, and in particular as measured by radiometry, radiant energy is the energy of electromagnetic^[1] and gravitational radiation.

https://en.wikipedia.org/wiki/Radiant_energy

https://en.wikipedia.org/wiki/Gravitational_wave

https://en.wikipedia.org/wiki/Scotopic_vision

https://en.wikipedia.org/wiki/Radiant_energy_density

https://en.wikipedia.org/wiki/Radiosity_(radiometry)

https://en.wikipedia.org/wiki/Sensation

https://en.wikipedia.org/wiki/Anion-conducting_channelrhodopsin

https://en.wikipedia.org/wiki/Voltage-sensitive_dye

https://en.wikipedia.org/wiki/Halorhodopsin

https://en.wikipedia.org/wiki/Hyperpolarization_(biology)

https://en.wikipedia.org/wiki/Shunting_inhibition

https://en.wikipedia.org/wiki/Reversal_potential

https://en.wikipedia.org/wiki/GABAA_receptor

https://en.wikipedia.org/wiki/Inhibitory_postsynaptic_potential

https://en.wikipedia.org/wiki/Cryptomonad

https://en.wikipedia.org/wiki/Model_organism

https://en.wikipedia.org/wiki/Bacteriorhodopsin

https://en.wikipedia.org/wiki/Electrochemical_gradient

https://en.wikipedia.org/wiki/Halobacterium_salinarum

Bacteriorhodopsin (Bop) is a protein used by Archaea, most notably by haloarchaea, a class of the Euryarchaeota.^[1] It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell.^[2] The resulting proton gradient is subsequently converted into chemical energy.^[3]

Function

Chemiosmotic coupling between bacteriorhodopsin and ATP synthase in the Halobacterium salinarum membrane

Bacteriorhodopsin is a light-driven H⁺ ion transporter found in some haloarchaea, most notably Halobacterium salinarum (formerly known as syn. H. halobium). The proton-motive force generated by the protein is used by ATP synthase to generate adenosine triphosphate (ATP). By expressing bacteriorhodopsin, the archaea cells are able to synthesise ATP in the absence of a carbon source.^[4]^[5]

https://en.wikipedia.org/wiki/Bacteriorhodopsin

https://en.wikipedia.org/wiki/Adenosine_triphosphate

Proton-motive force

Energy conversion by the inner mitochondrial membrane and chemiosmotic coupling between the chemical energy of redox reactions in the respiratory chain and the oxidative phosphorylation catalysed by the ATP synthase.^[6]^[7]

The movement of ions across the membrane depends on a combination of two factors:

Diffusion force caused by a concentration gradient - all particles tend to diffuse from higher concentration to lower.
Electrostatic force caused by electrical potential gradient - cations like protons H⁺ tend to diffuse down the electrical potential, from the positive (P) side of the membrane to the negative (N) side. Anions diffuse spontaneously in the opposite direction.

These two gradients taken together can be expressed as an electrochemical gradient.

Lipid bilayers of biological membranes, however, are barriers for ions. This is why energy can be stored as a combination of these two gradients across the membrane. Only special membrane proteins like ion channels can sometimes allow ions to move across the membrane (see also: Membrane transport). In the chemiosmotic hypothesis a transmembrane ATP synthases is central to convert energy of spontaneous flow of protons through them into chemical energy of ATP bonds.

Hence researchers created the term proton-motive force (PMF), derived from the electrochemical gradient mentioned earlier. It can be described as the measure of the potential energy stored (chemiosmotic potential) as a combination of proton and voltage (electrical potential) gradients across a membrane. The electrical gradient is a consequence of the charge separation across the membrane (when the protons H⁺ move without a counterion, such as chloride Cl⁻).

In most cases the proton-motive force is generated by an electron transport chain which acts as a proton pump, using the Gibbs free energy of redox reactions to pump protons (hydrogen ions) out across the membrane, separating the charge across the membrane. In mitochondria, energy released by the electron transport chain is used to move protons from the mitochondrial matrix (N side) to the intermembrane space (P side). Moving the protons out of the mitochondrion creates a lower concentration of positively charged protons inside it, resulting in excess negative charge on the inside of the membrane. The electrical potential gradient is about -170 mV ^[6], negative inside (N). These gradients - charge difference and the proton concentration difference both create a combined electrochemical gradient across the membrane, often expressed as the proton-motive force (PMF). In mitochondria, the PMF is almost entirely made up of the electrical component but in chloroplasts the PMF is made up mostly of the pH gradient because the charge of protons H⁺ is neutralized by the movement of Cl⁻ and other anions. In either case, the PMF needs to be greater than about 460 mV (45 kJ/mol) for the ATP synthase to be able to make ATP.

Equations

The proton-motive force is derived from the Gibbs free energy. Let N denote the inside of a cell, and let P denote the outside. Then^[6]

Δ G = z F Δ ψ + R T \ln \frac{[X^{z +}]_{N}}{[X^{z +}]_{P}}

where

$Δ G$ is the Gibbs free energy change per unit amount of cations transferred from P to N;
$z$ is the charge number of the cation $X^{z +}$ ;
$Δ ψ$ is the electric potential of N relative to P;
$[X^{z +}]_{P}$ and $[X^{z +}]_{N}$ are the cation concentrations at P and N, respectively;
$F$ is the Faraday constant;
$R$ is the gas constant; and
$T$ is the temperature.

The molar Gibbs free energy change $Δ G$ is frequently interpreted as a molar electrochemical ion potential $Δ μ_{X^{z +}} = Δ G$ .

For an electrochemical proton gradient $z = 1$ and as a consequence:

Δ μ_{H^{+}} = F Δ ψ + R T \ln \frac{[H^{+}]_{N}}{[H^{+}]_{P}} = F Δ ψ - (\ln 10) R T Δ p H

A diagram of chemiosmotic phosphorylation

where

Δ p H = {p H}_{N} - {p H}_{P}

Mitchell defined the proton-motive force (PMF) as

Δ p = - \frac{Δ μ_{H^{+}}}{F}

For example, $Δ μ_{H^{+}} = 1 k J {m o l}^{- 1}$ implies $Δ p = 10.4 m V$ . At $298 K$ this equation takes the form:

$Δ p = - Δ ψ + (59.1 m V) Δ p H$ .

Note that for spontaneous proton import from the P side (relatively more positive and acidic) to the N side (relatively more negative and alkaline), $Δ μ_{H^{+}}$ is negative (similar to $Δ G$ ) whereas PMF is positive (similar to redox cell potential $Δ E$ ).

It is worth noting that, as with any transmembrane transport process, the PMF is directional. The sign of the transmembrane electric potential difference $Δ ψ$ is chosen to represent the change in potential energy per unit charge flowing into the cell as above. Furthermore, due to redox-driven proton pumping by coupling sites, the proton gradient is always inside-alkaline. For both of these reasons, protons flow in spontaneously, from the P side to the N side; the available free energy is used to synthesize ATP (see below). For this reason, PMF is defined for proton import, which is spontaneous. PMF for proton export, i.e., proton pumping as catalyzed by the coupling sites, is simply the negative of PMF(import).

The spontaneity of proton import (from the P to the N side) is universal in all bioenergetic membranes.^[8] This fact was not recognized before the 1990s, because the chloroplast thylakoid lumen was interpreted as an interior phase, but in fact it is topologically equivalent to the exterior of the chloroplast. Azzone et al. stressed that the inside phase (N side of the membrane) is the bacterial cytoplasm, mitochondrial matrix, or chloroplast stroma; the outside (P) side is the bacterial periplasmic space, mitochondrial intermembrane space, or chloroplast lumen. Furthermore, 3D tomography of the mitochondrial inner membrane shows its extensive invaginations to be stacked, similar to thylakoid disks; hence the mitochondrial intermembrane space is topologically quite similar to the chloroplast lumen.:^[9]

The energy expressed here as Gibbs free energy, electrochemical proton gradient, or proton-motive force (PMF), is a combination of two gradients across the membrane:

the concentration gradient (via $Δ p H$ ) and
electric potential gradient $Δ ψ$ .

When a system reaches equilibrium, $Δ ρ = 0$ ; nevertheless, the concentrations on either side of the membrane need not be equal. Spontaneous movement across the potential membrane is determined by both concentration and electric potential gradients.

The molar Gibbs free energy $Δ G_{p}$ of ATP synthesis

{A D P}^{4 -} + H^{+} + {H O P O}_{3}^{2 -} \to {A T P}^{4 -} + H_{2} O

is also called phosphorylation potential. The equilibrium concentration ratio $[H^{+}] / [A T P]$ can be calculated by comparing $Δ p$ and $Δ G_{p}$ , for example in case of the mammalian mitochondrion:^[9]

H⁺ / ATP = ΔG_p / (Δp / 10.4 kJ·mol⁻¹/mV) = 40.2 kJ·mol⁻¹ / (173.5 mV / 10.4 kJ·mol⁻¹/mV) = 40.2 / 16.7 = 2.4. The actual ratio of the proton-binding c-subunit to the ATP-synthesizing beta-subunit copy numbers is 8/3 = 2.67, showing that under these conditions, the mitochondrion functions at 90% (2.4/2.67) efficiency.^[9]

In fact, the thermodynamic efficiency is mostly lower in eukaryotic cells because ATP must be exported from the matrix to the cytoplasm, and ADP and phosphate must be imported from the cytoplasm. This "costs" one "extra" proton import per ATP,^[6]^[7] hence the actual efficiency is only 65% (= 2.4/3.67).

In mitochondria

Directions of chemiosmotic proton transfer in the mitochondrion, chloroplast and in gram-negative bacterial cells (cellular respiration and photosynthesis). The bacterial cell wall is omitted, gram-positive bacterial cells do not have outer membrane.^[6]

The complete breakdown of glucose releasing its energy is called cellular respiration. The last steps of this process occur in mitochondria. The reduced molecules NADH and FADH₂ are generated by the Krebs cycle, glycolysis, and pyruvate processing. These molecules pass electrons to an electron transport chain, which releases the energy of oxygen to create a proton gradient across the inner mitochondrial membrane. ATP synthase then uses the energy stored in this gradient to make ATP. This process is called oxidative phosphorylation because it uses energy released by the oxidation of NADH and FADH₂ to phosphorylate ADP into ATP.

In plants

The light reactions of photosynthesis generate ATP by the action of chemiosmosis. The photons in sunlight are received by the antenna complex of Photosystem II, which excites electrons to a higher energy level. These electrons travel down an electron transport chain, causing protons to be actively pumped across the thylakoid membrane into the thylakoid lumen. These protons then flow down their electrochemical potential gradient through an enzyme called ATP-synthase, creating ATP by the phosphorylation of ADP to ATP. The electrons from the initial light reaction reach Photosystem I, then are raised to a higher energy level by light energy and then received by an electron acceptor and reduce NADP⁺ to NADPH. The electrons lost from Photosystem II get replaced by the oxidation of water, which is "split" into protons and oxygen by the oxygen-evolving complex (OEC, also known as WOC, or the water-oxidizing complex). To generate one molecule of diatomic oxygen, 10 photons must be absorbed by Photosystems I and II, four electrons must move through the two photosystems, and 2 NADPH are generated (later used for carbon dioxide fixation in the Calvin Cycle).

In prokaryotes

Chemiosmotic coupling between the energy of sunlight, bacteriorhodopsin and phosphorylation (chemical energy) during photosynthesis in the halophilic archaeal organism Halobacterium salinarum (syn. H. halobium). The archaeal cell wall is omitted. ^[6]^[7]

Bacteria and archaea also can use chemiosmosis to generate ATP. Cyanobacteria, green sulfur bacteria, and purple bacteria synthesize ATP by a process called photophosphorylation.^[6]^[7] These bacteria use the energy of light to create a proton gradient using a photosynthetic electron transport chain. Non-photosynthetic bacteria such as E. coli also contain ATP synthase. In fact, mitochondria and chloroplasts are the product of endosymbiosis and trace back to incorporated prokaryotes. This process is described in the endosymbiotic theory. The origin of the mitochondrion triggered the origin of eukaryotes, and the origin of the plastid the origin of the Archaeplastida, one of the major eukaryotic supergroups.^{[citation needed]}

Chemiosmotic phosphorylation is the third pathway that produces ATP from inorganic phosphate and an ADP molecule. This process is part of oxidative phosphorylation.

Emergence of chemiosmosis

Early cell powered by external proton gradient near a deep-sea hydrothermal vent. As long as the membrane (or passive ion channels within it) is permeable to protons, the mechanism can function without ion pumps.^[10]

Thermal cycling model

A stepwise model for the emergence of chemiosmosis, a key element in the origin of life on earth, proposes that primordial organisms used thermal cycling as an energy source (thermosynthesis), functioning essentially as a heat engine:^[11]

self-organized convection in natural waters causing thermal cycling →

added β-subunit of F₁ ATP Synthase

(generated ATP by thermal cycling of subunit during suspension in convection cell: thermosynthesis) →

added membrane and F_o ATP Synthase moiety

(generated ATP by change in electrical polarization of membrane during thermal cycling: thermosynthesis) →

added metastable, light-induced electric dipoles in membrane

(primitive photosynthesis) →

added quinones and membrane-spanning light-induced electric dipoles

(today's bacterial photosynthesis, which makes use of chemiosmosis).

External proton gradient model

Deep-sea hydrothermal vents, emitting hot acidic or alklaine water, would have created external proton gradients. These provided energy that primordial organisms could have exploited. To keep the flows separate, such an organism could have wedged itself in the rock of the hydrothermal vent, exposed to the hydrothermal flow on one side and the more alkaline water on the other. As long as the organism's membrane (or passive ion channels within it) is permeable to protons, the mechanism can function without ion pumps. Such a proto-organism could then have evolved further mechanisms such as ion pumps and ATP synthase.^[10]

Meteoritic quinones

A proposed alternative source to chemiosmotic energy developing across membranous structures is if an electron acceptor, ferricyanide, is within a vesicle and the electron donor is outside, quinones transported by carbonaceous meteorites pick up electrons and protons from the donor. They would release electrons across the lipid membrane by diffusion to ferricyanide within the vesicles and release protons which produces gradients above pH 2, the process is conducive to the development of proton gradients.^[12]^[13]

References

Mitchell P (July 1961). "Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism". Nature. 191 (4784): 144–148. Bibcode:1961Natur.191..144M. doi:10.1038/191144a0. PMID 13771349. S2CID 1784050.

Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). "Proton Gradients Produce Most of the Cell's ATP". Molecular Biology of the Cell. Garland. ISBN 0-8153-4072-9.

The Nobel Prize in Chemistry 1978.

Cooper GM (2000). "Figure 10.22: Electron transport and ATP synthesis during photosynthesis". The Cell: A Molecular Approach (2nd ed.). Sinauer Associates, Inc. ISBN 0-87893-119-8.

Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). "Figure 14-32: The importance of H⁺-driven transport in bacteria". Molecular Biology of the Cell. Garland. ISBN 0-8153-4072-9.

Nicholls D. G.; Ferguson S. J. (1992). Bioenergetics 2 (2nd ed.). San Diego: Academic Press. ISBN 9780125181242.

Stryer L (1995). Biochemistry (fourth ed.). New York - Basingstoke: W. H. Freeman and Company. ISBN 978-0716720096.

Azzone G, Benz R, Bertl A, Colombini M, Crofts A, Dilley R, Dimroth P, Dutton PL, Felle H, Harold F, Junge W (1993). "Transmembrane Measurements Across Bioenergetic Membranes". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1183 (1): 1–3. doi:10.1016/0005-2728(93)90002-W.

Silverstein TP (June 2014). "An exploration of how the thermodynamic efficiency of bioenergetic membrane systems varies with c-subunit stoichiometry of F₁F₀ ATP synthases". Journal of Bioenergetics and Biomembranes. 46 (3): 229–241. doi:10.1007/s10863-014-9547-y. PMID 24706236. S2CID 1840860.

Lane N (2015). The Vital Question: Why Is Life The Way It Is?. Profile Books. pp. 129–140. ISBN 978-1781250365.

Muller AW (2012). "Life explained by heat engines". Cellular Origin, Life in Extreme Environments and Astrobiology. Cellular Origin, Life in Extreme Habitats and Astrobiology. Springer. 22: 321–344. doi:10.1007/978-94-007-2941-4_19. ISBN 978-94-007-2940-7.

Damer B, Deamer D (April 2020). "The Hot Spring Hypothesis for an Origin of Life". Astrobiology. 20 (4): 429–452. doi:10.1089/ast.2019.2045. PMC 7133448. PMID 31841362.

Milshteyn D, Cooper G, Deamer D (August 2019). "Chemiosmotic energy for primitive cellular life: Proton gradients are generated across lipid membranes by redox reactions coupled to meteoritic quinones". Scientific Reports. 9 (1): 12447. doi:10.1038/s41598-019-48328-5. PMC 6713726. PMID 31462644.

External links

Chemiosmosis (University of Wisconsin)

Categories:

https://en.wikipedia.org/wiki/Chemiosmosis#Proton-motive_force

Chemiosmosis is the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient. An important example is the formation of adenosine triphosphate (ATP) by the movement of hydrogen ions (H⁺) across a membrane during cellular respiration or photosynthesis.

An ion gradient has potential energy and can be used to power chemical reactions when the ions pass through a channel (red).

Hydrogen ions, or protons, will diffuse from a region of high proton concentration to a region of lower proton concentration, and an electrochemical concentration gradient of protons across a membrane can be harnessed to make ATP. This process is related to osmosis, the movement of water across a selective membrane, which is why it is called "chemiosmosis".

ATP synthase is the enzyme that makes ATP by chemiosmosis. It allows protons to pass through the membrane and uses the free energy difference to phosphorylate adenosine diphosphate (ADP), making ATP. The generation of ATP by chemiosmosis occurs in mitochondria and chloroplasts, as well as in most bacteria and archaea. For instance, in chloroplasts during photosynthesis, an electron transport chain pumps H⁺ ions (protons) in the stroma (fluid) through the thylakoid membrane to the thylakoid spaces. The stored energy is used to photophosphorylate ADP, making ATP, as protons move through ATP synthase.

https://en.wikipedia.org/wiki/Chemiosmosis#Proton-motive_force

Structure

A bacteriorhodopsin trimer, showing the approximate positions of the extracellular and cytoplasmic sides of the membrane (red and blue lines respectively)

Bacteriorhodopsin is a 27 kDa integral membrane protein usually found in two-dimensional crystalline patches known as "purple membrane", which can occupy almost 50% of the surface area of the archaeal cell. The repeating element of the hexagonal lattice is composed of three identical protein chains, each rotated by 120 degrees relative to the others.^[6] Each monomer has seven transmembrane alpha helices and an extracellular-facing, two-stranded beta sheet.^[7]^[8]

Bacteriorhodopsin is synthesized as a protein precursor, known as bacterio-opsin, which is extensively modified after translation.^[9]^[10] The modifications are:

Covalent conjugation of a retinal molecule to residue Lys216, via a Schiff base, to create the retinylidene chromophore.^[11]
Cleavage of the signal peptide, the first 13 amino acids at the N-terminus, and the conversion of residue Gln14 to pyroglutamate^[12]
Removal of residue Asp262 at the C-terminus^[12]

Spectral properties

Bacteriorhodopsin molecule is purple and is most efficient at absorbing green light (in the wavelength range 500-650 nm). In the native membrane, the protein has a maximum absorbance at 553 nm, however addition of detergent disrupts the trimeric form, leading a loss of exciton coupling between the chromophores, and the monomeric form consequently has an absorption maximum of 568 nm.^[13]^[14]

Bacteriorhodopsin has a broad excitation spectrum. For a detection wavelength between 700 and 800 nm, it has an appreciable detected emission for excitation wavelengths between 470 nm and 650 nm (with a peak at 570 nm).^[15] When pumped at 633 nm, the emission spectrum has appreciable intensity between 650 nm and 850 nm.^[16]

Mechanism

Photocycle overview

Bacteriorhodopsin is a light-driven proton pump. It is the retinal molecule that changes its isomerization state from all-trans to 13-cis when it absorbs a photon. The surrounding protein responds to the change in the chromophore shape, by undergoing an ordered sequence of conformational changes (collectively known as the photocycle).^[17] The conformational changes alter the pK_a values of conserved amino acids in the core of the protein, including Asp85, Asp96 and the Schiff base N atom (Lys216). These sequential changes in acid dissociation constant, result in the transfer of one proton from the intracellular side to the extracellular side of the membrane for each photon absorbed by the chromophore.

The bacteriorhodopsin photocycle consists of nine distinct stages, starting from the ground or resting state, which is denoted 'bR'. The intermediates are identified by single letters and may be distinguished by their absorption spectra.^[18] The nine stages are:

bR + photon → K ⇌ L ⇌ M₁ ⇌ M₂ ⇌ M₂' ⇌ N ⇌ N' ⇌ O ⇌ bR^[18]

Ground state + photon → K state → L state

Conformational change, paired stereogram. The orange molecule is all-trans retinal and the red molecule is 13-cis retinal.

Bacteriorhodopsin in the ground state absorbs a photon and the retinal changes isomerization from all-trans 15-anti to the strained 13-cis 15-anti in the K state. The isomerisation reaction is fast and occurs in less than 1 ps. The retinal adopts a less strained conformation to form the L intermediate.

L state → M₁ state

Asp85 accepts a proton from the Schiff base N atom. In the M₁ intermediate, neither the Schiff base nor Asp85 are charged.

M₁ state → M₂ state

The Schiff base rotates away from the extracellular side of the protein towards the cytoplasmic side, in preparation to accept a new proton.

M₂ state → M₂' state

A proton is released from Glu204 and Glu194 to the extracellular medium.

M₂' state → N state

The retinal Schiff base accepts a proton from Asp96. In the N state, both Asp96 and the Schiff base are charged.

N state → N' state

Asp96 accepts a proton from the cytoplasmic side of the membrane and becomes uncharged.

N' state → O state

Retinal reisomerizes to the all-trans state.

O state → ground state

Asp85 transfers a proton to Glu194 and Glu204 ^[19] ^[20] on the extracellular face of the protein.

Homologs and other similar proteins

Bacteriorhodopsin belongs to the microbial rhodopsin family. Its homologs include the archaerhodopsins,^[21] the light-driven chloride pump halorhodopsin (for which the crystal structure is also known), and some directly light-activated channels such as channelrhodopsin.

Bacteriorhodopsin is similar to vertebrate rhodopsins, the pigments that sense light in the retina. Rhodopsins also contain retinal; however, the functions of rhodopsin and bacteriorhodopsin are different, and there is limited similarity in their amino acid sequences. Both rhodopsin and bacteriorhodopsin belong to the 7TM receptor family of proteins, but rhodopsin is a G protein-coupled receptor and bacteriorhodopsin is not. In the first use of electron crystallography to obtain an atomic-level protein structure, the structure of bacteriorhodopsin was resolved in 1990.^[22] It was then used as a template to build models of G protein-coupled receptors before crystallographic structures were also available for these proteins. It has been excessively studied on both mica^[23]^[24] and glass substrates using Atomic force microscopy and Femtosecond crystallography.^[25]

All other phototrophic systems in bacteria, algae, and plants use chlorophylls or bacteriochlorophylls rather than bacteriorhodopsin. These also produce a proton gradient, but in a quite different and more indirect way involving an electron transfer chain consisting of several other proteins. Furthermore, chlorophylls are aided in capturing light energy by other pigments known as "antennas"; these are not present in bacteriorhodopsin-based systems. It is possible that phototrophy independently evolved at least twice, once in bacteria and once in archaea.

Gallery

Bacteriorhodopsin single monomer with retinal molecule between 7 vertical alpha helixes (PDB ID: 1X0S ^[26]^[27]^[28]). One more small helix is light blue, beta sheet yellow.
Bacteriorhodopsin trimer with one retinal molecule in each subunit seen from the extracellular side EC (PDB ID: 1X0S ^[26]^[27]^[28]).

Literature

Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, McVeigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi (2020). "Halobacteria". NCBI Taxonomy: a comprehensive update on curation, resources and tools. National Center for Biotechnology Information. Retrieved 31 March 2021.

Voet, Judith G.; Voet, Donald (2004). Biochemistry. New York: J. Wiley & Sons. ISBN 978-0-471-19350-0.

"Bacteriorhodopsin: Pumping Ions".

Nicholls DG; Ferguson SJ (1992). Bioenergetics 2 (2nd ed.). San Diego: Academic Press. ISBN 9780125181242.

Stryer, Lubert (1995). Biochemistry (fourth ed.). New York - Basingstoke: WH Freeman and Company. ISBN 978-0716720096.

Essen LO, Siegert R, Lehman WD, Oesterhelt D (1998). "Lipid patches in membrane protein oligomers: Crystal structure of the bacteriorhodopsin-lipid complex". Proceedings of the National Academy of Sciences of the United States of America. 95 (20): 11673–11678. Bibcode:1998PNAS...9511673E. doi:10.1073/pnas.95.20.11673. PMC 21699. PMID 9751724.

Pebay-Peroua E, Rummel G, Rosenbusch JP, Landau EM (1997). "X-ray structure of bacteriorhodopsin at 2.5 Å from microcrystals grown in lipidic cubic phases". Science. 277 (5332): 1676–1681. doi:10.1126/science.277.5332.1676. PMID 9287223.

Luecke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK (1999). "Structure of bacteriorhodopsin at 1.55 Å resolution". Journal of Molecular Biology. 291 (4): 899–911. doi:10.1006/jmbi.1999.3027. PMID 10452895.

Oesterhelt, Dieter; Stoeckenius, Walther (1971). "Rhodopsin-like Protein from the Purple Membrane of Halobacterium halobium". Nature New Biology. 233 (39): 149–152. doi:10.1038/newbio233149a0. PMID 4940442.

Oesterhelt, Dieter (1982). "Reconstitution of the retinal proteins bacteriorhodopsin and halorhodopsin". Methods in Enzymology. 88: 10–17. doi:10.1016/0076-6879(82)88006-3. ISBN 9780121819880.

Bayley H, Huang KS, Radhakrishnan R, Ross AH, Takagaki Y, Khorana HG (1981). "Site of attachment of retinal in bacteriorhodopsin". Proceedings of the National Academy of Sciences of the United States of America. 78 (4): 2225–2229. Bibcode:1981PNAS...78.2225B. doi:10.1073/pnas.78.4.2225. PMC 319317. PMID 6941281.

Hoi KK, Bada Juarez JF, Judge PJ, Yen HY, Wu D, Vinals J, Taylor GF, Watts A, Robinson CV (2021). "Detergent-free Lipodisq Nanoparticles Facilitate High-Resolution Mass Spectrometry of Folded Integral Membrane Proteins". Nano Letters. 21 (7): 2824–2831. Bibcode:2021NanoL..21.2824H. doi:10.1021/acs.nanolett.0c04911. PMC 8050825. PMID 33787280.

Wang J, Link S, Heyes CD, El-Sayed MA (2002). "Comparison of the Dynamics of the Primary Events of Bacteriorhodopsin in Its Trimeric and Monomeric States". Biophysical Journal. 83 (3): 1557–1566. Bibcode:2002BpJ....83.1557W. doi:10.1016/S0006-3495(02)73925-8. PMC 1302253. PMID 12202380.

Pescitelli G, Woody RW (2012). "The Exciton Origin of the Visible Circular Dichroism Spectrum of Bacteriorhodopsin". Journal of Physical Chemistry B. 116 (23): 6751–6763. doi:10.1021/jp212166k. PMID 22329810.

Schenkl, Selma; Zgrablic, Goran; Portuondo-Campa, Erwin; Haacke, Stefan; Chergui, Majed (2007). "On the excitation wavelength dependence of the fluorescence of bacteriorhodopsin". Chemical Physics Letters. 441 (4–6): 322–326. Bibcode:2007CPL...441..322S. doi:10.1016/j.cplett.2007.04.086.

Ohtani, H.; Tsukamoto, Y.; Sakoda, Y.; Hamaguchi, H. (1995). "Fluorescence spectra of bacteriorhodopsin and the intermediates O and Q at room temperature". FEBS Lett. 359 (1): 65–68. doi:10.1016/0014-5793(94)01440-c. PMID 7851532.

Hayashi S, Tajkhorshid E, Schulten K (September 2003). "Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore". Biophysical Journal. 85 (3): 1440–9. Bibcode:2003BpJ....85.1440H. doi:10.1016/S0006-3495(03)74576-7. PMC 1303320. PMID 12944261.

Ernst OP, Lodowski DT, Elstner M, Hegeman P, Brown LS, Kandori H (2014). "Microbial and animal rhodopsins: Structures, functions and molecular mechanisms". Chemical Reviews. 114 (1): 126–163. doi:10.1021/cr4003769. PMC 3979449. PMID 24364740.

Dioumaev, A. K.; Richter, H. T.; Brown, L. S.; Tanio, M.; Tuzi, S.; Saito, H.; Kimura, Y.; Needleman, R.; Lanyi, J. K. (1998). "Existence of a proton transfer chain in bacteriorhodopsin: Participation of Glu-194 in the release of protons to the extracellular surface". Biochemistry. 37 (8): 2496–2906. doi:10.1021/bi971842m. PMID 9485398.

Balashov, S. P.; Lu, M.; Imasheva, E. S.; Govindjee, R.; Ebrey, T. G.; Othersen b, 3rd; Chen, Y.; Crouch, R. K.; Menick, D. R. (1999). "The proton release group of bacteriorhodopsin controls the rate of the final step of its photocycle at low pH". Biochemistry. 38 (7): 2026–2039. doi:10.1021/bi981926a. PMID 10026285.

Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TO, Hoi KK, Yen HY, Vial A, Milhiet PE, Robinson CV, Schapiro I, Moraes I, Watts A (2021). "Structures of the archaerhodopsin 3 transporter reveal that disordering of internal water networks underpins receptor sensitization". Nature Communications. 12 (1): 629. Bibcode:2021NatCo..12..629B. doi:10.1038/s41467-020-20596-0. PMC 7840839. PMID 33504778.

Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Downing KH (1990). "Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy". J Mol Biol. 213 (4): 899–929. doi:10.1016/S0022-2836(05)80271-2. PMID 2359127.

Müller, Daniel J.; Dufrêne, Yves F. (2008). "Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology". Nature Nanotechnology. 3 (5): 261–269. Bibcode:2008NatNa...3..261M. doi:10.1038/nnano.2008.100. ISSN 1748-3387. PMID 18654521.

Shibata, Mikihiro; Yamashita, Hayato; Uchihashi, Takayuki; Kandori, Hideki; Ando, Toshio (2010-02-14). "High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin". Nature Nanotechnology. 5 (3): 208–212. Bibcode:2010NatNa...5..208S. doi:10.1038/nnano.2010.7. hdl:2297/23872. ISSN 1748-3387. PMID 20154686.

Nango, Eriko; Royant, Antoine; Kubo, Minoru; Nakane, Takanori; Wickstrand, Cecilia; Kimura, Tetsunari; Tanaka, Tomoyuki; Tono, Kensuke; Song, Changyong (2016-12-23). "A three-dimensional movie of structural changes in bacteriorhodopsin". Science. 354 (6319): 1552–1557. Bibcode:2016Sci...354.1552N. doi:10.1126/science.aah3497. ISSN 0036-8075. PMID 28008064. S2CID 206651572.

Nishikawa, T.; Murakami, M. (2005-03-28). "Crystal structure of the 13-cis isomer of bacteriorhodopsin". RCSB Protein Data Bank (PDB). doi:10.2210/pdb1x0s/pdb. PDB ID: 1X0S. Retrieved 7 October 2012.

Nishikawa, T.; Murakami, M. (2005). "Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state". J. Mol. Biol. 352 (2): 319–328. doi:10.1016/j.jmb.2005.07.021. PMID 16084526. PDB ID: 1X0S.

Image created with RasTop (Molecular Visualization Software).

External links

Bacteriorhodopsin: Molecule of the Month, by David Goodsell, RCSB Protein Data Bank
Protein-Based Artificial Retina Manufacturing: Characterization of the Function and Stability of Bacteriorhodopsin Following Exposure to a Microgravity Environment, by Nicole Wagner & Jordan Greco

Categories:

https://en.wikipedia.org/wiki/Bacteriorhodopsin

Category:7TM receptors

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From Wikipedia, the free encyclopedia

This category contains the proteins belonging to the superfamily of G protein-coupled receptor-like proteins, including bacterial rhodopsins.

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G protein-coupled receptors‎ (13 C, 390 P)

Pages in category "7TM receptors"

The following 13 pages are in this category, out of 13 total. This list may not reflect recent changes.

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Halorhodopsin

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Membrane progesterone receptor

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Retinylidene protein

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https://en.wikipedia.org/wiki/G_protein-coupled_bile_acid_receptor

https://en.wikipedia.org/wiki/Deiodinase

https://en.wikipedia.org/wiki/Agamassan

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https://en.wikipedia.org/wiki/Water_oxidation_catalysis

https://en.wikipedia.org/wiki/Water_splitting

https://en.wikipedia.org/wiki/Membrane_gas_separation

https://en.wikipedia.org/wiki/Fluorine

https://en.wikipedia.org/wiki/Flue_gas

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https://en.wikipedia.org/wiki/Electrochemical_engineering

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https://en.wikipedia.org/wiki/Vacuum_cooling

https://en.wikipedia.org/wiki/Tungsten_hexafluoride

https://en.wikipedia.org/wiki/Timeline_of_low-temperature_technology

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https://en.wikipedia.org/wiki/Cryogenic_gas_plant

https://en.wikipedia.org/wiki/Cryogenic_fuel

https://en.wikipedia.org/wiki/Cryocooler

https://en.wikipedia.org/wiki/Compressed_hydrogen

https://en.wikipedia.org/wiki/Compressed_air_dryer

https://en.wikipedia.org/wiki/Supercritical_carbon_dioxide

https://en.wikipedia.org/wiki/Sulfur_hexafluoride

https://en.wikipedia.org/wiki/Radon

https://en.wikipedia.org/wiki/Refrigerant

https://en.wikipedia.org/wiki/Compressed_air

https://en.wikipedia.org/wiki/Coal_gasification

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https://en.wikipedia.org/wiki/Chemical_looping_reforming_and_gasification

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https://en.wikipedia.org/wiki/Carbon_dioxide_generator

https://en.wikipedia.org/wiki/Carbon_dioxide_clathrate

https://en.wikipedia.org/wiki/Carbogen

https://en.wikipedia.org/wiki/Calibration_gas

https://en.wikipedia.org/wiki/Inerting_system

https://en.wikipedia.org/wiki/Inert_gas_generator

https://en.wikipedia.org/wiki/Inhalant

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https://en.wikipedia.org/wiki/Blast_furnace_gas

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https://en.wikipedia.org/wiki/Oxy-fuel_welding_and_cutting

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Döbereiner's hydrogen lamp

Early understanding consisted of empirical evidence and the protoscience of alchemy; however with the advent of scientific method^[6] and the science of chemistry, these gases became positively identified and understood.

The timeline of attributed discovery for various gases are carbon dioxide (1754),^[7] hydrogen (1766),^[8]^[9] nitrogen (1772),^[8] nitrous oxide (1772),^[10] oxygen (1773),^[8]^[11]^[12] ammonia (1774),^[13] chlorine (1774),^[8] methane (1776),^[14] hydrogen sulfide (1777),^[15] carbon monoxide (1800),^[16] hydrogen chloride (1810),^[17] acetylene (1836),^[18] helium (1868) ^[8]^[19] fluorine (1886),^[8] argon (1894),^[8] krypton, neon and xenon (1898) ^[8] and radon (1899).^[8]

https://en.wikipedia.org/wiki/Industrial_gas

A gas evolution reaction is a chemical reaction in which one of the end products is a gas such as oxygen or carbon dioxide.^[1]^[2] Gas evolution reactions may be carried out in a fume chamber when the gases produced are poisonous when inhaled or explosive.^[3]

Examples

A replacement reaction concerning zinc metal and dilute sulfuric acid.

Zn + H_{2}^{} {SO}_{4}^{} (dil) ⟶ {ZnSO}_{4}^{} + H_{2}^{} ↑

In this example, diatomic hydrogen gas is released. Dilute hydrochloric acid can be used in place of dilute sulfuric acid.

A replacement reaction where gaseous hydrogen chloride and fluorine gas react to release diatomic chlorine gas (because fluorine is more electronegative):

2 HCl + F_{2}^{} ⟶ 2 HF + {Cl}_{2}^{} ↑

https://en.wikipedia.org/wiki/Gas_evolution_reaction

https://en.wikipedia.org/wiki/Diatomic_molecule

https://en.wikipedia.org/wiki/Electronegativity

https://en.wikipedia.org/wiki/Oxygen_evolution

https://en.wikipedia.org/wiki/Gasogene

https://en.wikipedia.org/wiki/Electrolysis_of_water

https://en.wikipedia.org/wiki/Photosystem_II

https://en.wikipedia.org/wiki/Cyanobacteria

https://en.wikipedia.org/wiki/Light-dependent_reactions

https://en.wikipedia.org/wiki/Photosynthesis#Overview

https://en.wikipedia.org/wiki/Monatomic_gas

https://en.wikipedia.org/wiki/Standard_temperature_and_pressure

https://en.wikipedia.org/wiki/Thermal_decomposition

https://en.wikipedia.org/wiki/Chemical_decomposition

The stability of a chemical compound is eventually limited when exposed to extreme environmental conditions such as heat, radiation, humidity, or the acidity of a solvent. Because of this chemical decomposition is often an undesired chemical reaction. However chemical decomposition can be desired, such as in various waste treatment processes.

https://en.wikipedia.org/wiki/Chemical_decomposition

Blog Archive

Thursday, May 11, 2023

05-11-2023-0415 - List of Rock Types

Igneous rocks

Sedimentary rocks

Metamorphic rocks

Specific varieties

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External links

Category:Geology-related lists

Subcategories

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G

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Pages in category "Geology-related lists"

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Gas mixtures for brewing

Controlled atmosphere manufacture and storage

Customized gas mixtures for analytical applications

Reverse RDF

ADF and NDB

VOR

Beam systems

Lorenz

Low-frequency radio range

Glide path and the localizer of ILS

Transponder systems

Radar and transponders

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Hyperbolic systems

Gee

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Other hyperbolic systems

Satellite navigation

International regulation

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Stations

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External links

Category:Wireless locating

Subcategories

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R