Relevant bibliographies by topics / Prototypical molecules

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Prototypical molecules'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Prototypical molecules"

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Borodin, Dmitriy, Igor Rahinov, Pranav R. Shirhatti, Meng Huang, Alexander Kandratsenka, Daniel J. Auerbach, Tianli Zhong, et al. "Following the microscopic pathway to adsorption through chemisorption and physisorption wells." Science 369, no. 6510 (September 17, 2020): 1461–65. http://dx.doi.org/10.1126/science.abc9581.

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Adsorption involves molecules colliding at the surface of a solid and losing their incidence energy by traversing a dynamical pathway to equilibrium. The interactions responsible for energy loss generally include both chemical bond formation (chemisorption) and nonbonding interactions (physisorption). In this work, we present experiments that revealed a quantitative energy landscape and the microscopic pathways underlying a molecule’s equilibration with a surface in a prototypical system: CO adsorption on Au(111). Although the minimum energy state was physisorbed, initial capture of the gas-phase molecule, dosed with an energetic molecular beam, was into a metastable chemisorption state. Subsequent thermal decay of the chemisorbed state led molecules to the physisorption minimum. We found, through detailed balance, that thermal adsorption into both binding states was important at all temperatures.
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Shao, Beiyue, and David A. Vanden Bout. "Probing the molecular weight dependent intramolecular interactions in single molecules of PCDTBT." Journal of Materials Chemistry C 5, no. 37 (2017): 9786–91. http://dx.doi.org/10.1039/c7tc02255g.

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Push–pull conjugated polymers have shown high performance in organic photovoltaic devices and yet, there have been fewer studies of the fundamental structure–property relationship in this class of materials compared to prototypical conjugated homopolymers MEH-PPV and P3HT.
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Hoffmann-Vogel, R. "Imaging prototypical aromatic molecules on insulating surfaces: a review." Reports on Progress in Physics 81, no. 1 (December 13, 2017): 016501. http://dx.doi.org/10.1088/1361-6633/aa8fda.

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Pitzer, Martin, Maksim Kunitski, Allan S. Johnson, Till Jahnke, Hendrik Sann, Felix Sturm, Lothar Ph H. Schmidt, et al. "Direct Determination of Absolute Molecular Stereochemistry in Gas Phase by Coulomb Explosion Imaging." Science 341, no. 6150 (September 5, 2013): 1096–100. http://dx.doi.org/10.1126/science.1240362.

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Bijvoet’s method, which makes use of anomalous x-ray diffraction or dispersion, is the standard means of directly determining the absolute (stereochemical) configuration of molecules, but it requires crystalline samples and often proves challenging in structures exclusively comprising light atoms. Herein, we demonstrate a mass spectrometry approach that directly images the absolute configuration of individual molecules in the gas phase by cold target recoil ion momentum spectroscopy after laser ionization–induced Coulomb explosion. This technique is applied to the prototypical chiral molecule bromochlorofluoromethane and the isotopically chiral methane derivative bromodichloromethane.
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Plehn, Thomas, Dirk Ziemann, and Volkhard May. "Charge separation at an organic/inorganic nano-hybrid interface: atomistic simulations of a para-sexiphenyl ZnO system." Physical Chemistry Chemical Physics 20, no. 42 (2018): 26870–84. http://dx.doi.org/10.1039/c8cp03978j.

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Ashfold, Michael N. R., Rebecca A. Ingle, Tolga N. V. Karsili, and Jingsong Zhang. "Photoinduced C–H bond fission in prototypical organic molecules and radicals." Physical Chemistry Chemical Physics 21, no. 26 (2019): 13880–901. http://dx.doi.org/10.1039/c8cp07454b.

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Kennedy, Linda M., and Kristina M. Gonzalez. "Taste quality coding in vertebrate receptor molecules and cells." Behavioral and Brain Sciences 31, no. 1 (February 2008): 82–83. http://dx.doi.org/10.1017/s0140525x08003439.

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AbstractRecent work on receptor molecules and cells used prototypical sweet, salty, sour, bitter, and umami stimuli. Labeled-line coding was supported, but it remains possible that the molecules and cells could respond to other tastants. Studies with other tastants are needed. The sensory message might contain two codes – one for attraction or aversion, the other, across-fiber patterning of stimulus quality.
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Endo, Tomoyuki, Simon P. Neville, Vincent Wanie, Samuel Beaulieu, Chen Qu, Jude Deschamps, Philippe Lassonde, et al. "Capturing roaming molecular fragments in real time." Science 370, no. 6520 (November 26, 2020): 1072–77. http://dx.doi.org/10.1126/science.abc2960.

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Since the discovery of roaming as an alternative molecular dissociation pathway in formaldehyde (H2CO), it has been indirectly observed in numerous molecules. The phenomenon describes a frustrated dissociation with fragments roaming at relatively large interatomic distances rather than following conventional transition-state dissociation; incipient radicals from the parent molecule self-react to form molecular products. Roaming has been identified spectroscopically through static product channel–resolved measurements, but not in real-time observations of the roaming fragment itself. Using time-resolved Coulomb explosion imaging (CEI), we directly imaged individual “roamers” on ultrafast time scales in the prototypical formaldehyde dissociation reaction. Using high-level first-principles simulations of all critical experimental steps, distinctive roaming signatures were identified. These were rendered observable by extracting rare stochastic events out of an overwhelming background using the highly sensitive CEI method.
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Thebeau, Lydia G., Sri P. Vagvala, Yee M. Wong, and Lynda A. Morrison. "B7 Costimulation Molecules Expressed from the Herpes Simplex Virus 2 Genome Rescue Immune Induction in B7-Deficient Mice." Journal of Virology 81, no. 22 (September 5, 2007): 12200–12209. http://dx.doi.org/10.1128/jvi.01224-07.

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ABSTRACT The interaction between B7 costimulation molecules on antigen-presenting cells and CD28 on antigen-responsive T cells is essential for T-cell activation and maturation of immune responses to herpes simplex virus (HSV) infection. Vaccine-induced immune responses also depend upon adequate upregulation of B7 costimulation molecules, but this signal may be limiting for replication-defective virus vaccines. We investigated whether expression of B7 costimulation molecules by a prototypical replication-defective antiviral vaccine could enhance immune responses to the vaccine and whether B7-1 and B7-2 would be similarly effective. We altered an ICP8− replication-defective strain of HSV type 2 (HSV-2), 5BlacZ, to encode either murine B7-1 or B7-2. B7 molecule expression was detected on the surface of cells infected in vitro and at the RNA level in tissue of immunized mice. Immunization of B7-1/B7-2 knockout mice with B7-encoding virus modestly expanded the number of gamma interferon-producing T cells and significantly augmented class-switched HSV-specific antibody responses compared with the parental virus. Mice immunized with either B7-expressing virus showed less replication of challenge virus in the genital mucosa than mice immunized with 5BlacZ, markedly fewer signs of genital and neurological disease, and little weight loss. Virtually all mice immunized with B7-encoding virus survived challenge with a large dose of HSV-2, whereas most 5BlacZ-immunized mice succumbed to infection. These results indicate that protective immune responses can be enhanced by the inclusion of host B7 costimulation molecules in a prototypical replication-defective HSV vaccine against HSV-2 genital infection and that B7-1 and B7-2 induce immune responses with similar capacities to fight HSV-2 infection.
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Prauzner-Bechcicki, Jakub S., Lukasz Zajac, Piotr Olszowski, Res Jöhr, Antoine Hinaut, Thilo Glatzel, Bartosz Such, Ernst Meyer, and Marek Szymonski. "Scanning probe microscopy studies on the adsorption of selected molecular dyes on titania." Beilstein Journal of Nanotechnology 7 (November 9, 2016): 1642–53. http://dx.doi.org/10.3762/bjnano.7.156.

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Titanium dioxide, or titania, sensitized with organic dyes is a very attractive platform for photovoltaic applications. In this context, the knowledge of properties of the titania–sensitizer junction is essential for designing efficient devices. Consequently, studies on the adsorption of organic dyes on titania surfaces and on the influence of the adsorption geometry on the energy level alignment between the substrate and an organic adsorbate are necessary. The method of choice for investigating the local environment of a single dye molecule is high-resolution scanning probe microscopy. Microscopic results combined with the outcome of common spectroscopic methods provide a better understanding of the mechanism taking place at the titania–sensitizer interface. In the following paper, we review the recent scanning probe microscopic research of a certain group of molecular assemblies on rutile titania surfaces as it pertains to dye-sensitized solar cell applications. We focus on experiments on adsorption of three types of prototypical dye molecules, i.e., perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA), phtalocyanines and porphyrins. Two interesting heteromolecular systems comprising molecules that are aligned with the given review are discussed as well.
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Dissertations / Theses on the topic "Prototypical molecules"

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Burke, Sarah Anne. "Building foundations for molecular electronics: growth of organic molecules on alkali halides as prototypical insulating substrates." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=32258.

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The epitaxy and growth of a series of organic molecules deposited on insulating surfaces were investigated by noncontact atomic force microscopy (nc-AFM). The molecules studied, C60 , 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA), 3,4,9,10-perylene tetracarboxlylic diimide (PTCDI), and copper (II) phthalocyanine (CuPc), were selected to investigate the effect of different molecular geometries, charge distributions and intermolecular interactions and as interesting candidates in molecular electronic applications. As it is known that the properties of molecules are influenced by their structural arrangements, an understanding of the interactions of molecules with substrates of interest as well as the dominant processes involved in growth are of great interest. Model insulating substrates KBr and NaCl were used for growth studies, due to the necessity of insulators in electrically isolating device regions. Dewetting processes were observed in several of these systems : C60 on KBr and NaCl, PTCDA on NaCl and PTCDI on NaCl. The specific influences of dewetting are discussed for each system, in particular the morphological impact of dewetting and the driving of dewetting by strained metastable monolayers. For C60 deposits, interesting branched structures are formed in the process of dewetting which are remarkably stable once formed, yet do not represent the equilibrium growth morphology. A determination of the large cell coincident epitaxy reveals a small, yet significant discrepancy between the observed overlayer and calculated stable adsorption sites indicating a dominance of the intermolecular interaction over the molecule–substrate interaction. For both PTCDA a
L'épitaxie et la croissance d'une série de molécules organiques déposées sur surface isolantes ont été étudiées par nc-AFM. Les molécules étudiées, C60, 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA), 3,4,9,10-perylene tetracarboxylic diimide (PTCDI), et Copper (II) Phthalocyanine (CuPc), ont été choisies pour examiner l'influence des géométries moléculaires, des distribution de charge, et de différentes interactions intermoléculaires, sur l'assemblage de candidats intéressants dans des applications en électronique moléculaire. Etant donné que les agencements structurels influencent leurs propriétés moléculaires, la compréhension des interactions entre molécules et substrats donnant lieu à la formation de couches mince est intéressant de plusieurs points de vue. Des surface isolantes modèles, KBr et NaCl, ont été utilisées pour les études de croissance, en raison de l'importance de l'isolement électronique de certaines régions des dispositifs. On a observé des processus de démouillage dans quelques systèmes: C60 sur KBr et NaCl, PTCDA sur NaCl, et PTCDI sur NaCl. Les influences de ces processus sont discutées pour chaque système, avec une emphase particulière sur l'impact morphologique du démouillage et la force d'entraînement par des mono-couches déformées. Dans le cas de C60, des îlots ramifiés se forment pendant le démouillage. Ces structures sont remarquablement stables un fois formées, mais ne représentent pas la structure en équilibre. La détermination d'une épitaxie coïncidente indique une petite, mais importante, difference entre la sur-couche observée et les sites d'adsorption stable calculés. Ce
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Lin, Ying. "Progress toward synthetic molecular motors : directed single bond rotation in a prototypical biaryl lactone system /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1324377621&sid=1&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2007.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 109-124). Also available for download via the World Wide Web; free to University of Oregon users.
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Dahl, Bartholomew James. "The design and synthesis of prototypical artificial molecular motors : studies of directed bond rotation in chiral biaryls /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1288652831&sid=3&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2007.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 151-165). Also available for download via the World Wide Web; free to University of Oregon users.
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Seier, Kerstin [Verfasser], and Davide [Gutachter] Calebiro. "Investigation of dynamic processes of prototypical class A GPCRs by single-molecule microscopy / Kerstin Seier ; Gutachter: Davide Calebiro." Würzburg : Universität Würzburg, 2020. http://d-nb.info/1205259058/34.

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Gao, Chao. "HOMOCYSTEINE-METHIONINE CYCLE IS A KEY METABOLIC SENSOR SYSTEM CONTROLLING METHYLATION-REGULATED PATHOLOGICAL SIGNALING - CD40 IS A PROTOTYPIC HOMOCYSTEINE-METHIONINE CYCLE REGULATED MASTER GENE." Master's thesis, Temple University Libraries, 2019. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/603000.

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Biomedical Sciences
M.S.
Homocysteine-Methionine (HM) cycle produces a universal methyl group donor S-adenosylmethionine (SAM), a competitive methylation inhibitor S-adenosylhomocysteine (SAH), and an intermediate amino acid product homocysteine (Hcy). Elevated plasma levels of Hcy is termed as hyperhomocycteinemia (HHcy) which is an established risk factor for cardiovascular disease (CVD) and neural degenerative disease. We were the first to describe methylation inhibition as a mediating biochemical mechanism for endothelial injury and inflammatory monocyte differentiation in HHcy-related CVD and diabetes. We proposed metabolism-associated danger signal (MADS) recognition as a novel mechanism for metabolic risk factor-induced inflammatory responses, independent from pattern recognition receptor (PRR)-mediated pathogen-associated molecular pattern (PAMP)/danger-associated molecular pattern (DAMP) recognition. In this study, we examined the relationship of HM cycle gene expression with methylation regulation in human disease. We selected 115 genes in the extended HM cycle, including 31 metabolic enzymes and 84 methyltransferases (MT), examined their mRNA levels in 35 human disease conditions using a set of public databases. We discovered that: 1) HM cycle senses metabolic risk factor and controls SAM/SAH-dependent methylation. 2) Most of metabolic enzymes in HM cycle (8/11) are located in cytosol, while most of the SAM-dependent MTs (61/84) are located in the nucleus, and Hcy metabolism is absent in the nucleus. 3) 11 up-regulated, 3 down-regulated and 24 differentially regulated SAM/SAH-responsive signal pathways are involved in 7 human disease categories. 4) 8 SAM/SAH-responsive H3/H4 hypomethylation sites are identified in 8 disease conditions. We conclude that HM cycle is a key metabolic sensor system which mediates receptor-independent MADS recognition and modulates SAM/SAH-dependent methylation in human disease. We propose that HM metabolism takes place in cytosol and that nuclear methylation equilibration requires nuclear-cytosol transfer of SAM, SAH and Hcy. CD40 is a cell surface molecule which is expressed on antigen presenting cells such as monocyte, macrophage, dendritic cells and neutrophils. The costimulatory pair, CD40 and CD40L, enhances T cell activation and induce chronic inflammatory disease. Also, DNA hypomethylation on CD40 promotor induces inflammatory monocyte differentiation in chronic kidney disease. In order to figure out if CD40 is a prototypic HM cycle regulated master gene, RNA-seq analysis were performed for CD40+ and CD40- monocytes from mouse peripheral blood and 1,093 differentially expressed genes (DEGs) were selected from those two groups. All the DEGs modulate as much as 15 functional gene groups such as cytokines, enzymes and transcriptional factors. Furthermore, CD40+ monocytes activated trained immunity pathways especially in Acetyl-CoA generation and mevalonate pathway. In HM cycle, CD40 is a prototypic HM cycle regulated master gene to induce the most of the Hcy metabolic enzymes as well as MT, which can further modulate the methylation-regulated pathological signaling.
Temple University--Theses
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Seier, Kerstin. "Investigation of dynamic processes of prototypical class A GPCRs by single-molecule microscopy." Doctoral thesis, 2020. https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-199739.

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In this work, two projects were pursued. In the first project, I investigated two different subtypes of opioid receptors, which play a key role as target for analgesia. A set of subtype specific fluorescent ligands for μ opioid receptor (MOR) and δ opioid receptor (DOR) was characterised and used to gain insights into the diffusion behaviour of those receptors. It was shown that the novel ligands hold photophysical and pharmacological properties making them suitable for single-molecule microscopy. Applying them to wild-type receptors expressed in living cells revealed that both sub-types possess a heterogeneous diffusion behaviour. Further- more, the fluorescent ligands for the MOR were used to investigate homodomerisation, a highly debated topic. The results reveal that only ≈ 5 % of the receptors are present as homodimers, and thus the majority is monomeric. G-protein coupled receptors (GPCRs) play a major role as drug targets. Accordingly, understanding the activation process is very important. For a long time GPCRs have been believed to be either active or inactive. In recent years several studies have shown, that the reality is more complex, involving more substates. [1, 2, 3, 4] In this work the α 2A AR was chosen to investigate the activation process on a single-molecule level, thus being able to distinguish also rare or short-lived events that are hidden in ensemble mea- surements. With this aim, the receptor was labelled intracellular with two fluorophores using supported membranes. Thus it was possible to acquire movies showing qualita- tively smFRET events. Unfortunately, the functionality of the used construct could not be demonstrated. To recover the functionality the CLIP-tag in the third intracellular loop was replaced successfully with an amber codon. This stop codon was used to insert an unnatural amino acid. Five different mutants were created and tested and the most promising candidate could be identified. First ensemble FRET measurements indicated that the functionality might be recovered but further improvements would be needed. Overall, I could show that single-molecule microscopy is a versatile tool to investigate the behaviour of typical class A GPCRs. I was able to show that MOR are mostly monomeric under physiological expression levels. Furthermore, I could establish intra- cellular labelling with supported membranes and acquire qualitative smFRET events
In dieser Arbeit wurden zwei Projekte verfolgt. Im ersten Projekt wurden zwei Subtypen der Opioidrezeptoren untersucht, die eine wichtige Rolle für die Wirksamkeit von Analgetika spielen. Ein Set von subtypspezifischen fluoreszierenden Liganden für den MOR und den DOR wurde charakterisiert und eingesetzt, um Einblicke in das Diffuionsverhalten der Rezeptoren zu gewinnen. Es konnte gezeigt werden, dass die neuartigen Liganden sowohl photophysikalische als auch pharmakologische Eigenschaften besitzen, die sie für die Einzelmolekülmikroskopie interessant machen. Versuche mit Opioidrezeptoren, die in lebenden Zellen exprimiert werden, zeigten, dass beide Subtypen heterogenes Diffuionsverhalten aufweisen. Des Weiteren wurden die fluoreszierenden Liganden für den MOR genutzt um Homodimerisierung zu untersuchen, da dies ein kontrovers diskutiertes Thema ist. Die Ergebnisse zeigen, dass lediglich ≈ 5% der Rezeptoren als Homodimere vorliegen und der Großteil monomerisch ist. GPCRs sind besonderem Interesse, weil sie Angriffspunkt vieler Medikamente sind. Deshalb ist es wichtig ihren Aktivierungsmechanismus besser zu verstehen. Lange Zeit wurde angenommen, dass GPCRs entweder aktiv oder inaktiv sind. Neuere Studien zeigten jedoch, dass die Realität komplexer ist und der Prozess Zwischenschritte involviert. [1, 2, 3, 4] In dieser Arbeit wurde der α 2A Adrenorezeptor als prototypischer Klasse A GPCR gewählt, um den Aktivierungsprozess auf Einzelmoleküllevel zu untersuchen. Durch die Betrachtung einzelner Rezeptoren ist es möglich auch seltene oder sehr kurzlebige Ereignisse zu unterscheiden, die in Kollektivmessungen untergehen. Um dies zu erreichen wurde der Rezeptor erfolgreich intrazellulär mit zwei Fluorophoren markiert. Dies gelang durch die Herstellung von „supported membranes", also Zellmembranen die auf einem Objektträger fixiert wurden. Dadurch war es möglich Videos aufzunehmen, die Einzelmolekül-FRET-Ereignisse zeigen. Jedoch gelang es nicht zu zeigen, dass der Rezeptor als Ganzes noch funktional war. Um einen funktionalen Rezeptor zu erhalten, wurde das CLIP-Tag in der dritten intrazellulären Schleife erfolgreich durch ein Stopcodon ersetzt, welches für eine nicht kanonische Aminosäure kodierte. Fünf verschiedene Mutanten wurden kloniert und getestet, wobei der vielversprechendste Mutant identifiziert werden konnte. Erste FRET-Kollektivmessungen deuten darauf hin, dass dieser Mutant funktional sein könnte. Jedoch sind weitere Verbesserungen nötig. Insgesamt konnte ich zeigen, dass Einzelmolekülmikroskopie vielseitige Möglichkeiten bietet um das Verhalten von GPCRs zu untersuchen. Ich konnte nachweisen, dass MOR unter physiologischen Bedingungen hauptsächlich als Monomere vorliegen. Des Weiteren konnte ich Dank supported membranes die Markierung durch Farbstoffe im Intrazellularbereich etablieren und qualitative smFRET Ereignisse aufnehmen
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Books on the topic "Prototypical molecules"

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Thygesen, K. S., and A. Rubio. Correlated electron transport in molecular junctions. Edited by A. V. Narlikar and Y. Y. Fu. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199533046.013.23.

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This article focuses on correlated electron transport in molecular junctions. More specifically, it considers how electronic correlation effects can be included in transport calculations using many-body perturbation theory within the Keldysh non-equilibrium Green’s function formalism. The article uses the GW self-energy method (G denotes the Green’s function and W is the screened interaction) which has been successfully applied to describe quasi-particle excitations in periodic solids. It begins by formulating the quantum-transport problem and introducing the non-equilibrium Green’s function formalism. It then derives an expression for the current within the NEGF formalism that holds for interactions in the central region. It also combines the GW scheme with a Wannier function basis set to study electron transport through two prototypical junctions: a benzene molecule coupled to featureless leads and a hydrogen molecule between two semi-infinite platinum chains. The results are analyzed using a generic two-level model of a molecular junction.
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Medjeral-Thomas, Nicholas, Anna Richards, and Matthew C. Pickering. Molecular basis of complement-mediated renal disease. Edited by Neil Turner. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199592548.003.0333.

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Abnormal regulation of complement is intimately associated with C3 glomerulopathy and atypical haemolytic uraemic syndrome. Atypical haemolytic uraemic syndrome is characterized by renal thrombotic microangiopathy due to an inability to regulate complement activation along the renal endothelium. The development of thrombosis is critically dependent on the ability to activate C5. Eculizumab, a monoclonal anti-C5 antibody, is an effective therapy for this condition. C3 glomerulopathy refers to glomerular lesions characterized by accumulation of C3 in the absence of immunoglobulin. The prototypic example is dense deposit disease. This condition is associated with impaired regulation of the alternative pathway in plasma. In other subtypes of C3 glomerulopathy, familial studies have identified mutations within the complement factor H-related protein family. Polymorphic variation within this protein family also influences susceptibility to IgA nephropathy. The mechanism underlying these associations remains unknown and is the subject of ongoing research efforts.
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Book chapters on the topic "Prototypical molecules"

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Kinosita, Kazuhiko. "F1-ATPase: A Prototypical Rotary Molecular Motor." In Viral Molecular Machines, 5–16. Boston, MA: Springer US, 2011. http://dx.doi.org/10.1007/978-1-4614-0980-9_2.

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Harwood, Adrian J. "Dictyostelium Development: A Prototypic Wnt Pathway?" In Methods in Molecular Biology, 21–32. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-60327-469-2_2.

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Rymarczyk, Dawid, Daniel Dobrowolski, and Tomasz Danel. "ProGReST: Prototypical Graph Regression Soft Trees for Molecular Property Prediction." In Proceedings of the 2023 SIAM International Conference on Data Mining (SDM), 379–87. Philadelphia, PA: Society for Industrial and Applied Mathematics, 2023. http://dx.doi.org/10.1137/1.9781611977653.ch43.

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Dunlap, Jay C., and Jennifer J. Loros. "Molecular Genetics of Circadian Rhythms inNeurosporaa Prototypic Circadian System." In Handbook of Behavioral Neurobiology, 335–50. Boston, MA: Springer US, 2001. http://dx.doi.org/10.1007/978-1-4615-1201-1_13.

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Degheidy, Heba, Dalia A. A. Salem, Constance M. Yuan, and Maryalice Stetler-Stevenson. "Chronic Lymphocytic Leukemia, the Prototypic Chronic Leukemia for Flow Cytometric Analysis." In Manual of Molecular and Clinical Laboratory Immunology, 226–34. Washington, DC, USA: ASM Press, 2016. http://dx.doi.org/10.1128/9781555818722.ch23.

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Chen, C. Julian. "Atomic Forces." In Introduction to Scanning Tunneling Microscopy, 93–130. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780198856559.003.0004.

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This chapter discusses the physics and properties of four types of atomic forces occurring in STM and AFM: the van der Waals force, the hard core repulsion, the ionic bond, and the covalent bond. The general mathematical form of the van der Waals force between a tip and a flat sample is derived. The focus of this chapter is the covalent-bond force, which is a key in the understanding of STM and AFM. The concept of covalent bond is illustrated by the hydrogen molecular ion, the prototypical molecule used by Pauling to illustrate Heisenberg’s concept of resonance. The Herring-Landau perturbation theory of the covalent bond, an analytical incarnation of the concept of resonance, is presented in great detail. It is then applied to molecules built from many-electron atoms, to show that the perturbation theory can be applied to practical systems to produce simple analytic results for measurable physical quantities with decent accuracy.
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Sakmar, Thomas P. "Rhodopsin: A Prototypical G Protein-Coupled Receptor." In Progress in Nucleic Acid Research and Molecular Biology, 1–34. Elsevier, 1997. http://dx.doi.org/10.1016/s0079-6603(08)61027-2.

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Bensimon, David, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick. "DNA Helicases." In Single-Molecule Studies of Nucleic Acids and Their Proteins, 155–76. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198530923.003.0008.

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This chapter discusses the application of single-molecule approaches in the study of helicases. It describes the main helicase families and possible mechanisms of their action, and the problems of bulk experiments on helicases resulting from rehybridization of unwound strands in the wake of the enzyme; this problem is absent for RecBCD, a helicase which also possesses exonuclease activity. Two mechanisms for helicase are then discussed: passive, whereby the helicase advances by trapping DNA fork fluctuations, and active, where the DNA forces itself through the double-helical molecule. It presents two prototypical examples: RecQ, an active enzyme, and gp41, a passive one . It then shows how single-molecule experiments can be used to estimate the enzymatic step size by analysing the unwinding noise. They further led to the discovery of strand-switching. Finally, FRET experiments can be used to study the mechanisms of helicases, as demonstrated by a study of the Rep helicase.
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Bernstein, Joel. "Computational aspects of polymorphism." In Polymorphism in Molecular Crystals, 215–72. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780199655441.003.0005.

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The application of computational techniques to polymorphic systems is reviewed. Topics covered include the energetics of molecular geometric features (bond lengths, bond angles, torsion angles) and the energetics of intermolecular interactions of various types. Methods and techniques for the presentation of polymorphic structures are described, followed by some historically important early examples of conformational polymorphism. The latter subject is treated in light of recent developments, including some exemplary studies of conformational polymorphism and the prototypical example of “ROY” is discussed in detail. The computational prediction and comparison of polymorphs is discussed in the framework of the computational prediction of crystal structures. Methods discussed on polymorphs include the comparison based on geometric criteria, comparison based on Hirshfeld surfaces, a comparison based on energetic environment, comparison of X-ray diffraction patterns, and the use of partitioned lattice energy to investigate the details of similarities and differences in polymorphic structures.
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Dunlap, Jay C., Jennifer J. Loros, Martha Merrow, Susan Crosthwaite, Deborah Bell-Pedersen, Norman Garceau, Mari Shinohara, Hyeseon Cho, and Chenghua Luo. "Chapter 2 The genetic and molecular dissection of a prototypic circadian system." In Progress in Brain Research, 11–27. Elsevier, 1996. http://dx.doi.org/10.1016/s0079-6123(08)60397-0.

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Conference papers on the topic "Prototypical molecules"

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Ahlheim, M., J. L. Brédas, M. Barzoukas, P. V. Bedworth, Y. Cai, C. Dehu, M. Blanchard-Desce, et al. "Experimental and Theoretical Studies of Nonlinear Optical Chromophores." In Organic Thin Films for Photonic Applications. Washington, D.C.: Optica Publishing Group, 1995. http://dx.doi.org/10.1364/otfa.1995.tud.1.

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We have described how the first hyperpolarizability, β, varies as a function of ground-state polarization and bond length alternation, BLA.1 Previously, our predictions of this relationship were derived by examining an prototypical push-pull polyene under the presence of static homogenous electric field.1 In order to develop a more realistic understanding of how real molecules behave in solution, we have now examined both p-nitroaniline and the push-pull polyene 1,1-dicyano-6-dibutylamino-hexatriene at the Hartree Fock ab initio level on the basis of an expanded Self Consistent Reaction-Field approach to simulate solvents with dielectric constants up to 37.5. The calculations were carried out using both spherical and elliptical cavities and taking into account multipole interactions up to 26 poles. Predictions were compared to Hyper-Rayleigh Scattering (HRS) results determined by Persoons et al. As had been shown earlier,2 the second-order NLO response of 1,1-dicyano-6-dibutylamino-hexatriene exhibits a peak as a function of solvent polarity, which was confirmed by the HRS measurements. Interestingly, we found that this peaked behavior of β as a function of solvent dielectric constant was predicted only when an elliptical cavity and the up to l = 6 pole contributions were taken into account, but was not observed when the calculations employed either an elliptical cavity and a dipole (l = 1) approximation, or a spherical cavity with up to l = 6 pole contributions. These results suggest that it is possible to model the geometric and electronic structure of polarizable molecules using a Self Consistent Reaction-Field approach, but it is necessary to build into the calculations mechanisms to account for the subtleties of the molecular charge distributions, not taken into account within a simple dipole approximation.
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Wittig, Curt. "Gas phase processes." In International Laser Science Conference. Washington, D.C.: Optica Publishing Group, 1986. http://dx.doi.org/10.1364/ils.1986.fa1.

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In condensed media, chemical reactions can be initiated with a great deal of geometric specificity, since the forces holding the molecules in place ensure that the reactants are aligned and oriented relative to one another. Unfortunately, the surrounding medium is in constant interaction with the reactive site and no signature characteristic of the eigenstates of isolated product species can be obtained. On the other hand, binary encounters in the gas phase are especially well suited for detecting nascent excitations. However, with isotropic samples the initial conditions are unbiased so that all angles and impact parameters are present. To exploit the virtues of each of these environments, we use weakly bound van der Waals-type complexes as precursors for studying elementary processes. A prototypical example is CO2 HBr, where the potential is minimum with the nuclei along a straight line. These complexes are prepared at 2K by supersonic expansion, and photodissociation of the HBr constituent propels the H-atom toward the CO2 with initial alignment, etc., determined mainly by zero-point fluctuations of the complex. Nascent products (e.g., OH, CO) can be detected by standard spectroscopic methods before collisions become troublesome. The technique can be used to peruse the system’s ability to avoid low energy channels (e.g., with an SCOHX precursor, can OH + CS be favored over SH + CO?), as well as provide stringent tests for different kinds of calculation.
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Endres, Christian, Sven Thorwirth, Stephan Schlemmer, Paola Caselli, Michael McCarthy, Luis Bonah, Oliver Zingsheim, J. C. Guillemin, Olivier Pirali, and Marie-Aline Martin-Drumel. "THE SOLEIL VIEW ON PROTOTYPICAL ORGANIC NITRILES: THE 13C SPECIES OF ETHYL CYANIDE." In 2022 International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2022. http://dx.doi.org/10.15278/isms.2022.fg07.

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Endo, T., S. P. Neville, P. Lassonde, C. Qu, H. Fujise, M. Fushitani, A. Hishikawa, et al. "Roaming in Formaldehyde – and how to get there." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 2022. http://dx.doi.org/10.1364/up.2022.m2a.5.

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Roaming molecular fragments in the prototypical formaldehyde dissociation-reaction are directly observed in real-time, using Coulomb explosion imaging and state-of-the-art theoretical modeling. How does the preparation of population ready to roam depend on the pump wavelength?
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Blodgett, Karl, Timothy Zwier, and Patrick Walsh. "SINGLE-CONFORMATION IR AND UV SPECTROSCOPY OF A PROTOTYPICAL HETEROGENEOUS α/β-PEPTIDE: IS IT A MIXED-HELIX FORMER?" In 71st International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2016. http://dx.doi.org/10.15278/isms.2016.mi12.

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Peebles, Rebecca, Brooks Pate, Sean Peebles, Rachel Dorris, Nathan Seifert, and Nathan Ulrich. "CHIRPED-PULSE FOURIER-TRANSFORM MICROWAVE SPECTROSCOPY OF THE PROTOTYPICAL C-H…π INTERACTION: THE BENZENE…ACETYLENE WEAKLY BOUND DIMER." In 69th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2014. http://dx.doi.org/10.15278/isms.2014.fd08.

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Bartenwerfer, Malte, and Sergej Fatikow. "Robotic nanowire handling for prototypic NEMS switching and resonator devices." In 2013 8th IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS). IEEE, 2013. http://dx.doi.org/10.1109/nems.2013.6559845.

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Endres, Christian, Sven Thorwirth, Stephan Schlemmer, Nadine Wehres, Olivier Pirali, Michael McCarthy, Marie-Aline Martin-Drumel, and Paola Caselli. "THE SOLEIL VIEW ON PROTOTYPICAL ORGANIC NITRILES: SELECTED VIBRATIONAL MODES OF ETHYL CYANIDE, C2H5CN, AND SPECTROSCOPIC ANALYSIS USING AN AUTOMATED SPECTRAL ASSIGNMENT PROCEDURE (ASAP)." In 71st International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2016. http://dx.doi.org/10.15278/isms.2016.fe01.

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Marisa, Laetitia, Laure Vescovo, Aurélien Reyniès, Alex Duval, Marie-Christine Etienne-Grimaldi, Marie-Pierre Gaub, Dominique Guenot, et al. "Abstract 5065: Gene expression profiling of colon adenocarcinomas reveals six prototypic molecular subtypes with distinct clinical and molecular characteristics." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-5065.

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Reports on the topic "Prototypical molecules"

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Lehotay, Steven J., and Aviv Amirav. Fast, practical, and effective approach for the analysis of hazardous chemicals in the food supply. United States Department of Agriculture, April 2007. http://dx.doi.org/10.32747/2007.7695587.bard.

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Background to the topic: For food safety and security reasons, hundreds of pesticides, veterinary drugs, and environmental pollutants should be monitored in the food supply, but current methods are too time-consuming, laborious, and expensive. As a result, only a tiny fraction of the food is tested for a limited number of contaminants. Original proposal objectives: Our main original goal was to develop fast, practical, and effective new approaches for the analysis of hazardous chemicals in the food supply. We proposed to extend the QuEChERS approach to more pesticides, veterinary drugs and pollutants, further develop GC-MS and LC-MS with SMB and combine QuEChERS with GC-SMB-MS and LC-SMB-EI-MS to provide the “ultimate” approach for the analysis of hazardous chemicals in food. Major conclusions, solutions and achievements: The original QuEChERS method was validated for more than 200 pesticide residues in a variety of food crops. For the few basic pesticides for which the method gave lower recoveries, an extensive solvent suitability study was conducted, and a buffering modification was made to improve results for difficult analytes. Furthermore, evaluation of the QuEChERS approach for fatty matrices, including olives and its oil, was performed. The QuEChERS concept was also extended to acrylamide analysis in foods. Other advanced techniques to improve speed, ease, and effectiveness of chemical residue analysis were also successfully developed and/or evaluated, which include: a simple and inexpensive solvent-in-silicone-tube extraction approach for highly sensitive detection of nonpolar pesticides in GC; ruggedness testing of low-pressure GC-MS for 3-fold faster separations; optimization and extensive evaluation of analyte protectants in GC-MS; and use of prototypical commercial automated direct sample introduction devices for GC-MS. GC-MS with SMB was further developed and combined with the Varian 1200 GCMS/ MS system, resulting in a new type of GC-MS with advanced capabilities. Careful attention was given to the subject of GC-MS sensitivity and its LOD for difficult to analyze samples such as thermally labile pesticides or those with weak or no molecular ions, and record low LOD were demonstrated and discussed. The new approach of electron ionization LC-MS with SMB was developed, its key components of sample vaporization nozzle and flythrough ion source were improved and was evaluated with a range of samples, including carbamate pesticides. A new method and software based on IAA were developed and tested on a range of pesticides in agricultural matrices. This IAA method and software in combination with GC-MS and SMB provide extremely high confidence in sample identification. A new type of comprehensive GCxGC (based on flow modulation) was uniquely combined with GC-MS with SMB, and we demonstrated improved pesticide separation and identification in complex agricultural matrices using this novel approach. An improved device for aroma sample collection and introduction (SnifProbe) was further developed and favorably compared with SPME for coffee aroma sampling. Implications, both scientific and agricultural: We succeeded in achieving significant improvements in the analysis of hazardous chemicals in the food supply, from easy sample preparation approaches, through sample analysis by advanced new types of GC-MS and LCMS techniques, all the way to improved data analysis by lowering LOD and providing greater confidence in chemical identification. As a result, the combination of the QuEChERS approach, new and superior instrumentation, and the novel monitoring methods that were developed will enable vastly reduced time and cost of analysis, increased analytical scope, and a higher monitoring rate. This provides better enforcement, an added impetus for farmers to use good agricultural practices, improved food safety and security, increased trade, and greater consumer confidence in the food supply.
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