diff --git a/_index.db b/_index.db index 4251f4321..79f1b27e0 100644 Binary files a/_index.db and b/_index.db differ diff --git a/data/en.wikipedia.org/wiki/Colorimeter_(chemistry)-0.md b/data/en.wikipedia.org/wiki/Colorimeter_(chemistry)-0.md new file mode 100644 index 000000000..91dbac6ee --- /dev/null +++ b/data/en.wikipedia.org/wiki/Colorimeter_(chemistry)-0.md @@ -0,0 +1,63 @@ +--- +title: "Colorimeter (chemistry)" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Colorimeter_(chemistry)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:23.481845+00:00" +instance: "kb-cron" +--- + +A colorimeter is a device used in colorimetry that measures the absorbance of particular wavelengths of light by a specific solution. It is commonly used to determine the concentration of a known solute in a given solution by the application of the Beer–Lambert law, which states that the concentration of a solute is proportional to the absorbance. + + +== Construction == + +The essential parts of a colorimeter are: + +a light source (often an ordinary low-voltage filament lamp); +an adjustable aperture; +a set of colored filters; +a cuvette to hold the working solution; +a detector (usually a photoresistor) to measure the transmitted light; +a meter to display the output from the detector. +In addition, there may be: + +a voltage regulator, to protect the instrument from fluctuations in mains voltage; +a second light path, cuvette and detector. This enables comparison between the working solution and a "blank", consisting of pure solvent, to improve accuracy. +There are many commercialized colorimeters as well as open source versions with construction documentation for education and for research. + + +=== Filters === +Changeable optics filters are used in the colorimeter to select the wavelength which the solute absorbs the most, in order to maximize accuracy. The usual wavelength range is from 400 to 700 nm. If it is necessary to operate in the ultraviolet range then some modifications to the colorimeter are needed. In modern colorimeters the filament lamp and filters may be replaced by several (light-emitting diode) of different colors. + + +=== Cuvettes === + +In a manual colorimeter the cuvettes are inserted and removed by hand. An automated colorimeter (as used in an AutoAnalyzer) is fitted with a flowcell through which solution flows continuously. + + +== Output == +The output from a colorimeter may be displayed by an analogue or digital meter and may be shown as transmittance (a linear scale from 0 to 100%) or as absorbance (a logarithmic scale from zero to infinity). The useful range of the absorbance scale is from 0 to 2 but it is desirable to keep within the range 0–1, because above 1 the results become unreliable due to scattering of light. +In addition, the output may be sent to a chart recorder, data logger, or computer. + + +== Applications in Biochemistry and Diagnostics == +In clinical laboratories, the colorimeter is commonly used to estimate various biochemical compounds in biological samples. In all methods where a colored product is formed in reaction with a specific analyte, the analyte can be quantitatively measured. For instance, it is used in the Folin–Wu method for measuring blood glucose, in which glucose is converted to a colored complex and absorbance is read at 680 nm; similarly, urea concentration in blood and urine is determined via enzymatic color reactions and color intensity is quantified by colorimetric measurement. + + +== See also == + +Spectronic 20 +Spectrophotometer +Lovibond Colorimeter + + +== Notes == + + +== References == +The Nuffield Foundation 2003. March 30, 2003. [1] Archived 4 December 2011 at the Wayback Machine +"Colour." Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc. (2011) Accessed 17 November 2011. [2] +"Colorimetry" Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc. (2011) 17 November 2011. [3] +Orion Colorimetry Theory. The Technical Edge. [4] \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Cosmic_Dust_Analyzer-0.md b/data/en.wikipedia.org/wiki/Cosmic_Dust_Analyzer-0.md new file mode 100644 index 000000000..1b3e1d0fa --- /dev/null +++ b/data/en.wikipedia.org/wiki/Cosmic_Dust_Analyzer-0.md @@ -0,0 +1,39 @@ +--- +title: "Cosmic Dust Analyzer" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Cosmic_Dust_Analyzer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:24.632084+00:00" +instance: "kb-cron" +--- + +The Cosmic Dust Analyzer (CDA) was a large-area (0.1 m2 total sensitive area) multi-sensor dust instrument included on the Cassini spacecraft, which was launched in 1997 and orbited Saturn from 2004 to 2017. The instrument included a chemical dust analyzer (time-of-flight mass spectrometer), a highly reliable impact ionization detector, and two high rate polarized polyvinylidene fluoride (PVDF) detectors. Over 7 years en route to Saturn, the CDA analysed the interplanetary dust cloud, the stream of interstellar dust, and Jupiter dust streams. During 13 years in orbit around Saturn, the CDA studied the E ring, dust in the plumes of Enceladus, and dust in Saturn's environment. + + +== Overview == + +The Cosmic Dust Analyzer was the seventh dust instrument from the Max Planck Institute for Nuclear Physics (MPIK), Heidelberg (Germany) following the dust detectors on the HEOS 2 satellite and dust detectors on the Galileo and Ulysses space probes and the more complex dust analyzers on the Helios spacecraft, the Giotto and VeGa spacecraft to Halley's Comet. The new dust analyzer system was developed by a team of scientists led by Eberhard Grün and engineers led by Dietmar Linkert to analyze dust in the Saturn system on board the Cassini spacecraft. This instrument employed a larger sensitive area (0.1 m2) impact detector, a smaller time-of-flight mass spectrometer chemical analyzer and two high rate polarized polyvinylidene fluoride (PVDF) detectors, in order to cope with the high fluxes during crossings of the E ring. The Max Planck Institute for Nuclear Physics in Heidelberg was responsible for the overall instrument development and test. Major contributions were provided by the DLR in Berlin-Adlershof (mechanics, cleanliness, thermal design, tests), Tony McDonnell from University of Canterbury (chemical analyzer, UK), Rutherford Appleton Laboratory (spectrometer electronics, UK) and G. Pahl (mechanical design, Munich, Ger). The PVDF detectors were provided by Tony Tuzzolino from the University of Chicago. +The proposing Principal Investigator for CDA was Eberhard Grün. In 1990 the PI-ship was handed over to Ralf Srama from the Max Planck Institute for Nuclear Physics, who is now at the University of Stuttgart, Germany. Ralf Srama got his degree “Dr.-Ing.” from the Technical University of Munich for his Thesis (10 Nov. 2000, in German), "From the Cosmic-Dust-Analyzer to a model describing scientific spacecraft". + +The main sensor of CDA was an impact ionization detector (IID), similar to the Galileo and Ulysses Dust Detectors. The center of the hemispherical target had the smaller (0.016 m2) Chemical Analyzer Target, CAT, at +1000 V electric potential. Three millimeters in front of the target was a grid at 0 V potential. Dust impacts onto CAT generated a plasma that was separated by the high electric field. Ions obtained an energy of ~1000eV and were focused towards the center collector. Ions were partly collected by the semi-transparent grid at 230 millimeter distance and the center electron multiplier. The waveforms of the charge signals were measured, stored and transmitted to ground. The multiplier signal represented a time-of-flight mass spectrum of the released ions. Two of the four grids at the entrance of the analyzer picked up the electric charge of the dust particle. With these capabilities, the CDA can be considered a prototype dust telescope. +CDA measured the micrometeoroid environment for 18 years, from 1999 until the last active seconds of Cassini in 2017 without major degradation. The instrument fly-away-cover was released in 1997 on day 317. Science planning and operations were managed by Max-Planck-Institute for Nuclear Physics and later by the University of Stuttgart. +The Cassini spacecraft was a three-axes stabilized spacecraft with the antenna occasionally pointing to Earth in order to download data and receive operational commands. In the mean time Cassini’s attitude was controlled by requested observations from one or more of the 12 instruments onboard. In order to obtain some more control of its pointing attitude, CDA employed a turntable between the spacecraft and the dust analyzer. + + +== Major discoveries and observations == + + +=== During interplanetary cruise === +From launch in 1997 until arrival at Saturn in 2004, Cassini–Huygens cruised interplanetary space from 0.7 to 10 AU. During this time there were long periods useful for observations of interplanetary and interstellar dust in the inner planetary system. Highlights were the detection of electrical charges of dust in interplanetary space and the determination of the composition of interplanetary dust particles. No measurements were possible during the crossing of the asteroid belt. During Jupiter flyby in 2000 there was a chance to analyze nanometer-sized dust stream particles and demonstrate their compositional relation to Jupiter's moon Io where they originate from. On approach to Saturn in 2004, similar streams of submicron grains with speeds in the order of 100 km/s were detected. These particles originate mostly from the outer parts of the dense rings. They were ejected by Saturn’s magnetic field until they become entrained in the solar wind magnetic field. The Saturn stream particles consist of silicate impurities of the primary icy ring particles. + + +=== In Saturn orbit === +During Cassini’s 292 orbits around Saturn (2004 to 2017) CDA measured several million dust impacts that characterize dust mostly in Saturn’s E ring. In this process CDA found that the E ring extends about twice as far from Saturn as optically observed. Measurements of variable dust charges depending on the magnetospheric plasma conditions (allowed the definition of a dynamical dust model of Saturn's E ring describing the observed properties. In 2005 during Cassini’s close flyby of Enceladus within 175 km from the surface CDA together with two other Cassini instruments discovered active ice geysers located at the south pole of Saturn's moon Enceladus. Later, detailed compositional analyses of the water ice grains in the vicinity of Enceladus led to the discovery of large reservoirs of liquid water oceans below the icy crust of Enceladus. During the Cassini spacecraft’s Grand Finale mission in 2017, it performed 22 traversals of the region between Saturn and its innermost D ring. During this path CDA detected of dust from Saturn's dense rings. Most analyzed grains were a few tens of nanometers in size and had silicate and water-ice composition. For most of Cassini’s orbital tour CDA observed a faint signature of interstellar dust in the largely dominant foreground of E ring water-ice particles. Mass spectra of the interstellar grains suggest the presence of magnesium-rich grains of silicate and oxide composition, some with iron inclusions. Major discoveries until 2011 were summarized in a dedicated paper. + + +== See also == +Galileo and Ulysses Dust Detectors + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/DNA_sequencer-0.md b/data/en.wikipedia.org/wiki/DNA_sequencer-0.md new file mode 100644 index 000000000..e56c5b423 --- /dev/null +++ b/data/en.wikipedia.org/wiki/DNA_sequencer-0.md @@ -0,0 +1,22 @@ +--- +title: "DNA sequencer" +chunk: 1/3 +source: "https://en.wikipedia.org/wiki/DNA_sequencer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:28.229170+00:00" +instance: "kb-cron" +--- + +A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine). This is then reported as a text string, called a read. Some DNA sequencers can be also considered optical instruments as they analyze light signals originating from fluorochromes attached to nucleotides. +The first automated DNA sequencer, invented by Lloyd M. Smith, was introduced by Applied Biosystems in 1987. It used the Sanger sequencing method, a technology which formed the basis of the "first generation" of DNA sequencers and enabled the completion of the Human Genome Project in 2001. This first generation of DNA sequencers are essentially automated electrophoresis systems that detect the migration of labelled DNA fragments. Therefore, these sequencers can also be used in the genotyping of genetic markers where only the length of a DNA fragment(s) needs to be determined (e.g. microsatellites, AFLPs). +The Human Genome Project spurred the development of cheaper, high throughput and more accurate platforms known as Next Generation Sequencers (NGS) to sequence the human genome. These include the 454, SOLiD and Illumina DNA sequencing platforms. Next generation sequencing machines have increased the rate of DNA sequencing substantially, as compared with the previous Sanger methods. DNA samples can be prepared automatically in as little as 90 mins, while a human genome can be sequenced at 15 times coverage in a matter of days. +More recent, third-generation DNA sequencers such as PacBio SMRT and Oxford Nanopore offer the possibility of sequencing long molecules, compared to short-read technologies such as Illumina SBS or MGI Tech's DNBSEQ. +Because of limitations in DNA sequencer technology, the reads of many of these technologies are short, compared to the length of a genome therefore the reads must be assembled into longer contigs. The data may also contain errors, caused by limitations in the DNA sequencing technique or by errors during PCR amplification. DNA sequencer manufacturers use a number of different methods to detect which DNA bases are present. The specific protocols applied in different sequencing platforms have an impact in the final data that is generated. Therefore, comparing data quality and cost across different technologies can be a daunting task. Each manufacturer provides their own ways to inform sequencing errors and scores. However, errors and scores between different platforms cannot always be compared directly. Since these systems rely on different DNA sequencing approaches, choosing the best DNA sequencer and method will typically depend on the experiment objectives and available budget. + +== History == +The first DNA sequencing methods were developed by Gilbert (1973) and Sanger (1975). Gilbert introduced a sequencing method based on chemical modification of DNA followed by cleavage at specific bases whereas Sanger's technique is based on dideoxynucleotide chain termination. The Sanger method became popular due to its increased efficiency and low radioactivity. The first automated DNA sequencer was the AB370A, introduced in 1986 by Applied Biosystems. The AB370A was able to sequence 96 samples simultaneously, 500 kilobases per day, and reaching read lengths up to 600 bases. This was the beginning of the "first generation" of DNA sequencers, which implemented Sanger sequencing, fluorescent dideoxy nucleotides and polyacrylamide gel sandwiched between glass plates - slab gels. The next major advance was the release in 1995 of the AB310 which utilized a linear polymer in a capillary in place of the slab gel for DNA strand separation by electrophoresis. These techniques formed the base for the completion of the Human Genome Project in 2001. The Human Genome Project spurred the development of cheaper, high throughput and more accurate platforms known as Next Generation Sequencers (NGS). In 2005, 454 Life Sciences released the 454 sequencer, followed by Solexa Genome Analyzer and SOLiD (Supported Oligo Ligation Detection) by Agencourt in 2006. Applied Biosystems acquired Agencourt in 2006, and in 2007, Roche bought 454 Life Sciences, while Illumina purchased Solexa. Ion Torrent entered the market in 2010 and was acquired by Life Technologies (now Thermo Fisher Scientific). And BGI started manufacturing sequencers in China after acquiring Complete Genomics under their MGI arm. These are still the most common NGS systems due to their competitive cost, accuracy, and performance. +More recently, a third generation of DNA sequencers was introduced. The sequencing methods applied by these sequencers do not require DNA amplification (polymerase chain reaction – PCR), which speeds up the sample preparation before sequencing and reduces errors. In addition, sequencing data is collected from the reactions caused by the addition of nucleotides in the complementary strand in real time. Two companies introduced different approaches in their third-generation sequencers. Pacific Biosciences sequencers utilize a method called Single-molecule real-time (SMRT), where sequencing data is produced by light (captured by a camera) emitted when a nucleotide is added to the complementary strand by enzymes containing fluorescent dyes. Oxford Nanopore Technologies is another company developing third-generation sequencers using electronic systems based on nanopore sensing technologies. + +== Manufacturers of DNA sequencers == +DNA sequencers have been developed, manufactured, and sold by the following companies, among others. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/DNA_sequencer-1.md b/data/en.wikipedia.org/wiki/DNA_sequencer-1.md new file mode 100644 index 000000000..d1c7d3d0d --- /dev/null +++ b/data/en.wikipedia.org/wiki/DNA_sequencer-1.md @@ -0,0 +1,34 @@ +--- +title: "DNA sequencer" +chunk: 2/3 +source: "https://en.wikipedia.org/wiki/DNA_sequencer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:28.229170+00:00" +instance: "kb-cron" +--- + +=== Roche === +The 454 DNA sequencer was the first next-generation sequencer to become commercially successful. It was developed by 454 Life Sciences and purchased by Roche in 2007. 454 utilizes the detection of pyrophosphate released by the DNA polymerase reaction when adding a nucleotide to the template strain. +Roche currently manufactures two systems based on their pyrosequencing technology: the GS FLX+ and the GS Junior System. The GS FLX+ System promises read lengths of approximately 1000 base pairs while the GS Junior System promises 400 base pair reads. A predecessor to GS FLX+, the 454 GS FLX Titanium system was released in 2008, achieving an output of 0.7G of data per run, with 99.9% accuracy after quality filter, and a read length of up to 700bp. In 2009, Roche launched the GS Junior, a bench top version of the 454 sequencer with read length up to 400bp, and simplified library preparation and data processing. +One of the advantages of 454 systems is their running speed. Manpower can be reduced with automation of library preparation and semi-automation of emulsion PCR. A disadvantage of the 454 system is that it is prone to errors when estimating the number of bases in a long string of identical nucleotides. This is referred to as a homopolymer error and occurs when there are 6 or more identical bases in row. Another disadvantage is that the price of reagents is relatively more expensive compared with other next-generation sequencers. +In 2013 Roche announced that they would be shutting down development of 454 technology and phasing out 454 machines completely in 2016 when its technology became noncompetitive. +Roche produces a number of software tools which are optimised for the analysis of 454 sequencing data. Such as, + +GS Run Processor converts raw images generated by a sequencing run into intensity values. The process consists of two main steps: image processing and signal processing. The software also applies normalization, signal correction, base-calling and quality scores for individual reads. The software outputs data in Standard Flowgram Format (or SFF) files to be used in data analysis applications (GS De Novo Assembler, GS Reference Mapper or GS Amplicon Variant Analyzer). +GS De Novo Assembler is a tool for de novo assembly of whole-genomes up to 3GB in size from shotgun reads alone or combined with paired end data generated by 454 sequencers. It also supports de novo assembly of transcripts (including analysis), and also isoform variant detection. +GS Reference Mapper maps short reads to a reference genome, generating a consensus sequence. The software is able to generate output files for assessment, indicating insertions, deletions and SNPs. Can handle large and complex genomes of any size. +Finally, the GS Amplicon Variant Analyzer aligns reads from amplicon samples against a reference, identifying variants (linked or not) and their frequencies. It can also be used to detect unknown and low-frequency variants. It includes graphical tools for analysis of alignments. + +=== Illumina === + +Illumina produces a number of next-generation sequencing machines using technology acquired from Manteia Predictive Medicine and developed by Solexa. Illumina makes a number of next generation sequencing machines using this technology including the HiSeq, Genome Analyzer IIx, MiSeq and the HiScanSQ, which can also process microarrays. +The technology leading to these DNA sequencers was first released by Solexa in 2006 as the Genome Analyzer. Illumina purchased Solexa in 2007. The Genome Analyzer uses a sequencing by synthesis method. The first model produced 1G per run. During the year 2009 the output was increased from 20G per run in August to 50G per run in December. In 2010 Illumina released the HiSeq 2000 with an output of 200 and then 600G per run which would take 8 days. At its release the HiSeq 2000 provided one of the cheapest sequencing platforms at $0.02 per million bases as costed by the Beijing Genomics Institute. +In 2011 Illumina released a benchtop sequencer called the MiSeq. At its release the MiSeq could generate 1.5G per run with paired end 150bp reads. A sequencing run can be performed in 10 hours when using automated DNA sample preparation. +The Illumina HiSeq uses two software tools to calculate the number and position of DNA clusters to assess the sequencing quality: the HiSeq control system and the real-time analyzer. These methods help to assess if nearby clusters are interfering with each other. + +=== Life Technologies === +Life Technologies (now Thermo Fisher Scientific) produces DNA sequencers under the Applied Biosystems and Ion Torrent brands. Applied Biosystems makes the SOLiD next-generation sequencing platform, and Sanger-based DNA sequencers such as the 3500 Genetic Analyzer. Under the Ion Torrent brand, Applied Biosystems produces four next-generation sequencers: the Ion PGM System, Ion Proton System, Ion S5 and Ion S5xl systems. The company is also believed to be developing their new capillary DNA sequencer called SeqStudio that will be released early 2018. +SOLiD systems was acquired by Applied Biosystems in 2006. SOLiD applies sequencing by ligation and dual base encoding. The first SOLiD system was launched in 2007, generating reading lengths of 35bp and 3G data per run. After five upgrades, the 5500xl sequencing system was released in 2010, considerably increasing read length to 85bp, improving accuracy up to 99.99% and producing 30G per 7-day run. +The limited read length of the SOLiD has remained a significant shortcoming and has to some extent limited its use to experiments where read length is less vital such as resequencing and transcriptome analysis and more recently ChIP-Seq and methylation experiments. The DNA sample preparation time for SOLiD systems has become much quicker with the automation of sequencing library preparations such as the Tecan system. +The colour space data produced by the SOLiD platform can be decoded into DNA bases for further analysis, however software that considers the original colour space information can give more accurate results. Life Technologies has released BioScope, a data analysis package for resequencing, ChiP-Seq and transcriptome analysis. It uses the MaxMapper algorithm to map the colour space reads. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/DNA_sequencer-2.md b/data/en.wikipedia.org/wiki/DNA_sequencer-2.md new file mode 100644 index 000000000..9c900b516 --- /dev/null +++ b/data/en.wikipedia.org/wiki/DNA_sequencer-2.md @@ -0,0 +1,26 @@ +--- +title: "DNA sequencer" +chunk: 3/3 +source: "https://en.wikipedia.org/wiki/DNA_sequencer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:28.229170+00:00" +instance: "kb-cron" +--- + +=== Beckman Coulter === +Beckman Coulter (now Danaher) has previously manufactured chain termination and capillary electrophoresis-based DNA sequencers under the model name CEQ, including the CEQ 8000. The company now produces the GeXP Genetic Analysis System, which uses dye terminator sequencing. This method uses a thermocycler in much the same way as PCR to denature, anneal, and extend DNA fragments, amplifying the sequenced fragments. + +=== Pacific Biosciences === +Pacific Biosciences produces the PacBio RS and Sequel sequencing systems using a single molecule real time sequencing, or SMRT, method. This system can produce read lengths of multiple thousands of base pairs. Higher raw read errors are corrected using either circular consensus - where the same strand is read over and over again - or using optimized assembly strategies. Scientists have reported 99.9999% accuracy with these strategies. The Sequel system was launched in 2015 with an increased capacity and a lower price. + +=== Oxford Nanopore === +Oxford Nanopore Technologies' MinION sequencer is based on evolving nanopore sequencing technology to nucleic acid analyses. The device is four inches long and gets power from a USB port. MinION decodes DNA directly as the molecule is drawn at the rate of 450 bases/second through a nanopore suspended in a membrane. Changes in electric current indicate which base is present. Initially, the device was 60 to 85 percent accurate, compared with 99.9 percent in conventional machines. Even inaccurate results may prove useful because it produces long read lengths. In early 2021, researchers from University of British Columbia has used special molecular tags and able to reduce the five-to-15 per cent error rate of the device to less than 0.005 per cent even when sequencing many long stretches of DNA at a time. There are two more product iterations based on MinION; the first one is the GridION which is a slightly larger sequencer that processes up to five MinION flow cells at once. And, the second one is the PromethION which uses as many as 100,000 pores in parallel, more suitable for high volume sequencing. + +=== MGI === +MGI produces high-throughput sequencers for scientific research and clinical applications such as DNBSEQ-G50, DNBSEQ-G400, and DNBSEQ-T7, under a proprietary DNBSEQ technology. It is based upon DNA nanoball sequencing and combinatorial probe anchor synthesis technologies, in which DNA nanoballs (DNBs) are loaded onto a patterned array chip via the fluidic system, and later a sequencing primer is added to the adaptor region of DNBs for hybridization. DNBSEQ-T7 can generate short reads at a very large scale—up to 60 human genomes per day. DNBSEQ-T7 was used to generate 150 bp paired-end reads, sequencing 30X, to sequence the genome of SARS-CoV-2 or COVID-19 to identify the genetic variants predisposition in severe COVID-19 illness. Using a novel technique the researchers from China National GeneBank sequenced PCR-free libraries on MGI's PCR-free DNBSEQ arrays to obtain for the first time a true PCR-free whole genome sequencing. MGISEQ-2000 was used in single-cell RNA sequencing to study the underlying pathogenesis and recovery in COVID-19 patients, as published in Nature Medicine. + +== Comparison == +Current offerings in DNA sequencing technology show a dominant player: Illumina (December 2019), followed by PacBio, MGI and Oxford Nanopore. + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/DU_spectrophotometer-0.md b/data/en.wikipedia.org/wiki/DU_spectrophotometer-0.md new file mode 100644 index 000000000..87a9ecffa --- /dev/null +++ b/data/en.wikipedia.org/wiki/DU_spectrophotometer-0.md @@ -0,0 +1,25 @@ +--- +title: "DU spectrophotometer" +chunk: 1/5 +source: "https://en.wikipedia.org/wiki/DU_spectrophotometer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:29.374364+00:00" +instance: "kb-cron" +--- + +The DU spectrophotometer or Beckman DU, introduced in 1941, was the first commercially viable scientific instrument for measuring the amount of ultraviolet light absorbed by a substance. This model of spectrophotometer enabled scientists to easily examine and identify a given substance based on its absorption spectrum, the pattern of light absorbed at different wavelengths. Arnold O. Beckman's National Technical Laboratories (later Beckman Instruments) developed three in-house prototype models (A, B, C) and one limited distribution model (D) before moving to full commercial production with the DU. Approximately 30,000 DU spectrophotometers were manufactured and sold between 1941 and 1976. +Sometimes referred to as a UV–Vis spectrophotometer because it measured both the ultraviolet (UV) and visible spectra, the DU spectrophotometer is credited as being a truly revolutionary technology. It yielded more accurate results than previous methods for determining the chemical composition of a complex substance, and substantially reduced the time needed for an accurate analysis from weeks or hours to minutes. The Beckman DU was essential to several critical secret research projects during World War II, including the development of penicillin and synthetic rubber. + +== Background == +Before the development of the DU spectrophotometer, analysis of a test sample to determine its components was a long, costly, and often inaccurate process. A classical wet laboratory contained a wide variety of complicated apparatus. Test samples were run through a series of awkward and time-consuming qualitative processes to separate out and identify their components. Determining quantitative concentrations of those components in the sample involved further steps. Processes could involve techniques for chemical reactions, precipitations, filtrations and dissolutions. Determination of the concentrations of known impurities in a known inorganic substance such as molten iron could be done in under thirty minutes. The determination of complex organic structures such as chlorophyll using wet and dry methods could take decades. +Spectroscopic methods for observing the absorption of electromagnetic radiation in the visible spectrum were known as early as the 1860s. +Scientists had observed that light traveling through a medium would be absorbed at different wavelengths, depending on the matter-composition of the medium involved. A white light source would emit light at multiple wavelengths over a range of frequencies. A prism could be used to separate a light source into specific wavelengths. Shining the light through a sample of a material would cause some wavelengths of light to be absorbed, while others would be unaffected and continue to be transmitted. Wavelengths in the resulting absorption spectrum would differ depending upon the atomic and molecular composition if the material involved. +Spectroscopic methods were predominantly used by physicists and astrophysicists. Spectroscopic techniques were rarely taught in chemistry classes and were unfamiliar to most practicing chemists. Beginning around 1904, Frank Twyman of the London instrument making firm Adam Hilger, Ltd. tried to develop spectroscopic instruments for chemists, but his customer base was consistently made up of physicists rather than chemists. + By the 1930s he had developed a niche market in metallurgy, where his instruments were well adapted to the types of problems that chemists were solving. +By the 1940s, both academic and industrial chemists were becoming increasingly interested in problems involving the composition and detection of biological molecules. Biological molecules, including proteins and nucleic acids, absorb light energy in both the ultraviolet and visible range. The spectrum of visible light was not broad enough to enable scientists to examine substances such as vitamin A. Accurate characterization of complex samples, particularly of biological materials, would require the accurate reading of absorption frequencies in the ultraviolet and infrared (IR) sections of the spectrum in addition to visible light. Existing instruments such as the Cenco "Spectrophotelometer" and the Coleman Model DM Spectrophotometer could not be effectively used to examine wavelengths in the ultraviolet range. +The array of equipment needed to measure light energy reaching beyond the visible spectrum towards the ultraviolet could cost a laboratory as much as $3,000, a huge amount in 1940. Repeated readings of a sample were taken to produce photographic plates showing the absorption spectrum of a material at different wavelengths. An experienced human could compare these to the known images to identify a match. Then information from the plates had to be combined to create a graph showing the spectrum as a whole. Ultimately, the accuracy of such approaches was dependent on accurate, consistent development of the photographic plates, and on human visual acuity and practice in reading the wavelengths. + +== Development == +The DU was developed at National Technical Laboratories (later Beckman Instruments) under the direction of Arnold Orville Beckman, an American chemist and inventor. Beginning in 1940, National Technical Laboratories developed three in-house prototype models (A, B, C) and one limited distribution model (D) before moving to full commercial production with the DU in 1941. Beckman's research team was led by Howard Cary, who went on to co-found Applied Physics Corporation (later Cary Instruments) which became one of Beckman Instruments' strongest competitors. Other scientists included Roland Hawes and Kenyon George. +Coleman Instruments had recently coupled a pH meter with an optical phototube unit to examine the visual spectrum (the Coleman Model DM). Beckman had already developed a successful pH meter for measuring acidity of solutions, his company's breakthrough product. Seeing the potential to build upon their existing expertise, Beckman made it a goal to create an easy-to-use integrated instrument which would both register and report specific wavelengths extending into the ultraviolet range. Rather than depending on development of photographic plates, or a human observer's visual ability to detect wavelengths in the absorption spectrum, phototubes would be used to register and report the specific wavelengths that were detected. This had the potential to increase the instrument's accuracy and reliability as well as its speed and ease of use. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/DU_spectrophotometer-1.md b/data/en.wikipedia.org/wiki/DU_spectrophotometer-1.md new file mode 100644 index 000000000..91c1f94fa --- /dev/null +++ b/data/en.wikipedia.org/wiki/DU_spectrophotometer-1.md @@ -0,0 +1,33 @@ +--- +title: "DU spectrophotometer" +chunk: 2/5 +source: "https://en.wikipedia.org/wiki/DU_spectrophotometer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:29.374364+00:00" +instance: "kb-cron" +--- + +=== Model A (prototype) === +The first prototype Beckman spectrophotometer, the Model A, was created at National Technologies Laboratories in 1940. It used a tungsten light source with a glass Fery prism as a monochromator. Tungsten was used for incandescent light filaments because it was strong, withstood heat, and emitted a steady light. Types of light sources differed in the range of wavelengths of light that they emitted. Tungsten lamps were useful in the visible light range but gave poor coverage in the ultraviolet range. However, they had the advantage of being readily available because they were used as automobile headlamps. An external amplifier from the Beckman pH meter and a vacuum tube photocell were used to detect wavelengths. + +=== Model B (prototype) === + +It was quickly realized that a glass dispersive prism was not suitable for use in the ultraviolet spectrum. Glass absorbed electromagnetic radiation below 400 millimicrons rather than dispersing it. In the Model B, a quartz prism was substituted for the earlier glass. +A tangent bar mechanism was used to adjust the monochromator. The mechanism was highly sensitive and required a skilled operator. Only two Model B prototypes were made. One was sold: in February 1941, to the University of California Chemistry department in Los Angeles. +The Model B prototype should be distinguished from a later production model of spectrophotometer that was also referred to as the Model "B". The production Model "B" was introduced in 1949 as a less-expensive, simple-to-use alternative to the Beckman DU. It used a glass Fery prism as a chromator and operated in a narrower range, roughly from 320 millimicrons to 950 millimicrons, and 5 to 20 Å. + +=== Model C (prototype) === +Three Model C instruments were then built, improving the instrument's wavelength resolution. The Model B's rotary cell compartment was replaced with a linear sample chamber. The tangent bar mechanism was replaced by a scroll drive mechanism, which could be more precisely controlled to reset the quartz prism and select the desired wavelength. With this new mechanism, results could be more easily and reliably obtained, without requiring a highly skilled operator. This set the pattern for all of Beckman's later quartz prism instruments. Although only three Model B prototypes were built, all were sold, one to Caltech and the other two to companies in the food industry. + +=== Model D (limited production) === + +The A, B, and C prototype models all coupled an external Beckman pH meter to the optical component to obtain readouts. In developing the Model D, Beckman took the direct-coupled amplifier circuit from the pH meter and combined the optical and electronic components in a single housing, making it more economical. +Moving from a prototype to production of the Model D involved challenges. +Beckman originally approached Bausch and Lomb about making quartz prisms for the spectrophotometer. When they turned down the opportunity, National Technical Laboratories designed its own optical system, including both a control mechanism and a quartz prism. Large, high optical quality quartz suitable for creating prisms was difficult to obtain. It came from Brazil, and was in demand for wartime radio oscillators. Beckman had to obtain a wartime priority listing for the spectrophotometer to get access to suitable quartz supplies. +Beckman had previously attempted to find a source of reliable hydrogen lamps, seeking better sensitivity to wavelengths in the ultraviolet range than was possible with tungsten. As described in July 1941, the Beckman spectrophotometer could use a "hot cathode hydrogen discharge tube" or a tungsten light source interchangeably. However, Beckman was still unsatisfied with the available hydrogen lamps. National Technical Laboratories designed its own hydrogen lamp, an anode enclosed in a thin blown-glass window. By December 1941, the in-house design was being used in production of the Model D. +The instrument's design also required a more sensitive phototube than was commercially available at that time. Beckman was able to obtain small batches of an experimental phototube from RCA for the first Model D instruments. +The Model D spectrophotometer, using the experimental RCA phototube, was shown at MIT's Summer Conference on Spectroscopy in July 1941. The paper that Cary and Beckman presented there was published in the Journal of the Optical Society of America. In it, Cary and Beckman compared designs for a modified self-collimating quartz Fery prism, a mirror-collimated quartz Littrow prism, and various gratings. The Littrow prism was a half-prism, which had a mirrored back face, so that the light went through the front face twice. Use of a tungsten light source with the quartz Littrow prism as a monochromator was reported to minimize light scattering within the instrument. +The Model D was the first model to enter actual production. A small number of Model D instruments were sold, beginning in July 1941, before it was superseded by the DU. + +=== Model DU === \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/DU_spectrophotometer-2.md b/data/en.wikipedia.org/wiki/DU_spectrophotometer-2.md new file mode 100644 index 000000000..9d10b0cbc --- /dev/null +++ b/data/en.wikipedia.org/wiki/DU_spectrophotometer-2.md @@ -0,0 +1,29 @@ +--- +title: "DU spectrophotometer" +chunk: 3/5 +source: "https://en.wikipedia.org/wiki/DU_spectrophotometer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:29.374364+00:00" +instance: "kb-cron" +--- + +When RCA could not meet Beckman's demand for experimental phototubes, National Technical Laboratories again had to design its own components in-house. They developed a pair of phototubes, sensitive to the red and blue areas of the spectrum, capable of amplifying the signals they received. With the incorporation of Beckman's UV-sensitive phototubes, the Model D became the Model DU UV–Vis spectrophotometer. Its designation as a "UV–Vis" spectrophotometer indicates its ability to measure light in both the visible and ultraviolet spectra. +The DU was the first commercially viable scientific instrument for measuring the amount of ultraviolet light absorbed by a substance. As he had done with the pH meter, Beckman had replaced an array of complicated equipment with a single, easy-to-use instrument. One of the first fully integrated instruments or "black boxes" used in modern chemical laboratories, it sold for $723 in 1941. +It is generally assumed that the "DU" in the name was a combination of "D" for the Model D on which it was based, and "U" for the ultraviolet spectrum. However, it has been suggested that "DU" may also reference Beckman's fraternity at the University of Illinois, Delta Upsilon, whose members were called "DU"s. +A publication in the scholarly literature compared the optical quality of the DU to the Cary 14 Spectrophotometer, another leading UV–Vis spectrophotometer of the time. + +== Design == + +From 1941 until 1976, when it was discontinued, the Model DU spectrophotometer was built upon what was essentially the same design. It was a single beam instrument. +The DU spectrophotometers used a quartz prism to separate light from a lamp into its absorption spectrum and a phototube to electrically measure the light energy across the spectrum. This allowed the user to plot the light absorption spectrum of a substance to obtain a standardized "fingerprint" characteristic of a compound. All modern UV–Vis spectrophotometer are built on the same basic principles as the DU spectrophotometer. + +"Light from the tungsten lamp is focused by the condensing mirror and directed in a beam to the diagonal slit entrance mirror. The entrance mirror deflects the light through the entrance slit and into the monochromator to the collimating mirror. Light falling on the collimating mirror is rendered parallel and reflected to the quartz prism where it undergoes refraction. The back surface of the prism is aluminized so that light refracted at the first surface is reflected back through the prism, undergoing further refraction as it emerges from the prism. The desired wavelength of light is selected by rotating the Wavelength Selector which adjusts the position of the prism. The spectrum is directed back to the collimating mirror which centers the chosen wavelength on the exit slit and sample. Light passing through the sample strikes the phototube, causing a current gain. The current gain is amplified and registered on the null meter." Model DU Optical System +Although the default light source for the instrument was tungsten, a hydrogen or mercury lamp could be substituted depending on the optimal range of measurement for which the instrument was to be used. The tungsten lamp was suitable for transmittance of wavelengths between 320 and 1000 millimicrons; the hydrogen lamp for 220 to 320 millimicrons, and the mercury lamp for checking the calibration of the spectrophotometer. + +As advertised in the 1941 News Edition of the American Chemical Society, the Beckman Spectrophotometer used an autocollimating quartz crystal prism for a monochromator, capable of covering a range from the ultraviolet (200 millimicrons) to the infrared (2000 millimicrons), with a nominal bandwidth of 2 millimicrons or less for most of its spectral range. The slit mechanism was continuously adjustable from .01 to 2.0 mm and claimed to have less than 1/10% of stray light over most of the spectral range. It featured an easy-to-read wavelength scale, simultaneously reporting % Transmission and Density information. +The sample holder held up to 4 cells. Cells could be moved into the light path via an external control, allowing the user to take multiple readings without opening the cell compartment. As described in the DU's manual, absorbance measurements of a sample were made in comparison to a blank, or standard, "a solution identical in composition with the sample except that the absorbing material being measured is absent." The standard could be a cell filled with a solvent such as distilled water or a prepared solvent of a known concentration. At each wavelength two measurements are made: with the sample and with the standard in the light beam. This enables the ratio, transmittance, to be obtained. For quantitative measurements transmittance is converted to absorbance which is proportional to the solute concentration according to Beer's law. This makes possible the quantitative determination of the amount of a substance in solution. +The user could also switch between phototubes without removing the sample holder. A 1941 advertisement indicates that three types of phototubes were available, with maximum sensitivity to red, blue and ultraviolet light ranges. +The 1954 DU spectrophotometer differs in that it claims to be useful from 200 to 1000 millimicrons, and does not mention the ultraviolet phototube. The wavelength selector, however, still ranged from 200 to 2000 millimicrons. and an "Ultraviolet accessory set" was available. This shift away from using the DU for infrared measurement is understandable, since by 1954 Beckman Instruments was marketing a separate infrared spectrophotometer. Beckman developed the IR-1 infrared spectrophotometer during World War II, and redesigned it as the IR-4 between 1953 and 1956. + +== Use == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/DU_spectrophotometer-3.md b/data/en.wikipedia.org/wiki/DU_spectrophotometer-3.md new file mode 100644 index 000000000..2098779b1 --- /dev/null +++ b/data/en.wikipedia.org/wiki/DU_spectrophotometer-3.md @@ -0,0 +1,34 @@ +--- +title: "DU spectrophotometer" +chunk: 4/5 +source: "https://en.wikipedia.org/wiki/DU_spectrophotometer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:29.374364+00:00" +instance: "kb-cron" +--- + +The Beckman spectrophotometer was the first easy-to-use single instrument containing both the optical and electronic components needed for ultraviolet-absorption spectrophotometry within a single housing. The user could insert a cell tray with standard and sample cells, dial up the desired wavelength of light, confirm that the instrument was properly set by measuring the standard, and then measure the amount of absorption of the sample, reading the frequency from a simple meter. A series of readings at different wavelengths could be taken without disturbing the sample. The DU spectrophotometer's manual scanning method was extremely fast, reducing analysis times from weeks or hours to minutes. + +It was accurate in both the visible and ultraviolet ranges. +Working in both the ultraviolet and the visible regions of the spectrum, the model DU produced accurate absorption spectra which could be obtained with relative ease and accurately replicated. The National Bureau of Standards ran tests to certify that the DU's results were accurate and repeatable and recommended its use. +Other advantages included its high resolution and the minimization of stray light in the ultraviolet region. Although it was not cheap, its initial price of $723 made it available to the average laboratory. In comparison, in 1943, the GE Hardy Spectrophotometer cost $6,400. Practical and reliable, the DU rapidly established itself as a standard for laboratory equipment. + +== Impact == + +Credited with having "brought about a breakthrough in optical spectroscopy", the Beckman DU has been identified as "an indispensable tool for chemistry" and "the Model T of laboratory instruments". Approximately 30,000 DU spectrophotometers were manufactured and sold between 1941 and 1976. +The DU enabled researchers to perform easier analysis of substances by quickly taking measurements at more than one wavelength to produce an absorption spectrum describing the complete substance. For example, the standard method of analysis of the vitamin A content of shark liver oil, before the introduction of the DU spectrophotometer, involved feeding the oil to rats for 21 days, then cutting off the rats' tails and examining their bone structure. With the DU's UV technology, vitamin A content of shark liver oil could be determined directly in a matter of minutes. +The Scripps Research Institute and the Massachusetts Institute of Technology credit the DU with improving both accuracy and speed of chemical analysis. MIT states: "This device forever simplified and streamlined chemical analysis, by allowing researchers to perform a 99.9% accurate quantitative measurement of a substance within minutes, as opposed to the weeks required previously for results of only 25% accuracy." +Inorganic chemist and philosopher of science Theodore L. Brown states that it "revolutionized the measurement of light signals from samples". Nobel laureate Bruce Merrifield is quoted as calling the DU spectrophotometer "probably the most important instrument ever developed towards the advancement of bioscience." Historian of science Peter J. T. Morris identifies the introduction of the DU and other scientific instruments in the 1940s as the beginning of a Kuhnian revolution. +For the Beckman company, the DU was one of three foundational inventions – the pH meter, the DU spectrophotometer, and the helipot potentiometer – that established the company on a secure financial basis and enabled it to expand. + +=== Vitamins === +Development of the spectrophotometer had direct relevance to World War II and the American war effort. The role of vitamins in health was of significant concern, as scientists wanted to identify Vitamin A-rich foods to keep soldiers healthy. Previous methods of assessing Vitamin A levels involved feeding rats a food for several weeks and then performing a biopsy to estimate ingested Vitamin A levels. In contrast, examining a food sample with a DU spectrophotometer yielded better results in a matter of minutes. The DU spectrophotometer could be used to study both vitamin A and its precursor carotenoids, and rapidly became the preferred method of spectrophotometric analysis. + +=== Penicillin === +The DU spectrophotometer was also an important tool for scientists studying and producing the new wonder drug penicillin. +The development of penicillin was a secret national mission, involving 17 drug companies, with the goal of providing penicillin to all U.S. Forces engaged in World War II. It was known that penicillin was more effective than sulfa drugs, and that its use reduced mortality, severity of long-term wound trauma, and recovery time. However, its structure was not understood, isolation procedures used to create pure cultures were primitive, and production using known surface culture techniques was slow. +At Northern Regional Research Laboratory in Peoria, Illinois, researchers collected and examined more than 2,000 specimens of molds (as well as other microorganisms). An extensive research team included Robert Coghill, Norman Heatley, Andrew Moyer, Mary Hunt, Frank H. Stodola and Morris E. Friedkin. Friedkin recalls that an early model of the Beckman DU spectrophotometer was used by the penicillin researchers in Peoria. The Peoria lab was successful in isolating and commercially producing superior strains of the mold, which were 200 times more effective than the original forms discovered by Alexander Fleming. By the end of the war, American pharmaceutical companies were producing 650 billion units of penicillin each month. Much of the work done in this area during World War II was kept secret until after the war. + +=== Hydrocarbons === +The DU spectrophotometer was also used for critical analysis of hydrocarbons. A number of hydrocarbons were of interest to the war effort. Toluene, a hydrocarbon in crude oil, was used in production of TNT for military use. Benzene and butadienes were used in the production of synthetic rubber. Rubber, used in tires for jeeps, airplanes and tanks, was in critically short supply because the United States was cut off from foreign supplies of natural rubber. The Office of Rubber Reserve organized researchers at universities and in industry to secretly work on the problem. The demand for synthetic rubber caused Beckman Instruments to develop infrared spectrophotometers. Infrared spectrophotometers were better suited than UV–Vis spectrophotometers to the analysis of C4 hydrocarbons, particularly for applications in petroleum refining and gasoline production. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/DU_spectrophotometer-4.md b/data/en.wikipedia.org/wiki/DU_spectrophotometer-4.md new file mode 100644 index 000000000..9f62c3071 --- /dev/null +++ b/data/en.wikipedia.org/wiki/DU_spectrophotometer-4.md @@ -0,0 +1,34 @@ +--- +title: "DU spectrophotometer" +chunk: 5/5 +source: "https://en.wikipedia.org/wiki/DU_spectrophotometer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:29.374364+00:00" +instance: "kb-cron" +--- + +=== Enzyme assays and DNA research === +Gerty Cori and her husband Carl Ferdinand Cori won the Nobel Prize in Physiology or Medicine in 1947 in recognition of their work on enzymes. They made several discoveries critical to understanding carbohydrate metabolism, including the isolation and discovery of the Cori ester, glucose 1-phosphate, and the understanding of the Cori cycle. They determined that the enzyme phosphorylase catalyzes formation of glucose 1-phosphate, which is the beginning and ending step in the conversions of glycogen into glucose and blood glucose to glycogen. Gerty Cori was also the first to show that a defect in an enzyme can be the cause of a human genetic disease. The Beckman DU spectrophotometer was used in the Cori laboratory to calculate enzyme concentrations, including phosphorylase. +Another researcher who spent six months in 1947 at the Cori laboratory, "the most vibrant place in biochemistry" at that time, was Arthur Kornberg. Kornberg was already familiar with the DU spectrophotometer, which he had used at Severo Ochoa's laboratory at New York University. The "new and scarce" Beckman DU, loaned to Ochoa by the American Philosophical Society, was highly prized and in constant use. Kornberg used it to purify aconitase, an enzyme in the citric acid cycle. + +"The enzyme could be assayed in a few minutes by coupling it to isocitrate dehydrogenase and in measuring the NADH formed using the Beckman DU spectrophotometer, an instrument that transformed biochemistry." +Kornberg and Bernard L. Horecker used the Beckman DU spectrophotometer for enzyme assays measuring NADH and NADPH. They determined their extinction coefficients, establishing a basis for quantitative measurements in reactions involving nucleotides. This work became one of the most cited papers in biochemistry. Kornberg went on to study nucleotides in DNA synthesis, isolating the first DNA polymerizing enzyme (DNA polymerase I) in 1956 and receiving the Nobel Prize in Physiology or Medicine with Severo Ochoa in 1959. +The bases of DNA absorbed ultraviolet light near 260 nm. Inspired by the work of Oswald Avery on DNA, Erwin Chargaff used a DU spectrophotometer in the 1940s in measuring the relative concentrations of bases in DNA. Based on this research, he formulated Chargaff's rules. In the first complete quantitative analysis of DNA, he reported the near-equal correspondence of pairs of bases in DNA, with the number of guanine units equaling the number of cytosine units, and the number of adenine units equaling the number of thymine units. He further demonstrated that the relative amounts of guanine, cytosine, adenine and thymine varied between species. In 1952, Chargaff met Francis Crick and James D. Watson, discussing his findings with them. Watson and Crick built upon his ideas in their determination of the structure of DNA. + +=== Biotechnology === +Ultraviolet spectroscopy has wide applicability in molecular biology, particularly the study of photosynthesis. It has been used to study a wide variety of flowering plants and ferns by researchers in departments of biology, plant physiology and agriculture science as well as molecular genetics. +Particularly useful in detecting conjugated double bonds, the new technology made it possible for researchers like Ralph Holman and George O. Burr to study dietary fats, work that had significant implications for human diet. The DU spectrophotometer was also used in the study of steroids by researchers like Alejandro Zaffaroni, who helped to develop the birth control pill, the nicotine patch, and corticosteroids. + +== Later models == + +The Beckman team eventually developed additional models, as well as a number of accessories or attachments which could be used to modify the DU for different types of work. One of the first accessories was a flame attachment with a more powerful photo multiplier to enable the user to examine flames such as potassium, sodium and cesium (1947). +In the 1950s, Beckman Instruments developed the DR and the DK, both of which were double-beam ultraviolet spectrophotometers. The DK was named for Wilbur I. Kaye, who developed it by modifying the DU to expand its range into the near-infrared. He did the initial work while at Tennessee Eastman Kodak, and later was hired by Beckman Instruments. The DKs introduced an automatic recording feature. The DK-1 used a non-linear scroll, and the DK-2 used a linear scroll to automatically record the spectra. +The DR incorporated a "robot operator" which would reset the knobs on the DU to complete a sequence of measurements at different wavelengths, just like a human operator would to generate results for a full spectrum. It used a linear shuttle with four positions, and a superstructure to change the knobs. It had a moving chart recorder to plot results, with red, green and black dots. The price of recording spectrophotometers was substantially higher than non-recording machines. +The DK was ten times faster than the DR, but not quite as accurate. It used a photomultiplier, which had introduced a source of error. The DK's speed made it preferred to the DR. Kaye eventually developed the DKU, combining infrared and ultraviolet features in one instrument, but it was more expensive than other models. +The last DU spectrophotometer was produced on July 6, 1976. By the 1980s, computers were being incorporated into scientific instruments such as Bausch & Lomb's Spectronic 2000 UV–Vis spectrophotometer, to improve data acquisition and provide instrument control. Specialized spectrophotometers designed for specific tasks now tend to be used rather than general "all-purpose machines" like the DU. + +== References == + +== External links == +Jaehnig, Kenton G. Finding Aid to the Beckman historical collection, 1911–2011 (bulk 1934–2004). Science History Institute. OCLC 899243886. Retrieved 6 February 2018. Links on landing page go to full documents. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Deposit_gauge-0.md b/data/en.wikipedia.org/wiki/Deposit_gauge-0.md new file mode 100644 index 000000000..12a2c9ce5 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Deposit_gauge-0.md @@ -0,0 +1,47 @@ +--- +title: "Deposit gauge" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Deposit_gauge" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:25.831510+00:00" +instance: "kb-cron" +--- + +A deposit gauge is a large, funnel-like scientific instrument used for capturing and measuring atmospheric particulates, notably soot, carried in air pollution and deposited back down to ground. + + +== Design and construction == +Deposit gauges are similar to rain gauges. They have a large circular funnel on top, made of a material that will not be corroded by acid rain (such as stone, in early versions, or anodized aluminium, in modern ones). This is mounted on a simple wooden or metal stand, which drains down into a collection bottle beneath. Typically the funnel has a wire-mesh screen around its perimeter to deter perching birds. They are made to a standardized design, which means the pollution collected in different places can be systematically studied and compared. The bottle is removed after a period of time (usually from a week to a month) and the contents taken away for analysis of water (such as rain, fog, and snow), insoluble matter (such as soot), and soluble matter. + + +=== Standard designs === +The various standardized designs include: + +The standard deposit gauge, introduced in 1916 and formalized in a British Standard in 1951 +The International Standard (ISO/DIS 4222.2) deposit gauge +The Norwegian NILU gauge, which is similar to the ISO gauge +The German Standard VDI 2119 +ASTM D1739 + + +== Early history == +The first gauges of this type were developed in the early 20th century by W.J. Russell of St Bartholomew's Hospital and the Coal Smoke Abatement Society. Between 1910 and 1916, the design was refined and standardized by the Committee for the Investigation of Atmospheric Pollution, a group of expert, volunteer scientists studying air pollution of which Sir Napier Shaw, first director of the Met Office, was chair. The first scientific paper featuring deposit gauge measurements was titled "The Sootfall of London: Its Amount, Quality, and Effects" and published in The Lancet in January 1912. Thanks to the introduction of the deposit gauge, air quality in Britain was monitored systematically from 1914 onward and this played an important role in determining the effectiveness of efforts to control pollution. By 1927, some deposit gauges were already showing 50 percent reductions in "deposited matter", although air pollution remained a major problem. +Over the next few decades, deposit gauges were deployed in many British towns and cities, allowing rough comparisons to be made of pollution in different parts of the country. According to pollution historian Stephen Mosley, by 1949, some 177 gauges had been deployed across Britain, so creating the world's first large-scale pollution monitoring network, but the number increased dramatically after the Great London Smog of 1952, reaching 615 in 1954 and 1066 in 1966. + + +== Modern use == +Although deposit gauges were inaccurate and their limitations were well known from the start, their widespread introduction still represented a considerable advance in the study and comparison of pollution at different times of the year and in different places. In his book State, Science and the Skies: Governmentalities of the British Atmosphere, Mark Whitehead, a geography lecturer at Aberystywth University, has described the deposit gauge as "perhaps the most important technological device in the history of Britain's air pollution monitoring". Even so, from the mid-20th century, it was gradually superseded by more accurate instruments and better methods of data collection and analysis. +Today, although air pollution is more likely to be measured with automated electronic sensors, deposit gauges are still used. Modern variants of the standard deposit gauge include the so-called "frisbee" gauge, in which the deposit collector is shaped like an inverted frisbee; the Bergerhoff gauge, in which a single glass vessel mounted on a stand acts as both the collector and deposit bottle; and the directional dust deposit gauge (DDDG), which has four tall, removable bottles to collect and compare deposits arriving from different directions. + + +== See also == +Rain gauge +Air pollution measurement + + +== References == + + +== Further reading == +Brimblecombe, Peter (1987). The Big Smoke: A History of Air Pollution in London Since Medieval Times. Routledge. pp. 147–160. ISBN 9781136703294. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Dichroscope-0.md b/data/en.wikipedia.org/wiki/Dichroscope-0.md new file mode 100644 index 000000000..880e12513 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Dichroscope-0.md @@ -0,0 +1,21 @@ +--- +title: "Dichroscope" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Dichroscope" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:27.051509+00:00" +instance: "kb-cron" +--- + +A dichroscope is a pocket instrument used in the field of gemology, and can be used to test transparent gemstones (crystals). Experienced gemologists, observing the pleochroism of some gems, can successfully detect gemstones from other artificial stones using this instrument. + +There are two types of dichroscopes available: calcite and polarizing. Of the two, calcite gives better results and is widely used by experienced gemologists. With the polarizing type, only one pleochroic color can be seen at a time. This makes the process time-consuming and difficult, though it is the most economical way to get results. +The dichroscope has been used since at least the start of the nineteenth century. + + +== Calcite dichroscope == +A calcite dichroscope shows a gem's pleochroic colors in contrast with one another, allowing the viewer to easily determine whether the stone is singly or doubly refractive (uniaxial or biaxial, respectively). Singly refractive stones do not split light that enters them, leaving light as a single beam as it exits the stone. On the contrary, doubly refractive stones may split an entering light beam into two rays (an ordinary ray and an extraordinary ray) depending on the angle, a property known as birefringence. Calcite dichroscopes are effective because the inner calcite component is able to split the entering light beam coming through the stone, revealing whether the stone is isotropic, uniaxial or biaxial. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Dual-polarization_interferometry-0.md b/data/en.wikipedia.org/wiki/Dual-polarization_interferometry-0.md new file mode 100644 index 000000000..eaf473afc --- /dev/null +++ b/data/en.wikipedia.org/wiki/Dual-polarization_interferometry-0.md @@ -0,0 +1,31 @@ +--- +title: "Dual-polarization interferometry" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Dual-polarization_interferometry" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:30.582869+00:00" +instance: "kb-cron" +--- + +Dual-polarization interferometry (DPI) is an analytical technique that probes molecular layers adsorbed to the surface of a waveguide using the evanescent wave of a laser beam. It is used to measure the conformational change in proteins, or other biomolecules, as they function (referred to as the conformation activity relationship). + + +== Instrumentation == +DPI focuses laser light into two waveguides. One of these functions as the "sensing" waveguide having an exposed surface while the second one functions to maintain a reference beam. A two-dimensional interference pattern is formed in the far field by combining the light passing through the two waveguides. The DPI technique rotates the polarization of the laser, to alternately excite two polarization modes of the waveguides. Measurement of the interferogram for both polarizations allows both the refractive index and the thickness of the adsorbed layer to be calculated. The polarization can be switched rapidly, allowing real-time measurements of chemical reactions taking place on a chip surface in a flow-through system. These measurements can be used to infer conformational information about the molecular interactions taking place, as the molecule size (from the layer thickness) and the fold density (from the RI) change. DPI is typically used to characterize biochemical interactions by quantifying any conformational change at the same time as measuring reaction rates, affinities and thermodynamics. +The technique is quantitative and real-time (10 Hz) with a dimensional resolution of 0.01 nm. +Extensions of dual-polarization interferometry also exist, namely multiple pathlength dual-polarization interferometry (MPL-DPI) and absorption enhanced DPI. In MPL-DPI quantification of both layer thickness and refractive index (density) and therefore mass per unit area can be made for in situ and ex-situ coated films, where normal DPI can only calculate film properties if the interferogram is constantly monitored. Absorption enhanced DPI (AE-DPI) is used to separate the mass of different molecules on the surface, exploiting the absorption of one of the molecular species compared to the other species on the surface. + + +== Applications == +A novel application for dual-polarization interferometry emerged in 2008, where the intensity of light passing through the waveguide is extinguished in the presence of crystal growth. This has allowed the very earliest stages in protein crystal nucleation to be monitored. Later versions of dual-polarization interferometers also have the capability to quantify the order and disruption in birefringent thin films. This has been used, for example, to study the formation of lipid bilayers and their interaction with membrane proteins. + + +== References == + + +== Further reading == +Cross, GH; Ren, Y; Freeman, NJ (1999). "Young's fringes from vertically integrated slab waveguides: Applications to humidity sensing" (PDF). Journal of Applied Physics. 86 (11): 6483. Bibcode:1999JAP....86.6483C. doi:10.1063/1.371712. S2CID 121706760. +Cross, G (2003). "A new quantitative optical biosensor for protein characterisation". Biosensors and Bioelectronics. 19 (4): 383–90. doi:10.1016/S0956-5663(03)00203-3. PMID 14615097. +Freeman, NJ; Peel, LL; Swann, MJ; Cross, GH; Reeves, A; Brand, S; Lu, JR (2004). "Real time, high resolution studies of protein adsorption and structure at the solid–liquid interface using dual polarization interferometry". Journal of Physics: Condensed Matter. 16 (26): S2493–S2496. Bibcode:2004JPCM...16S2493F. doi:10.1088/0953-8984/16/26/023. S2CID 250737643. +Khan, TR; Grandin, HM; Mashaghi, A; Textor, M; Reimhult, E; Reviakine, I (2008). "Lipid redistribution in phosphatidylserine-containing vesicles adsorbing on titania". Biointerphases. 3 (2): FA90. doi:10.1116/1.2912098. PMID 20408675. S2CID 28632810. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Ecotron-0.md b/data/en.wikipedia.org/wiki/Ecotron-0.md new file mode 100644 index 000000000..14638303e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Ecotron-0.md @@ -0,0 +1,28 @@ +--- +title: "Ecotron" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Ecotron" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:31.755715+00:00" +instance: "kb-cron" +--- + +An Ecotron is an experimental instrument in ecology consisting of a controlled environment which makes it possible to simultaneously condition the environment of natural, simplified, or completely artificial ecosystems and measure the processes generated by living beings present in these ecosystems, in particular the flow of matter and energy. + + +== Design == +Its principle is to confine ecosystems in totally or partially waterproof enclosures which are permeable to energy flow and capable of generating a range of physical and chemical conditions applied to terrestrial or aquatic ecosystems, continental or marine. Environmental control and real-time measurements are precise enough to test hypotheses or operating models. For this purpose, the enclosures are fitted with significant equipment allowing continuous measurement of fluxes, states or biological characteristics. Other specific measurements, in situ and ex situ, on samples taken complete these online measurements. A sufficient number of independent confinement chambers is necessary to study several interacting factors in a framework of statistical inference. +Depending on the case, we speak of a macrocosm when the space is large enough to study several m3 of reconstituted ecosystem over a period of time, generally measured in years (3-5 years or more for example), of microcosm for volumes measuring in cubic decimeters (study of fungal, bacterial, soil ecosystems, etc.) and mesocosm for intermediate situations. + + +== References == + + +== Bibliography == + + +== External links == +Paris CEREEP – ECOTRON IDF +Montpellier European Ecotron +Deep Soil Ecotron \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Filar_micrometer-0.md b/data/en.wikipedia.org/wiki/Filar_micrometer-0.md new file mode 100644 index 000000000..bb1aa2fe8 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Filar_micrometer-0.md @@ -0,0 +1,40 @@ +--- +title: "Filar micrometer" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Filar_micrometer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:32.890741+00:00" +instance: "kb-cron" +--- + +A filar micrometer is a specialized eyepiece used in astronomical telescopes for astrometry measurements, in microscopes for specimen measurements, and in alignment and surveying telescopes for measuring angles and distances on nearby objects. "Filar" derives from the Latin filum ("thread"). It refers to the fine threads or wires used in the device. + + +== Construction and use == + +A typical filar micrometer consists of a reticle that has two fine parallel wires or threads that can be moved by the observer using a micrometer screw mechanism. The wires are placed in the focal image plane of the eyepiece so they remain sharply superimposed over the object under observation, while the micrometer motion moves the wires across the focal plane. Other designs employ a fixed reticle, against which one wire or a second reticle moves. By rotating the eyepiece assembly in the eyetube, the measurement axis can be aligned to match the orientation of the two points of observation. +At one time, it was common to use spider silk as a thread. +By placing one wire over one point of interest and moving the other to a second point, the distance between the two wires can be measured with the micrometer portion of the instrument. Given this precise distance measurement at the image plane, a trigonometric calculation with the objective focal length yields the angular distance between the two points seen in a telescope. In a microscope, a similar calculation yields the spatial distance between two points on a specimen. +In an alignment telescope, the precise micrometric measurement of the eyepiece image directly indicates the real distance of a nearby observed point from the line of sight. This absolute measurement is independent of the distance to the object, due to the telecentricity principle. +A common use of filar micrometers in astronomical telescopes was measuring the distance between double stars. +Filar micrometers are little used in modern astronomy, having been replaced by digital photographic techniques where digital pixels provide a precise reference for image distance. Filar eyepieces are still used in teaching astronomy and by some amateur astronomers. + + +== Prior devices == +The precursor to the filar micrometer was the micrometer eyepiece, invented by William Gascoigne. +Earlier measures of angular distances relied on inserting into the eyepiece a thin metal sheet cut in the shape of a narrow, isosceles triangle. The sheet was pushed into the eyepiece until the two adjacent edges of the metal sheet simultaneously occulted the two objects of interest. By carefully measuring the position where the objects were extinguished and knowing the focal length of the objective lens, the angular distance could be calculated. Christiaan Huygens used such a device. + + +== See also == +Micrometer + + +== Notes == + + +== References == + + +== External links == +Photographs of the Filar micrometer circa 1930 used at the Lick Observatory from the Lick Observatory Records Digital Archive, UC Santa Cruz Library's Digital Collection Archived 2015-05-20 at the Wayback Machine \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-0.md b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-0.md new file mode 100644 index 000000000..034866fe2 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-0.md @@ -0,0 +1,24 @@ +--- +title: "Fourier-transform infrared spectroscopy" +chunk: 1/5 +source: "https://en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:34.037453+00:00" +instance: "kb-cron" +--- + +Fourier transform infrared spectroscopy (FTIR) is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid, or gas. An FTIR spectrometer collects high-resolution spectral data over a wide spectral range. This confers a significant advantage over a dispersive spectrometer, which measures intensity over a narrow range of wavelengths at a time. +The term Fourier transform infrared spectroscopy originates from the fact that a Fourier transform (a mathematical process) is required to convert the raw data into the actual spectrum. + +== Conceptual introduction == + +Absorption spectroscopy techniques (FTIR, ultraviolet-visible ("UV-vis") spectroscopy, etc.) measure how much light a sample absorbs at each wavelength. The most straightforward way to do this, the "dispersive spectroscopy" technique, is to shine a monochromatic light beam at a sample, measure how much of the light is absorbed, and repeat for each different wavelength (this is also how some UV–vis spectrometers take measurements). +Fourier transform spectroscopy is a less intuitive way to obtain the same information. Rather than shining a monochromatic beam of light (a beam composed of only a single wavelength) at the sample, this technique shines a beam containing many frequencies of light at once and measures how much of that beam is absorbed by the sample. Next, the beam is modified to contain a different combination of frequencies, giving a second data point. This process is rapidly repeated many times over a short time span. Afterwards, a computer takes all this data and works backward to infer what the absorption is at each wavelength. +The beam described above is generated by starting with a broadband light source—one containing the full spectrum of wavelengths to be measured. The light shines into a Michelson interferometer—a certain configuration of mirrors, one of which is moved by a motor. As this mirror moves, each wavelength of light in the beam is periodically blocked, transmitted, blocked, transmitted, by the interferometer, due to wave interference. Different wavelengths are modulated at different rates, so that at each moment or mirror position the beam coming out of the interferometer has a different spectrum. +As mentioned, computer processing is required to turn the raw data (light absorption for each mirror position) into the desired result (light absorption for each wavelength). The processing required turns out to be a common algorithm called the Fourier transform. The Fourier transform converts one domain (in this case displacement of the mirror in cm) into its inverse domain (wavenumbers in cm−1). The raw data is called an "interferogram". + +== History == +The first low-cost spectrophotometer capable of recording an infrared spectrum was the Perkin-Elmer Infracord produced in 1957. This instrument covered the wavelength range from 2.5 μm to 15 μm (wavenumber range 4,000 cm−1 to 660 cm−1). The lower wavelength limit was chosen to encompass the highest known vibration frequency due to a fundamental molecular vibration. The upper limit was imposed by the fact that the dispersing element was a prism made from a single crystal of rock-salt (sodium chloride), which becomes opaque at wavelengths longer than about 15 μm; this spectral region became known as the rock-salt region. Later instruments used potassium bromide prisms to extend the range to 25 μm (400 cm−1) and caesium iodide 50 μm (200 cm−1). The region beyond 50 μm (200 cm−1) became known as the far-infrared region; at very long wavelengths it merges into the microwave region. Measurements in the far infrared needed the development of accurately ruled diffraction gratings to replace the prisms as dispersing elements, since salt crystals are opaque in this region. More sensitive detectors than the bolometer were required because of the low energy of the radiation. One such was the Golay detector. An additional issue is the need to exclude atmospheric water vapour because water vapour has an intense pure rotational spectrum in this region. Far-infrared spectrophotometers were cumbersome, slow and expensive. The advantages of the Michelson interferometer were well-known, but considerable technical difficulties had to be overcome before a commercial instrument could be built. Also an electronic computer was needed to perform the required Fourier transform, and this only became practicable with the advent of minicomputers, such as the PDP-8, which became available in 1965. Digilab pioneered the world's first commercial FTIR spectrometer (Model FTS-14) in 1969. Digilab FTIRs are now a part of Agilent Technologies's molecular product line after Agilent acquired spectroscopy business from Varian. + +== Michelson interferometer == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-1.md b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-1.md new file mode 100644 index 000000000..c12e69407 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-1.md @@ -0,0 +1,22 @@ +--- +title: "Fourier-transform infrared spectroscopy" +chunk: 2/5 +source: "https://en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:34.037453+00:00" +instance: "kb-cron" +--- + +In a Michelson interferometer adapted for FTIR, light from the polychromatic infrared source, approximately a black-body radiator, is collimated and directed to a beam splitter. Ideally 50% of the light is refracted towards the fixed mirror and 50% is transmitted towards the moving mirror. Light is reflected from the two mirrors back to the beam splitter and some fraction of the original light passes into the sample compartment. There, the light is focused on the sample. On leaving the sample compartment the light is refocused on to the detector. The difference in optical path length between the two arms to the interferometer is known as the retardation or optical path difference (OPD). An interferogram is obtained by varying the OPD and recording the signal from the detector for various values of the OPD. The form of the interferogram when no sample is present depends on factors such as the variation of source intensity and splitter efficiency with wavelength. This results in a maximum at zero OPD, when there is constructive interference at all wavelengths, followed by series of "wiggles". The position of zero OPD is determined accurately by finding the point of maximum intensity in the interferogram. When a sample is present the background interferogram is modulated by the presence of absorption bands in the sample. +Commercial spectrometers use Michelson interferometers with a variety of scanning mechanisms to generate the path difference. Common to all these arrangements is the need to ensure that the two beams recombine exactly as the system scans. The simplest systems have a plane mirror that moves linearly to vary the path of one beam. In this arrangement the moving mirror must not tilt or wobble as this would affect how the beams overlap as they recombine. Some systems incorporate a compensating mechanism that automatically adjusts the orientation of one mirror to maintain the alignment. Arrangements that avoid this problem include using cube corner reflectors instead of plane mirrors as these have the property of returning any incident beam in a parallel direction regardless of orientation. + +Systems where the path difference is generated by a rotary movement have proved very successful. One common system incorporates a pair of parallel mirrors in one beam that can be rotated to vary the path without displacing the returning beam. Another is the double pendulum design where the path in one arm of the interferometer increases as the path in the other decreases. +A quite different approach involves moving a wedge of an IR-transparent material such as KBr into one of the beams. Increasing the thickness of KBr in the beam increases the optical path because the refractive index is higher than that of air. One limitation of this approach is that the variation of refractive index over the wavelength range limits the accuracy of the wavelength calibration. + +== Measuring and processing the interferogram == +The interferogram has to be measured from zero path difference to a maximum length that depends on the resolution required. In practice the scan can be on either side of zero resulting in a double-sided interferogram. Mechanical design limitations may mean that for the highest resolution the scan runs to the maximum OPD on one side of zero only. +The interferogram is converted to a spectrum by Fourier transformation. This requires it to be stored in digital form as a series of values at equal intervals of the path difference between the two beams. To measure the path difference a laser beam is sent through the interferometer, generating a sinusoidal signal where the separation between successive maxima is equal to the wavelength of the laser (typically a 633 nm HeNe laser is used). This can trigger an analog-to-digital converter to measure the IR signal each time the laser signal passes through zero. Alternatively, the laser and IR signals can be measured synchronously at smaller intervals with the IR signal at points corresponding to the laser signal zero crossing being determined by interpolation. This approach allows the use of analog-to-digital converters that are more accurate and precise than converters that can be triggered, resulting in lower noise. + +The result of Fourier transformation is a spectrum of the signal at a series of discrete wavelengths. The range of wavelengths that can be used in the calculation is limited by the separation of the data points in the interferogram. The shortest wavelength that can be recognized is twice the separation between these data points. For example, with one point per wavelength of a HeNe reference laser at 0.633 μm (15800 cm−1) the shortest wavelength would be 1.266 μm (7900 cm−1). Because of aliasing, any energy at shorter wavelengths would be interpreted as coming from longer wavelengths and so has to be minimized optically or electronically. The spectral resolution, i.e. the separation between wavelengths that can be distinguished, is determined by the maximum OPD. The wavelengths used in calculating the Fourier transform are such that an exact number of wavelengths fit into the length of the interferogram from zero to the maximum OPD as this makes their contributions orthogonal. This results in a spectrum with points separated by equal frequency intervals. +For a maximum path difference d adjacent wavelengths λ1 and λ2 will have n and (n+1) cycles, respectively, in the interferogram. The corresponding frequencies are ν1 and ν2: \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-2.md b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-2.md new file mode 100644 index 000000000..96f2fb8cf --- /dev/null +++ b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-2.md @@ -0,0 +1,30 @@ +--- +title: "Fourier-transform infrared spectroscopy" +chunk: 3/5 +source: "https://en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:34.037453+00:00" +instance: "kb-cron" +--- + +The separation is the inverse of the maximum OPD. For example, a maximum OPD of 2 cm results in a separation of 0.5 cm−1. This is the spectral resolution in the sense that the value at one point is independent of the values at adjacent points. Most instruments can be operated at different resolutions by choosing different OPD's. Instruments for routine analyses typically have a best resolution of around 0.5 cm−1, while spectrometers have been built with resolutions as high as 0.001 cm−1, corresponding to a maximum OPD of 10 m. The point in the interferogram corresponding to zero path difference has to be identified, commonly by assuming it is where the maximum signal occurs. This so-called centerburst is not always symmetrical in real world spectrometers so a phase correction may have to be calculated. The interferogram signal decays as the path difference increases, the rate of decay being inversely related to the width of features in the spectrum. If the OPD is not large enough to allow the interferogram signal to decay to a negligible level there will be unwanted oscillations or sidelobes associated with the features in the resulting spectrum. To reduce these sidelobes the interferogram is usually multiplied by a function that approaches zero at the maximum OPD. This so-called apodization reduces the amplitude of any sidelobes and also the noise level at the expense of some reduction in resolution. +For rapid calculation the number of points in the interferogram has to equal a power of two. A string of zeroes may be added to the measured interferogram to achieve this. More zeroes may be added in a process called zero filling to improve the appearance of the final spectrum although there is no improvement in resolution. Alternatively, interpolation after the Fourier transform gives a similar result. + +== Advantages == +There are three principal advantages for an FT spectrometer compared to a scanning (dispersive) spectrometer. + +The multiplex or Fellgett's advantage (named after Peter Fellgett). This arises from the fact that information from all wavelengths is collected simultaneously. It results in a higher signal-to-noise ratio for a given scan-time for observations limited by a fixed detector noise contribution (typically in the thermal infrared spectral region where a photodetector is limited by generation-recombination noise). For a spectrum with m resolution elements, this increase is equal to the square root of m. Alternatively, it allows a shorter scan-time for a given resolution. In practice multiple scans are often averaged, increasing the signal-to-noise ratio by the square root of the number of scans. +The throughput or Jacquinot's advantage (named after Pierre Jacquinot). This results from the fact that in a dispersive instrument, the monochromator has entrance and exit slits which restrict the amount of light that passes through it. The interferometer throughput is determined only by the diameter of the collimated beam coming from the source. Although no slits are needed, FTIR spectrometers do require an aperture to restrict the convergence of the collimated beam in the interferometer. This is because convergent rays are modulated at different frequencies as the path difference is varied. Such an aperture is called a Jacquinot stop. For a given resolution and wavelength this circular aperture allows more light through than a slit, resulting in a higher signal-to-noise ratio. +The wavelength accuracy or Connes's advantage (named after Janine Connes). The wavelength scale is calibrated by a laser beam of known wavelength that passes through the interferometer. This is much more stable and accurate than in dispersive instruments where the scale depends on the mechanical movement of diffraction gratings. In practice, the accuracy is limited by the divergence of the beam in the interferometer which depends on the resolution. +Another minor advantage is less sensitivity to stray light, that is radiation of one wavelength appearing at another wavelength in the spectrum. In dispersive instruments, this is the result of imperfections in the diffraction gratings and accidental reflections. In FT instruments there is no direct equivalent as the apparent wavelength is determined by the modulation frequency in the interferometer. + +=== Resolution === +The interferogram belongs in the length dimension. Fourier transform (FT) inverts the dimension, so the FT of the interferogram belongs in the reciprocal length dimension([L−1]), that is the dimension of wavenumber. The spectral resolution in cm−1 is equal to the reciprocal of the maximal OPD in cm. Thus a 4 cm−1 resolution will be obtained if the maximal OPD is 0.25 cm; this is typical of the cheaper FTIR instruments. Much higher resolution can be obtained by increasing the maximal OPD. This is not easy, as the moving mirror must travel in a near-perfect straight line. The use of corner-cube mirrors in place of the flat mirrors is helpful, as an outgoing ray from a corner-cube mirror is parallel to the incoming ray, regardless of the orientation of the mirror about axes perpendicular to the axis of the light beam. +A spectrometer with 0.001 cm−1 resolution is now available commercially. The throughput advantage is important for high-resolution FTIR, as the monochromator in a dispersive instrument with the same resolution would have very narrow entrance and exit slits. +In 1966 Janine Connes measured the temperature of the atmosphere of Venus by recording the vibration-rotation spectrum of Venusian CO2 at 0.1 cm−1 resolution. Michelson himself attempted to resolve the hydrogen Hα emission band in the spectrum of a hydrogen atom into its two components by using his interferometer. p25 + +== Motivation == +FTIR is a method of measuring infrared absorption and emission spectra. For a discussion of why people measure infrared absorption and emission spectra, i.e. why and how substances absorb and emit infrared light, see the article: Infrared spectroscopy. + +== Components == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-3.md b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-3.md new file mode 100644 index 000000000..c502ffb27 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-3.md @@ -0,0 +1,48 @@ +--- +title: "Fourier-transform infrared spectroscopy" +chunk: 4/5 +source: "https://en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:34.037453+00:00" +instance: "kb-cron" +--- + +=== IR sources === +FTIR spectrometers are mostly used for measurements in the mid and near IR regions. For the mid-IR region, 2−25 μm (5,000–400 cm−1), the most common source is a silicon carbide (SiC) element heated to about 1,200 K (930 °C; 1,700 °F) (Globar). The output is similar to a blackbody. Shorter wavelengths of the near-IR, 1−2.5 μm (10,000–4,000 cm−1), require a higher temperature source, typically a tungsten-halogen lamp. The long wavelength output of these is limited to about 5 μm (2,000 cm−1) by the absorption of the quartz envelope. For the far-IR, especially at wavelengths beyond 50 μm (200 cm−1) a mercury discharge lamp gives higher output than a thermal source. + +=== Detectors === +Far-IR spectrometers commonly use pyroelectric detectors that respond to changes in temperature as the intensity of IR radiation falling on them varies. The sensitive elements in these detectors are either deuterated triglycine sulfate (DTGS) or lithium tantalate (LiTaO3). These detectors operate at ambient temperatures and provide adequate sensitivity for most routine applications. To achieve the best sensitivity the time for a scan is typically a few seconds. Cooled photoelectric detectors are employed for situations requiring higher sensitivity or faster response. Liquid nitrogen cooled mercury cadmium telluride (MCT) detectors are the most widely used in the mid-IR. With these detectors an interferogram can be measured in as little as 10 milliseconds. Uncooled indium gallium arsenide photodiodes or DTGS are the usual choices in near-IR systems. Very sensitive liquid-helium-cooled silicon or germanium bolometers are used in the far-IR where both sources and beamsplitters are inefficient. + +=== Beam splitter === + +An ideal beam-splitter transmits and reflects 50% of the incident radiation. However, as any material has a limited range of optical transmittance, several beam-splitters may be used interchangeably to cover a wide spectral range. +In a simple Michelson interferometer, one beam passes twice through the beamsplitter but the other passes through only once. To correct for this, an additional compensator plate of equal thickness is incorporated. +For the mid-IR region, the beamsplitter is usually made of KBr with a germanium-based coating that makes it semi-reflective. KBr absorbs strongly at wavelengths beyond 25 μm (400 cm−1), so CsI or KRS-5 are sometimes used to extend the range to about 50 μm (200 cm−1). ZnSe is an alternative where moisture vapour can be a problem, but is limited to about 20 μm (500 cm−1). +CaF2 is the usual material for the near-IR, being both harder and less sensitive to moisture than KBr, but cannot be used beyond about 8 μm (1,200 cm−1). +Far-IR beamsplitters are mostly based on polymer films, and cover a limited wavelength range. + +=== Attenuated total reflectance === + +Attenuated total reflectance (ATR) is one accessory of FTIR spectrophotometer to measure surface properties of solid or thin film samples rather than their bulk properties. Generally, ATR has a penetration depth of around 1 or 2 micrometers depending on sample conditions. + +=== Fourier transform === +The interferogram in practice consists of a set of intensities measured for discrete values of OPD. The difference between successive OPD values is constant. Thus, a discrete Fourier transform is needed. The fast Fourier transform (FFT) algorithm is used. + +== Spectral range == + +=== Far-infrared === +The first FTIR spectrometers were developed for far-infrared range. The reason for this has to do with the mechanical tolerance needed for good optical performance, which is related to the wavelength of the light being used. For the relatively long wavelengths of the far infrared, ~10 μm tolerances are adequate, whereas for the rock-salt region tolerances have to be better than 1 μm. A typical instrument was the cube interferometer developed at the NPL and marketed by Grubb Parsons. It used a stepper motor to drive the moving mirror, recording the detector response after each step was completed. + +=== Mid-infrared === +With the advent of cheap microcomputers it became possible to have a computer dedicated to controlling the spectrometer, collecting the data, doing the Fourier transform and presenting the spectrum. This provided the impetus for the development of FTIR spectrometers for the rock-salt region. The problems of manufacturing ultra-high precision optical and mechanical components had to be solved. A wide range of instruments are now available commercially. Although instrument design has become more sophisticated, the basic principles remain the same. Nowadays, the moving mirror of the interferometer moves at a constant velocity, and sampling of the interferogram is triggered by finding zero-crossings in the fringes of a secondary interferometer lit by a helium–neon laser. In modern FTIR systems the constant mirror velocity is not strictly required, as long as the laser fringes and the original interferogram are recorded simultaneously with higher sampling rate and then re-interpolated on a constant grid, as pioneered by James W. Brault. This confers very high wavenumber accuracy on the resulting infrared spectrum and avoids wavenumber calibration errors. + +=== Near-infrared === + +The near-infrared region spans the wavelength range between the rock-salt region and the start of the visible region at about 750 nm. Overtones of fundamental vibrations can be observed in this region. It is used mainly in industrial applications such as process control and chemical imaging. + +== Applications == +FTIR can be used in all applications where a dispersive spectrometer was used in the past (see external links). In addition, the improved sensitivity and speed have opened up new areas of application. Spectra can be measured in situations where very little energy reaches the detector. Fourier transform infrared spectroscopy is used in geology, chemistry, materials, botany and biology research fields. + +=== Nano and biological materials === +FTIR is also used to investigate various nanomaterials and proteins in hydrophobic membrane environments. Studies show the ability of FTIR to directly determine the polarity at a given site along the backbone of a transmembrane protein. The bond features involved with various organic and inorganic nanomaterials and their quantitative analysis can be done with the help of FTIR. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-4.md b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-4.md new file mode 100644 index 000000000..a3fc0486d --- /dev/null +++ b/data/en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy-4.md @@ -0,0 +1,38 @@ +--- +title: "Fourier-transform infrared spectroscopy" +chunk: 5/5 +source: "https://en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T03:13:34.037453+00:00" +instance: "kb-cron" +--- + +=== Microscopy and imaging === +An infrared microscope allows samples to be observed and spectra measured from regions as small as 5 microns across. Images can be generated by combining a microscope with linear or 2-D array detectors. The spatial resolution can approach 5 microns with tens of thousands of pixels. The images contain a spectrum for each pixel and can be viewed as maps showing the intensity at any wavelength or combination of wavelengths. This allows the distribution of different chemical species within the sample to be seen. This technique has been applied in various biological applications including the analysis of tissue sections as an alternative to conventional histopathology, examining the homogeneity of pharmaceutical tablets, and for differentiating morphologically-similar pollen grains. + +=== Nanoscale and spectroscopy below the diffraction limit === +The spatial resolution of FTIR can be further improved below the micrometer scale by integrating it into scanning near-field optical microscopy platform. The corresponding technique is called nano-FTIR and allows for performing broadband spectroscopy on materials in ultra-small quantities (single viruses and protein complexes) and with 10 to 20 nm spatial resolution. + +=== FTIR as detector in chromatography === +The speed of FTIR allows spectra to be obtained from compounds as they are separated by a gas chromatograph. However this technique is little used compared to GC-MS (gas chromatography-mass spectrometry) which is more sensitive. The GC-IR method is particularly useful for identifying isomers, which by their nature have identical masses. Liquid chromatography fractions are more difficult because of the solvent present. One notable exception is to measure chain branching as a function of molecular size in polyethylene using gel permeation chromatography, which is possible using chlorinated solvents that have no absorption in the area in question. + +=== TG-IR (thermogravimetric analysis-infrared spectrometry) === +Measuring the gas evolved as a material is heated allows qualitative identification of the species to complement the purely quantitative information provided by measuring the weight loss. + +=== Water content determination in plastics and composites === +FTIR analysis is used to determine water content in fairly thin plastic and composite parts, more commonly in the laboratory setting. Such FTIR methods have long been used for plastics, and became extended for composite materials in 2018, when the method was introduced by Krauklis, Gagani and Echtermeyer. FTIR method uses the maxima of the absorbance band at about 5200 cm−1, which correlates with the true water content in the material. + +== See also == +Discrete Fourier transform – Function in discrete mathematics − for computing periodicity in evenly spaced data +Fourier transform – Mathematical transform that expresses a function of time as a function of frequency +Fourier transform spectroscopy – Spectroscopy based on time- or space-domain dataPages displaying short descriptions of redirect targets +Least-squares spectral analysis – Periodicity computation method − for computing periodicity in unevenly spaced data + +== References == + +== External links == +Infracord spectrometer photograph +The Grubb-Parsons-NPL cube interferometer Spectroscopy, part 2 by Dudley Williams, page 81 +Infrared materials Properties of many salt crystals and useful links. +University FTIR lab example Archived 2017-01-10 at the Wayback Machine from the University of Bristol \ No newline at end of file