Journal articles on the topic 'Dimers'
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Dey, Sumitra, and Ahmed Hassan. "Asymmetric Carbon Nanotube Dimers for Novel Sensing Applications." Applied Computational Electromagnetics Society 35, no. 11 (February 4, 2021): 1320–21. http://dx.doi.org/10.47037/2020.aces.j.351129.
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In this work, we study the use of asymmetric carbon nanotube (CNT) dimers for the contactless detection of foreign nano-particles. Asymmetric CNT dimers create a unique field distribution, through the electromagnetic coupling, which in turn generates two distinct resonances representing the bonding and anti-bonding modes. The presence of a foreign nano-particle (NP) in the vicinity of the CNT dimer perturbs the dimer’s field distribution and causes the bonding and anti-bonding resonances to shift by unequal amounts depending on the NP location. By studying the difference in the shift of the bonding and the anti-bonding resonances, we show that the NP relative location can be reconstructed. The computational experiments performed in this work show how asymmetric CNT dimers can be used for novel sensing applications.
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Gould, Katherine A., Xiao-Su Pan, Robert J. Kerns, and L. Mark Fisher. "Ciprofloxacin Dimers Target Gyrase in Streptococcus pneumoniae." Antimicrobial Agents and Chemotherapy 48, no. 6 (June 2004): 2108–15. http://dx.doi.org/10.1128/aac.48.6.2108-2115.2004.
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ABSTRACT We have examined the antipneumococcal activities of novel quinolone dimers in which ciprofloxacin was tethered to itself or to pipemidic acid by linkage of C-7 piperazinyl rings. Symmetric 2,6-lutidinyl- and trans-butenyl-linked ciprofloxacin dimers (dimers 1 and 2, respectively) and a pipemidic acid-ciprofloxacin dimer (dimer 3) had activities against Streptococcus pneumoniae strain 7785 that were comparable to that of ciprofloxacin, i.e., MICs of 2, 1, and 4 to 8 μg/ml versus an MIC of 1 to 2 μg/ml, respectively. Surprisingly, unlike ciprofloxacin (which targets topoisomerase IV), several lines of evidence revealed that the dimers act through gyrase in S. pneumoniae. First, ciprofloxacin-resistant parC mutants of strain 7785 remained susceptible to dimers 1 to 3, whereas a gyrA mutation conferred a four- to eightfold increase in the dimer MIC but had little effect on ciprofloxacin activity. Second, dimer 1 selected first-step gyrA (S81Y or S81F) mutants (MICs, 8 to 16 μg/ml) that carried wild-type topoisomerase IV parE-parC genes. Third, dimers 1 and 2 promoted comparable DNA cleavage by S. pneumoniae gyrase and topoisomerase IV, whereas ciprofloxacin-mediated cleavage was 10-fold more efficient with topoisomerase IV than with gyrase. Fourth, the GyrA S81F and ParC S79F enzymes were resistant to dimers, confirming that the resistance phenotype is largely silent in parC mutants. Although a dimer molecule could bind very tightly by bridging quinolone binding sites in the enzyme-DNA complex, the greater potency of ciprofloxacin against gyrase and topoisomerase IV suggests that dimers 1 to 3 bind in a monomeric fashion. The bulky C-7 side chain may explain dimer targeting of gyrase and activity against efflux mutants. Tethered quinolones have potential as mechanistic tools and as novel antimicrobial agents.
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Прасолов, Н. Д., А. А. Гуткин, and П. Н. Брунков. "Исследование с помощью молекулярной динамики образования димеров на поверхности (001) GaAs при низких температурах." Физика и техника полупроводников 55, no. 2 (2021): 134. http://dx.doi.org/10.21883/ftp.2021.02.50498.9516.
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The simulation of dimers formation during the low-temperature reconstruction of GaAs (001) surface terminated with Ga or As atoms was performed by the molecular dynamics method using the analytical Bond-Order Potential based on quantum mechanical theory incorporating both σ- and π- bonds between atoms. A decrease in values of potential energy of the atoms during formation of isolated surface dimer have been determined. It has been found that potential energy of an atom in As-dimer is several tenths of an eV lower than in Ga-dimer. Kinetics of the initial stages of Ga-dimers formation in the temperature range of 25 - 40 K was studied. It was found that the characteristic thermal activation energy of single isolated Ga-dimers formation is ~ 29 meV, which is lower than the same value for As-dimers (~ 38 meV). Time constants characterizing the average rate of transformation of one dimer into a chain of two dimers at temperature range of 28 - 37 K were estimated. Inverse values of these parameters for paired Ga- and As-dimers are in the ranges of 10^11 – 10^12 s^-1 and 10^9 – 10^10 s^-1, respectively, while corresponding parameters for the formation of single dimers are in the ranges of 4·10^6 – 10^8 s^-1 and 1.4·10^6 – 7.4·10^7 s^-1.
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Abramov-Harpaz, Karina, and Yifat Miller. "Insights into Non-Proteolytic Inhibitory Mechanisms of Polymorphic Early-Stage Amyloid β Oligomers by Insulin Degrading Enzyme." Biomolecules 12, no. 12 (December 16, 2022): 1886. http://dx.doi.org/10.3390/biom12121886.
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Insulin degrading enzyme (IDE) has been detected in the cerebrospinal fluid media and plays a role in encapsulating and degrading the amyloid β (Aβ) monomer, thus regulating the levels of Aβ monomers. The current work illustrates a first study by which IDE encapsulates polymorphic early-stage Aβ oligomers. The main goal of this study was to investigate the molecular mechanisms of IDE activity on the encapsulated early-stage Aβ dimers: fibril-like and random coil/α-helix dimers. Our work led to several findings. First, when the fibril-like Aβ dimer interacts with IDE-C domain, IDE does not impede the contact between the monomers, but plays a role as a ‘dead-end’ chaperone protein. Second, when the fibril-like Aβ dimer interacts with the IDE-N domain, IDE successfully impedes the contacts between monomers. Third, the inhibitory activity of IDE on random coil/α-helix dimers depends on the stability of the dimer. IDE could impede the contacts between monomers in relatively unstable random coil/α-helix dimers, but gets hard to impede in stable dimers. However, IDE encapsulates stable dimers and could serve as a ‘dead-end’ chaperone. Our results examine the molecular interactions between IDE and the dimers, and between the monomers within the dimers. Hence, this study provides insights into the inhibition mechanisms of the primary nucleation of Aβ aggregation and the basic knowledge for rational design to inhibit Aβ aggregation.
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Jang, Hyunbum, Serena Muratcioglu, Attila Gursoy, Ozlem Keskin, and Ruth Nussinov. "Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers." Biochemical Journal 473, no. 12 (June 10, 2016): 1719–32. http://dx.doi.org/10.1042/bcj20160031.
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Are the dimer structures of active Ras isoforms similar? This question is significant since Ras can activate its effectors as a monomer; however, as a dimer, it promotes Raf's activation and MAPK (mitogen-activated protein kinase) cell signalling. In the present study, we model possible catalytic domain dimer interfaces of membrane-anchored GTP-bound K-Ras4B and H-Ras, and compare their conformations. The active helical dimers formed by the allosteric lobe are isoform-specific: K-Ras4B-GTP favours the α3 and α4 interface; H-Ras-GTP favours α4 and α5. Both isoforms also populate a stable β-sheet dimer interface formed by the effector lobe; a less stable β-sandwich interface is sustained by salt bridges of the β-sheet side chains. Raf's high-affinity β-sheet interaction is promoted by the active helical interface. Collectively, Ras isoforms’ dimer conformations are not uniform; instead, the isoform-specific dimers reflect the favoured interactions of the HVRs (hypervariable regions) with cell membrane microdomains, biasing the effector-binding site orientations, thus isoform binding selectivity.
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Habets, Thomas, Dennis Lensen, Sylvia Speller, and Johannes A. A. W. Elemans. "Self-Assembly of Covalently Linked Porphyrin Dimers at the Solid–Liquid Interface." Molecules 24, no. 16 (August 20, 2019): 3018. http://dx.doi.org/10.3390/molecules24163018.
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The synthesis and surface self-assembly behavior of two types of metal-porphyrin dimers is described. The first dimer type consists of two porphyrins linked via a rigid conjugated spacer, and the second type has an alkyne linker, which allows rotation of the porphyrin moieties with respect to each other. The conjugated dimers were equipped with two copper or two manganese centers, while the flexible dimers allowed a modular built-up that also made the incorporation of two different metal centers possible. The self-assembly of the new porphyrin dimers at a solid–liquid interface was investigated at the single-molecule scale using scanning tunneling microscopy (STM). All dimers formed monolayers, of which the stability and the internal degree of ordering of the molecules depended on the metal centers in the porphyrins. While in all monolayers the dimers were oriented coplanar with respect to the underlying surface (‘face-on’), the flexible dimer containing a manganese and a copper center could be induced, via the application of a voltage pulse in the STM setup, to self-assemble into monolayers in which the porphyrin dimers adopted a non-common perpendicular (‘edge-on’) geometry with respect to the surface.
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Klingelhöfer, Jörg, Oscar Y. Laur, Regina B. Troyanovsky, and Sergey M. Troyanovsky. "Dynamic Interplay between Adhesive and Lateral E-Cadherin Dimers." Molecular and Cellular Biology 22, no. 21 (November 1, 2002): 7449–58. http://dx.doi.org/10.1128/mcb.22.21.7449-7458.2002.
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ABSTRACT E-cadherin, an adhesive transmembrane protein of epithelial adherens junctions, forms two types of detergent-resistant dimers: adhesive dimers consisting of cadherin molecules derived from two neighboring cells and lateral dimers incorporating cadherins of the same cell. Both dimers depend on the integrity of the same residue, Trp156. While the relative amounts of these complexes are not certain, we show here that in epithelial A-431 cells, adhesive dimers may be a prevalent form. Inactivation of the calcium-binding sites, located between successive cadherin ectodomains, drastically reduced the amount of adhesive dimers and concomitantly increased the amount of lateral dimers. A similar interdependence of adhesive and lateral dimers was observed in digitonin-permeabilized cells. In these cells, adhesive dimers immediately disassembled after lowering the Ca2+ concentration below 0.1 mM. The disappearance of adhesive dimers was counterbalanced by an increase in Trp156-dependent lateral dimers. Increasing the calcium concentration to a normal level rapidly restored the original balance between adhesive and lateral dimers. We also present evidence that E-cadherin dimers in vivo have a short lifetime. These observations suggest that cadherin-mediated adhesion is based on the dynamic cycling of E-cadherin between monomeric and adhesive dimer states.
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Troyanovsky, Regina B., Eugene P. Sokolov, and Sergey M. Troyanovsky. "Endocytosis of Cadherin from Intracellular Junctions Is the Driving Force for Cadherin Adhesive Dimer Disassembly." Molecular Biology of the Cell 17, no. 8 (August 2006): 3484–93. http://dx.doi.org/10.1091/mbc.e06-03-0190.
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The adhesion receptor E-cadherin maintains cell–cell junctions by continuously forming short-lived adhesive dimers. Here mixed culture cross-linking and coimmunoprecipitation assays were used to determine the dynamics of adhesive dimer assembly. We showed that the amount of these dimers increased dramatically minutes after the inhibition of endocytosis by ATP depletion or by hypertonic sucrose. This increase was accompanied by the efficient recruitment of E-cadherin into adherens junctions. After 10 min, when the adhesive dimer amount had reached a plateau, the assembly of new dimers stalled completely. These cells, in a striking difference from the control, became unable to disintegrate both their intercellular contacts and adhesive dimers in response to calcium depletion. The same effects, but after a slightly longer time course, were obtained using acidic media, another potent approach inhibiting endocytosis. These data suggest that endocytosis is the main pathway for the dissociation of E-cadherin adhesive dimers. Its inhibition blocks the replenishment of the monomeric cadherin pool, thereby inhibiting new dimer formation. This suggestion has been corroborated by immunoelectron microscopy, which revealed cadherin-enriched coated pit-like structures in close association with adherens junctions.
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Pita, M. Luisa, and Ricardo A. Mosquera. "Computational Study on the Conformational Preferences of Neutral, Protonated and Deprotonated Glycine Dimers." Compounds 2, no. 4 (October 12, 2022): 252–66. http://dx.doi.org/10.3390/compounds2040021.
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A conformational analysis has been carried out for monoprotonated, unprotonated and deprotonated glycine dimers in the gas phase and an aqueous solution. MP2/6-311++(d,p), B3LYP/6-311++(d,p) and M06/6-311++(d,p) optimizations were performed for more than 200 initial conformations comprising nonionic (COOH–CH2–NH2) (N) and zwitterionic (COO−–CH2–NH3+) (Z) structures for neutral monomers. All the methods indicate that Z monomers are preferred over N ones for the neutral and deprotonated dimers in aqueous solutions, whereas the reverse trend is observed in the gas phase (including also protonated dimers). NC and ZC structures coexist in aqueous solutions for the protonated glycine dimer. The preferred geometries are significantly different depending on the media and total dimer charge. Moreover, several minima display close energies in each series (media and total dimer charge). New conformers, not previously reported, are found to be significantly populated in those conformational mixtures. Dimers containing Z monomers are associated with larger absolute solvation energies and are more prone than N-containing ones to experience protonation and deprotonation in the gas phase, whereas the reverse trend is observed in the aqueous solution. The Quantum Theory of Atoms in Molecules (QTAIM) analysis reveals that uncharged dimers display trifling electron density transfer between monomers, whereas it is significant in anionic and cationic dimers.
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Cheng, Jie, Jing Chuan Zhu, and Bo Liu. "Molecular Modeling of the Dimers from Cyclo-[(1R, 3S)-γ-Acc-D-Phe]3." Key Engineering Materials 353-358 (September 2007): 2244–47. http://dx.doi.org/10.4028/www.scientific.net/kem.353-358.2244.
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Four kinds of dimers from cyclic peptide [-(1R, 3S)-γ-Acc-D-Phe]3 were investigated using molecular modeling based on the density functional theory (DFT), molecular mechanics (MM) and molecular dynamics (MD). The equilibrium dimer structures reveal that these dimers can be divided into two different types according to stacking formation, in which one type dimer is more stable due to the effect of side chain groups. In each type of dimers, only one can transport CHCl3. When the terminal N-substituent methyl is introduced, the transport character is reversed. Analysis of 500 ps MD trajectory suggests that the inner and terminal sizes of the dimers are the main factor that affects the transport of CHCl3. The modeling results can provide a new way for designing and synthesizing cyclic peptide transport channels.
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Zhou, Yuehui, W. E. Baker, P. M. Kazmaier, and E. Buncel. "Phenanthroimidazole dimers: structure and free radical reactivity; piezochromism, thermochromism, and photochromism." Canadian Journal of Chemistry 76, no. 6 (June 1, 1998): 884–95. http://dx.doi.org/10.1139/v98-085.
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A series of 2-phenyl phenanthroimidazole dimers was synthesized by means of a two-phase preparative method, which allowed their isolation in pure form. Definitive proof of structure was obtained by means of 1H and 13C NMR spectroscopy; five of the six possible structural isomers of the dimer could thus be eliminated. The dimers exhibited thermochromic and piezochromic behavior, but not photochromic. The colored species were shown to be free radicals formed on dissociation of the dimers; this was confirmed through ESR measurements. The electronic absorption spectra of the radicals were influenced by substituents on the phenyl ring. The UV-VIS measurements allowed the evaluation of the dimer-radical equilibrium constants, which were also found to be dependent on substituents on the phenyl ring.Key words: phenanthroimidazole dimers, free radical equilibrium, piezochromism, thermochromism, photochromism.
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Ploegh, Hidde, and Philippe Benaroch. "MHC class II dimer of dimers." Nature 364, no. 6432 (July 1993): 16–17. http://dx.doi.org/10.1038/364016d0.
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Yamane, Tsutomu, Takahiro Nakayama, Toru Ekimoto, Masao Inoue, Keigo Ikezaki, Hiroshi Sekiguchi, Masahiro Kuramochi, et al. "Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study." International Journal of Molecular Sciences 24, no. 20 (October 21, 2023): 15423. http://dx.doi.org/10.3390/ijms242015423.
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Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.
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Reyna-Rosas, Edgar, Hugo I. Contreras-Treviño, Renato León-Rodríguez, Leticia Rocha-Zavaleta, Tzvetanka D. Dinkova, and Luis Padilla-Noriega. "The accumulation of rotavirus NSP3 dimers does not correlate with the extent of host cell translation inhibition." Future Virology 15, no. 9 (September 2020): 565–76. http://dx.doi.org/10.2217/fvl-2020-0259.
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Aim: We aimed to determine the functionality of rotavirus NSP3 dimers. Materials & methods: We expressed rhesus rotavirus NSP3 and determined the kinetics of host cell translation inhibition and the levels of accumulated dimerization intermediates and dimers. Results: We observed a linear kinetics of host cell translation inhibition, which correlated well with the sum of the dimerization intermediates and dimers. Treatment with 17-dimethylaminoethylamino-17-demethoxygeldanamycin reduced the accumulation of NSP3 dimers and potentiated host cell translation inhibition. Conclusion: Our results show that NSP3 dimer formation does not correlate with host cell translation inhibition and suggest that both NSP3 dimers and dimerization intermediates are functional and inhibit host cell translation.
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Wang, Junqiao, Jia Zhang, Yongzhi Tian, Kaijun Mu, Chunzhen Fan, Shu Chen, and Pei Ding. "Fano resonances in nanorod dimers antenna." Modern Physics Letters B 31, no. 18 (June 27, 2017): 1750202. http://dx.doi.org/10.1142/s0217984917502025.
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Without losing symmetry, plasmonic Fano resonances have been observed and investigated in multiple nanorod dimers antennae in this paper. The dipole–dipole Fano resonance in three nanorod dimers can be excited simultaneously due to the resonance detuning, and the induced currents of nanorod dimers on both sides are in-phase and out-of-phase with the middle nanorod dimer, respectively. The sharp Fano dip excited in three nanorod dimers antennae can be used to realize the high sensitive sensing of 1116 nm/RIU in the visible and near infrared regions. Furthermore, the Fano resonance is also observed in plasmonic nanoantennae with four nanorod dimers.
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Zawadzki, Paweł, Anita Nowak, and Lukasz Dzieciuchowicz. "Factors affecting D-dimer levels in patients with uncomplicated primary varicose veins." Polish Journal of Surgery 93, no. 5 (June 23, 2021): 1–5. http://dx.doi.org/10.5604/01.3001.0014.9658.
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Objectives The diagnosis of deep venous thrombosis (DVT) is hampered in patients with primary varicose veins due to similarity of symptoms of DVT and PVV and elevated levels of D-dimers. The purpose of this study was to analyze factors that influence the D-dimer concentration in patients with PVV in order to redefine its diagnostic value. Methods Forty- one patients with non-complicated PVV were enrolled in the study, in whom D-dimer level was determined by immunoturbidimetric assay. The influence of selected clinical factors on the concentration of D-dimers was determined with univariate and bivariate analysis. Besides descriptive statistics the D-dimers levels were compared to the age -adjusted cutoff values. Results The median concentration of D-dimer was 630.0 ng/ml (440.0-1140.0 ng/ml) and was above the age-adjusted level in 21 (52%) of patients. There was a positive correlation between the patient’s age and and D-dimer concentration (p = 0.035, Spearman correlation coefficient rs=0,33. The bivariate analysis showed a significant interaction between age and weight p=0,02. Conclusions In patients with PVV the diagnostic value of D-dimers is limited especially in older and overweight subjects.
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Kasai, Rinshi S., Kenichi G. N. Suzuki, Eric R. Prossnitz, Ikuko Koyama-Honda, Chieko Nakada, Takahiro K. Fujiwara, and Akihiro Kusumi. "Full characterization of GPCR monomer–dimer dynamic equilibrium by single molecule imaging." Journal of Cell Biology 192, no. 3 (February 7, 2011): 463–80. http://dx.doi.org/10.1083/jcb.201009128.
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Receptor dimerization is important for many signaling pathways. However, the monomer–dimer equilibrium has never been fully characterized for any receptor with a 2D equilibrium constant as well as association/dissociation rate constants (termed super-quantification). Here, we determined the dynamic equilibrium for the N-formyl peptide receptor (FPR), a chemoattractant G protein–coupled receptor (GPCR), in live cells at 37°C by developing a single fluorescent-molecule imaging method. Both before and after liganding, the dimer–monomer 2D equilibrium is unchanged, giving an equilibrium constant of 3.6 copies/µm2, with a dissociation and 2D association rate constant of 11.0 s−1 and 3.1 copies/µm2s−1, respectively. At physiological expression levels of ∼2.1 receptor copies/µm2 (∼6,000 copies/cell), monomers continually convert into dimers every 150 ms, dimers dissociate into monomers in 91 ms, and at any moment, 2,500 and 3,500 receptor molecules participate in transient dimers and monomers, respectively. Not only do FPR dimers fall apart rapidly, but FPR monomers also convert into dimers very quickly.
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Lu, Tieyi, Wen Guo, Prathamesh M. Datar, Yue Xin, E. Neil G. Marsh, and Zhan Chen. "Probing protein aggregation at buried interfaces: distinguishing between adsorbed protein monomers, dimers, and a monomer–dimer mixture in situ." Chemical Science 13, no. 4 (2022): 975–84. http://dx.doi.org/10.1039/d1sc04300e.
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SFG spectra analyzed by the developed Hamiltonian method show that adsorbed BSA molecules on silicone oil are dimers. On treatment with dithiothreitol, some BSA dimers dissociate, resulting in 60% dimer and 40% monomer on the silicone oil surface.
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Apelblat, Alexander. "Dimerization and continuous association including formation of cyclic dimers." Canadian Journal of Chemistry 69, no. 4 (April 1, 1991): 638–47. http://dx.doi.org/10.1139/v91-097.
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New aspects of the theory of ideal associated mixtures related to a differentiation between formed cyclic and linear dimers are discussed. A mathematical analysis is presented for the dimerization model, A + B + A2, the continuous association (Mecke–Kempter) model, [Formula: see text], both coupled with the cyclic dimmer → linear dimer transformation and for the unsymmetrical (mixed) dimer formation model, A + B + A2 + B2 + AB. Introduction of the standard reaction enthalpies and volumes associated with transformations of dimers leads to a considerable change in behavior and symmetry properties of the excess thermodynamic functions. In terms of the modified Mecke–Kempter model, a consistent representation of the excess Gibbs energy of mixing GE, heat of mixing HE, and excess molar volume VE is reported for the acetic acid – water system at 298.15 K. Key words: association, dimerization, linear dimers, cyclic dimers, hydrogen bonding, carboxylic acids, alcohols, aqueous solutions.
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Schwarzbauer, J. E., C. S. Spencer, and C. L. Wilson. "Selective secretion of alternatively spliced fibronectin variants." Journal of Cell Biology 109, no. 6 (December 1, 1989): 3445–53. http://dx.doi.org/10.1083/jcb.109.6.3445.
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We demonstrate that the alternatively spliced variable (V) region of fibronectin (FN) is required for secretion of FN dimers during biosynthesis. Alternative splicing of the V segment of the rat FN transcript generates three subunit variants (V120, V95, V0) that differ by the inclusion or omission of an additional 120 or 95 amino acids. We are exploring the functions of this segment by expressing variant cDNAs in normal and transformed fibroblasts. Like FN itself, the cDNA-encoded polypeptides (deminectins [DNs]) containing the V120 or V95 segment are efficiently secreted as disulfide-bonded homodimers. However, few homodimers of DNs lacking this region, V0 DNs, are secreted. V0 homodimers do form inside the cell, as demonstrated by biosynthetic analyses of dimer formation and secretion using pulse-chase and time course experiments, but these dimers seldom reach the cell surface and are probably degraded intracellularly. Coexpression of V0 and V120 subunits results in intracellular formation of three types of dimers, V0-V0, V0-V120, and V120-V120, but only the V120-containing dimers are secreted. This selective retention of V0 homodimers indicates that the V region is required for formation and secretion of native FN dimers. In an analogous in vivo situation, we show that plasma FN also lacks V0-V0 dimers and consists of V0-V+ and V+-V+ combinations. Dissection of V region sequences by deletion mapping localizes the major site involved in DN dimer secretion to an 18-amino acid segment within V95. In addition, high levels of dimer secretion can be restored by insertion of V into a heterologous site 10 kD COOH terminal to its normal location. We discuss the potential role of intracellular protein-protein interactions in FN dimer formation.
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Caliezi, Holtz, and Wuillemin. "Case 16: Use of D-dimer assay in suspected deep vein thrombosis or pulmonary embolism." Therapeutische Umschau 56, no. 9 (September 1, 1999): 529–32. http://dx.doi.org/10.1024/0040-5930.56.9.529.
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D-Dimere sind Abbauprodukte des quervernetzten Fibrins nach fibrinolytischer Spaltung durch Plasmin. D-Dimere können im Plasma oder im Vollblut mittels gegen Epitope des D-Dimers gerichteter monoklonaler Antikörper nachgewiesen werden. Erhöhte D-Dimer-Werte finden sich bei Patienten mit tiefer Venenthrombose (TVT) oder Lungenembolie (LE), aber auch z.B. bei Patienten mit Infektionen, malignen Tumoren oder Herzinsuffizienz. Die Bestimmung der D-Dimere hat sich als früher Abklärungsschritt in der Diagnostik venöser Thromboembolien (TVT/LE) etabliert. Die hohe Sensitivität verschiedener ELISA-Teste ermöglicht es, die Diagnose einer TVT oder LE zuverlässig auszuschließen, falls die Konzentration der D-Dimere unterhalb einer kritischen Schwelle (sog. cut-off) liegt. Bei ambulanten Patienten gelingt es so, in rund 30% der Fälle mit Hilfe eines gut validierten Testes eine venöse Thromboembolie auszuschließen und auf weitere diesbezügliche Untersuchungen zu verzichten.
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Tellinghuisen, Timothy L., Rushika Perera, and Richard J. Kuhn. "In Vitro Assembly of Sindbis Virus Core-Like Particles from Cross-Linked Dimers of Truncated and Mutant Capsid Proteins." Journal of Virology 75, no. 6 (March 15, 2001): 2810–17. http://dx.doi.org/10.1128/jvi.75.6.2810-2817.2001.
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ABSTRACT A nucleic acid-bound capsid protein dimer was previously identified using a Sindbis virus in vitro nucleocapsid assembly system and cross-linking reagents. Cross-link mapping, in combination with a model of the nucleocapsid core, suggested that this dimer contained one monomer from each of two adjacent capsomeres. This intercapsomere dimer is believed to be the initial intermediate in the nucleocapsid core assembly mechanism. This paper presents the purification of cross-linked dimers of a truncated capsid protein and the partial purification of cross-linked dimers of a full-length assembly-defective mutant. The assembly of core-like particles from these cross-linked capsid protein dimers is demonstrated. Core-like particles generated from cross-linked full-length mutant CP(19-264)L52D were examined by electron microscopy and appeared to have a morphology similar to that of wild-type in vitro-assembled core-like particles, although a slight size difference was often visible. Truncated cross-linked CP(81-264) dimers generated core-like particles as well. These core-like particles could subsequently be disassembled when reversible cross-linking reagents were used to form the dimers. The ability of the covalent intercapsomere cross-link to rescue capsid proteins with assembly defects or truncations in the amino-terminal region of the capsid protein supports the previous model of assembly and suggests a possible role for the amino-terminal region of the protein.
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Mühleip, Alexander W., Friederike Joos, Christoph Wigge, Achilleas S. Frangakis, Werner Kühlbrandt, and Karen M. Davies. "Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria." Proceedings of the National Academy of Sciences 113, no. 30 (July 11, 2016): 8442–47. http://dx.doi.org/10.1073/pnas.1525430113.
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F1Fo-ATP synthases are universal energy-converting membrane protein complexes that synthesize ATP from ADP and inorganic phosphate. In mitochondria of yeast and mammals, the ATP synthase forms V-shaped dimers, which assemble into rows along the highly curved ridges of lamellar cristae. Using electron cryotomography and subtomogram averaging, we have determined the in situ structure and organization of the mitochondrial ATP synthase dimer of the ciliate Paramecium tetraurelia. The ATP synthase forms U-shaped dimers with parallel monomers. Each complex has a prominent intracrista domain, which links the c-ring of one monomer to the peripheral stalk of the other. Close interaction of intracrista domains in adjacent dimers results in the formation of helical ATP synthase dimer arrays, which differ from the loose dimer rows in all other organisms observed so far. The parameters of the helical arrays match those of the cristae tubes, suggesting the unique features of the P. tetraurelia ATP synthase are directly responsible for generating the helical tubular cristae. We conclude that despite major structural differences between ATP synthase dimers of ciliates and other eukaryotes, the formation of ATP synthase dimer rows is a universal feature of mitochondria and a fundamental determinant of cristae morphology.
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Mughal, Sabeeha, C. Grazia Bezzu, Emma Carter, Simon J. A. Pope, and Neil B. McKeown. "The tetratriptycenoporphyrazines revisited." Journal of Porphyrins and Phthalocyanines 17, no. 08n09 (August 2013): 778–84. http://dx.doi.org/10.1142/s1088424613500351.
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The spectroscopic behavior of octa-t-butyltetra-2,3-triptycenotetraazaporphyrin and some of its metal complexes ( Cu 2+, Zn 2+ and Co 2+) were examined. UV-visible and electron paramagnetic resonance spectroscopy indicate that these phthalocyanine derivatives form cofacial dimers in pentane solution. Modeling suggests that the lowest energy configuration of the dimer is a self-complementary embrace in which the two phthalocyanine cores are staggered at an angle of 45° relative to each other. This configuration results in a remarkably intense and sharp absorption band (~635 nm; ε = ~4.0 × 105 M-1.cm-1) arising from excitonic coupling within the dimer, a unique property for self-assembled dimers but analogous to the behavior of certain μ-oxo-dimers of silicon phthalocyanine. Introduction of methyl substituents into the bridgehead positions of the triptycene subunits prevents dimer formation.
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Wei, Dongdong, Yongliang Qin, Zhipeng Xu, Hui Liu, Ranran Chen, Yang Yu, and Di Wang. "Study of Molecular Dimer Morphology Based on Organic Spin Centers: Nitronyl Nitroxide Radicals." Molecules 29, no. 9 (April 28, 2024): 2042. http://dx.doi.org/10.3390/molecules29092042.
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In this work, in order to investigate the short-range interactions between molecules, the spin-magnetic unit nitronyl nitroxide (NN) was introduced to synthesize self-assembly single radical molecules with hydrogen bond donors and acceptors. The structures and magnetic properties were extensively investigated and characterized by UV-Vis absorption spectroscopy, electron paramagnetic resonance (EPR), and superconducting quantum interference devices (SQUIDs). Interestingly, it was observed that the single molecules can form two different dimers (ring-closed dimer and “L”-type dimer) in different solvents, due to hydrogen bonding, when using EPR to track the molecular spin interactions. Both dimers exhibit ferromagnetic properties (for ring-closed dimer, J/kB = 0.18 K and ΔES−T = 0.0071 kcal/mol; for “L”-type dimer, the values were J/kB = 9.26 K and ΔES−T = 0.037 kcal/mol). In addition, the morphologies of the fibers formed by the two dimers were characterized by transmission electron microscopy (TEM) and atomic force microscopy (AFM).
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Thomas, Hans Günter, Michael Rasp, and Gerhard Raabe. "Anodische Oxidation von 2-Thiobarbitursäuren unter Bildung neuartiger, tetracyclischer Dimerer / Anodic Oxidation of 2-Thiobarbituric Acids under Formation of New Tetracyclic Dimers." Zeitschrift für Naturforschung B 57, no. 2 (February 1, 2002): 215–25. http://dx.doi.org/10.1515/znb-2002-0213.
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2-Thiobarbituric acids 1 can be dimerized anodically in acceptable yields if the special ultrasonic electrolysis cell described here is used. In some cases two isomeric dimers 2 and 4 were isolated. 2 is of the same type as the corresponding barbituric acid dimers. The other dimer 4 has a completely different, tetracyclic structure characterized by NMR spectra and X-ray diffraction. The mechanism postulated for the formation of the tetracyclic dimers is supported by cyclovoltammetric measurements.
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Breslow, Ronald, Sandro Belvedere, Leland Gershell, and David Leung. "The chelate effect in binding, catalysis, and chemotherapy." Pure and Applied Chemistry 72, no. 3 (January 1, 2000): 333–42. http://dx.doi.org/10.1351/pac200072030333.
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Cyclodextrin (CD) dimers bind amino acid side chains, and such binding can dissociate aggregated proteins, including citrate synthase (dimer) and lactic dehydrogenase (tetramer). A CD dimer can bind a hydrophobic photosensitizer that, upon irradiation, generates singlet oxygen. This cleaves the dimer and releases the photosensitizer. CD dimers in a cytochrome P-450 mimic steer catalyzed hydroxylation to a bound steroid with geometric control. Chelate binding has also led to a group of cytodifferentiating agents whose mechanism has been recently established. They have promising anticancer properties, and are currently entering human trials as therapeutic agents.
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Li, W., S. Nagaraja, G. P. Delcuve, M. J. Hendzel, and J. R. Davie. "Effects of histone acetylation, ubiquitination and variants on nucleosome stability." Biochemical Journal 296, no. 3 (December 15, 1993): 737–44. http://dx.doi.org/10.1042/bj2960737.
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The properties of the nucleosomes of a salt-soluble, transcriptionally active gene-enriched fraction of chicken erythrocyte chromatin were evaluated by hydroxyapatite dissociation chromatography. We have demonstrated previously that the salt-soluble, transcriptionally active gene-enriched polynucleosomes are enriched in dynamically acetylated and ubiquitinated histones, and in an atypical U-shaped nucleosome that possessed about 20% less protein than a typical nucleosome. Further, newly synthesized histones H2A and H2B exchange preferentially with the nucleosomal histones H2A and H2B of this salt-soluble chromatin fraction. Analysis of the histones eluting from the hydroxyapatite-bound chromatin demonstrated that hyperacetylated and ubiquitinated (u), including multi-ubiquitinated, H2A-H2B.1 dimers dissociated at lower concentrations of NaCl than unmodified dimers or dimers with histone variants H2A.Z and/or H2B.2. Cross-linking studies revealed that at least 50% of uH2B.1 was paired with uH2A. uH2A-uH2B.1 dimers dissociated at lower NaCl concentrations than H2A-uH2B.1 dimers. Hyperacetylated histone (H3-H4)2 tetramers also eluted at lower concentrations of NaCl than unmodified tetramers. Our results support the idea that acetylation and ubiquitination of histones H2A and H2B.1 increase the lability of H2A-H2B.1 dimers in transcriptionally active nucleosomes. In contrast, our observations suggest that histone variants H2A.Z and H2B.2. stabilize the association of the H2A-H2B dimer in nucleosomes. The elevated lability of the H2A-H2B dimer may facilitate processes such as the exchange of these dimers with newly synthesized histones, the elongation process of transcription and transcription factor binding.
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Kong, Qingjun, Qingzhi Zeng, Jia Yu, Hongxi Xiao, Jun Lu, and Xueyan Ren. "Mechanism of Resveratrol Dimers Isolated from Grape Inhibiting 1O2 Induced DNA Damage by UHPLC-QTOF-MS2 and UHPLC-QQQ-MS2 Analyses." Biomedicines 9, no. 3 (March 8, 2021): 271. http://dx.doi.org/10.3390/biomedicines9030271.
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Resveratrol dimers have been extensively reported on due to their antioxidative activity. Previous studies revealed that resveratrol dimer has been shown to selectively quench singlet oxygen (1O2), and could protect DNA from oxidative damage. The mechanism of resveratrol dimers protecting DNA against oxidative damage is still not clear. Therefore, in this project, the reactants and products of resveratrol dimers protecting guanine from oxidative damage were qualitatively monitored and quantitatively analyzed by UHPLC-QTOF-MS2 and UHPLC-QQQ-MS2. Results showed that when guanine and resveratrol dimers were attacked by 1O2, mostly resveratrol dimers were oxidized, which protected guanine from oxidation. Resveratrol dimers’ oxidation products were identified and quantified at m/z 467.1134 [M-H]− and 467.1118 [M-H]−, respectively. The resorcinol of resveratrol dimers reacted with singlet oxygen to produce p-benzoquinone, protecting guanine from 1O2 damage. Therefore, it is hereby reported for the first time that the resorcinol ring is the characteristic structure in stilbenes inhibiting 1O2 induced-DNA damage, which provides a theoretical basis for preventing and treating DNA damage-mediated diseases.
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Lazaroff, Carolyn, David Peeney, Sadeechya Gurung, and William G. Stetler-Stevenson. "Abstract 3837: The physiological relevance of TIMP dimer formation." Cancer Research 82, no. 12_Supplement (June 15, 2022): 3837. http://dx.doi.org/10.1158/1538-7445.am2022-3837.
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Abstract Tissue inhibitors of metalloproteinases (TIMPs) are a family of four paralogous genes that modulate the activity of matrix metalloproteinases (MMPs) and are vital for tissue homeostasis. Additionally, TIMPs display activities that are independent of their MMP inhibitory activities. Dysregulation and perturbations within this system can lead to complex tissue-specific pathologies. TIMP2 is the most abundantly expressed member of the TIMP family and has been shown to display potential therapeutic uses in cancer and other diseases. We have noted the persistent presence of SDS-stable TIMP2 dimers/multimers in SDS-PAGE at a level of ~5% total protein. The goal of this study is to determine the stability and biological relevance of SDS-stable dimer formation of TIMP2 in in vitro and in vivo. We found that TIMP2 dimers display an enhanced ability to inhibit MMP2 activity in reverse zymography assays. Immunoblotting revealed gel extracted TIMP2 dimer entered an equilibrium with monomeric TIMP2, while the extracted monomer did not form new dimer. In addition, MMP2 activity assays do not corroborate the enhanced MMP2 inhibitory activity observed in reverse zymograms but are consistent with the observation that isolated TIMP2 dimers re-equilibrate with monomers. This implies that structural or sequence difference mediates the formation of dimers. Dimer/multimer formation is observed across the TIMP family. Mass spectrometry analysis of gel extracted TIMP monomers and dimers show that monomer and dimer forms of TIMPs display unique post-translation modification (PTM) profiles. We propose that understanding the interplay between TIMP multimers and PTMs will reveal new biological functions within this intriguing family of proteins. We are currently working to resolve the functional differences between monomer and dimer and reveal the underlying mechanisms at play. Citation Format: Carolyn Lazaroff, David Peeney, Sadeechya Gurung, William G. Stetler-Stevenson. The physiological relevance of TIMP dimer formation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3837.
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Seligmann, Jenny F., Peter Hall, Patrick Hamilton, Simon Richard Lord, Paul Baxter, Maria Marples, and Daniel P. Stark. "D-dimers as a tumor marker in GIST: Can it reduce the frequency of CT scanning in patients receiving palliative imatinib?" Journal of Clinical Oncology 30, no. 4_suppl (February 1, 2012): 119. http://dx.doi.org/10.1200/jco.2012.30.4_suppl.119.
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119 Background: Treatment with palliative imatinib has improved outcomes in advanced GISTs, with a reported 2 year PFS of 50%. Guidelines suggest monitoring during imatinib by CT scan at 12 week intervals. There are no validated biomarkers to assist in disease evaluation. High d-dimer levels are associated with poor prognosis in several cancers and are predictive of disease progression during chemotherapy. In the diagnosis of venous thromboembolism, low D-dimer levels have a high negative predictive value (npv) for thrombosis. We investigated whether low d-dimers have a clinically useful npv for GIST progression. Methods: We retrospectively identified all patients treated with palliative Imatinib for GIST in a single tertiary referral centre using a systematic search of an electronic clinical database. Every 12 weeks during treatment patients were assessed by clinical evaluation, CT and a d-dimer measurement (HemosIL HS assay). The prognostic value of d-dimers was assessed by Cox regression. The clinical utility of d-dimers as a biomarker for radiological progression (rPD) was evaluated using radio operator curve (ROC) analysis. Results: 50 patients treated between Jan 2002 and June 2011 met criteria for inclusion. D-dimers were prognostic for progression free survival and overall survival, when analysed by level or over time (p <0.05). Over 460 clinical observations with CT and d-dimer were analysed. Scans demonstrating rPD were associated with higher d-dimer levels and a rising trend (p <0.05). D-dimer levels <1000 had a npv for rPD of 85%. An asymptomatic patient with a d-dimer level <1000 and a falling level over time was seen in 32% of observations, and had a npv for rPD of 92%. Conclusions: D-dimers may have a useful role in disease monitoring for GIST patients treated with palliative imatinib, particularly as a negative predictor of progression. This may reduce the burden of CT scanning in a useful percentage of patients but will require further validation.
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Liyasova, Mariya, Michael Slade, Julie Fortier, Ravi Vij, Mark Fiala, Liqiang Yang, and Bin Ma. "Novel Assay for Quantification of Free Light Chain (FLC) Dimers in Serum of Patients with Plasma Cell Dyscrasias." Blood 142, Supplement 1 (November 28, 2023): 2292. http://dx.doi.org/10.1182/blood-2023-186583.
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Free light chains (FLCs) are a well-established biomarker of plasma cell dyscrasias. FLCs exist as monomers, dimers and oligomers. Lambda FLC is particularly prone to form dimers and oligomers. Under certain pathological conditions, FLC dimerization changes towards the increased dimer formation. For instance, high levels of FLC dimers were found in AL amyloidosis and multiple myeloma (MM) even when the total FLC concentrations were near the normal levels. Thus, FLC dimer quantification can be used as a tool to diagnose and monitor AL amyloidosis and MM. Here we report a novel assay to detect and quantify FLC dimers with mass spectrometry. To demonstrate the power of the assay, we quantified FLC dimers in LC-only MM serum samples and compared the results to the gold standard Freelite assay. FLC dimer quant assay relies on the detection and quantification of constant region dimeric peptides of lambda and kappa LCs in serum with targeted mass spectrometry. The serum sample is enzymatically digested under non-reducing condition for 1 hour, specific disulfide-bridged dimeric peptides are then separated by Evosep One liquid chromatography and analyzed with parallel reaction monitoring (PRM) on Orbitrap Exploris mass spectrometer. FLC dimers can be quantified relative to control serum samples and by absolute quant using stable isotope labelled (SIL) peptides resulting in mg/dL values. The identities of the peptides were confirmed by mass spectrometry analysis of synthetic dimeric peptides and recombinant FLCs. To determine the lower limit of quantification (LLoQ) the control pooled serum was spiked with the increasing amounts of recombinant FLC. The assay demonstrated exceptional linearity from 0.78 to 50 mg/dL of spiked FLC kappa or lambda (R 2=0.999 for both). The assay only requires 10 μL of serum without the need for a diagnostic sample and can be performed at any time point, as frequently as needed. FLC dimer quant assay was compared to Freelite assay for 17 newly diagnosed patients with LC-only MM. All patients underwent autologous stem cell transplant (ASCT) and had banked serum samples at diagnosis and day 100 post-ASCT. 15 patients (88%) reached CR at day 100 post-ASCT. 8 patients had lambda LC MM, while 9 patients had kappa LC MM. At diagnosis the median involved FLC was 250 mg/dL (range: 26.1 - 1440), while at day 100 post-ASCT the median involved FLC was 1.1 mg/dL (range 0 - 2.5). The FLC dimer quant results were reported as a ratio to control, whereby the FLC dimer amount in control pooled serum was set to 1. FLC dimers were detected at all time points in all patients. The median involved FLC dimer ratio to control at diagnosis was 23.3 (range: 4.5 - 445.7), while the median involved FLC dimer ratio to control at day 100 post-ASCT was 1.0 (range: 0.3 - 3.8). Strong correlation (R 2=0.993 for lambda and R 2=0.931 for kappa) was observed between FLC dimer and Freelite assays (Fig.1). To conclude, we developed a novel assay to measure FLC dimer with mass spectrometry. The assay demonstrated a good correlation to Freelite assay. This study establishes an FLC dimer assay as a promising diagnostic and monitoring tool in LC MM patients. Large clinical studies are needed to establish reference ranges for kappa and lambda dimers in healthy population and demonstrate clinical utility in other plasma cell dyscrasias.
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Capps, G. G., B. E. Robinson, K. D. Lewis, and M. C. Zúñiga. "In vivo dimeric association of class I MHC heavy chains. Possible relationship to class I MHC heavy chain-beta 2-microglobulin dissociation." Journal of Immunology 151, no. 1 (July 1, 1993): 159–69. http://dx.doi.org/10.4049/jimmunol.151.1.159.
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Abstract Class I MHC molecules have been thought to occur in vivo both as class I MHC heavy chain-beta 2-m heterodimers, which are or are not associated with antigenic peptide, and as free class I MHC heavy chains. Class I MHC molecules are now found also to occur in another type of structure: a heavy chain-heavy chain dimer. Biochemical studies show that heavy chain dimers are disulfide-linked via a conserved cytoplasmic domain cysteine. H-2Ld, H-2Db, and H-2Dd class I dimers fail to react with certain alpha 1 and alpha 2 domain-specific antibodies. Furthermore, although beta 2-m-specific antibodies coprecipitate class I MHC heavy chains, they do not coprecipitate class I MHC heavy chain dimers. Pulse-chase studies show that heavy chain dimer formation occurs at different points in the biosynthesis of class I MHC molecules in beta 2-m+ and beta 2-m- cells: in beta 2-m+ cells, heavy chain dimers form after the class I molecules have traversed the medial Golgi cisternae, whereas in beta 2-m- cells they form immediately. Culturing of beta 2-m+ cells with exogenous beta 2-m prevents the formation of H-2Ld/Db heavy chain dimers. We conclude that dimer formation occurs as a consequence of loss or unavailability of beta 2-m. Class I MHC heavy chain dimerization may provide a mechanism for removal of immunologically dysfunctional molecules.
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KATIRCIOĞLU, ŞENAY. "DISSOCIATION OF PH3 AND AsH3 ON Ge(100)(2x1) SURFACE." Surface Review and Letters 14, no. 03 (June 2007): 507–15. http://dx.doi.org/10.1142/s0218625x07009451.
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The most stable structures for the dissociation of phosphine and arsine on Ge (100)(2x1) surface have been investigated by relative total energy calculations based on Density Functional Theory. It has been found that the thermodynamically preferred structures in the dissociation path of phosphine and arsine are the same; PH 2 and AsH 2 products prefer to be on a single Ge dimer bond, but PH and AsH prefer to be between the adjacent Ge dimers. According to the optimization calculations, the dissociation path started with the adsorption of PH 3( AsH 3) on the electron deficient side of the Ge dimer bond is ended with the formation of P – P ( As – As ) dimers parallel to the dimers of Ge .
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Briz, Montserrat, Helen Marr, Kate Talks, John Hanley, and Patrick Kesteven. "Serial D-Dimer Measurements Are Useful in Predicting the Recurrence of Venous Thromboembolism after Discontinuation of Anticoagulation." Blood 112, no. 11 (November 16, 2008): 525. http://dx.doi.org/10.1182/blood.v112.11.525.525.
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Abstract The optimal duration of anticoagulation following a venous thromboembolism (VTE) is influenced by the site of the event and the presence of risk factors. After anticoagulation is discontinued, approximately 10% of patients will have a recurrent event. At present, there is no accurate method of identifying this group of patients, in whom the benefits of reanticoagulation may outweigh the bleeding risks. In 2006, Palaretti et al reported the use of a single qualitative d-dimer measurement, 4 weeks after stopping anticoagulation for a spontaneous VTE, to identify patients at increased risk of a recurrent VTE. Our observational study investigates whether serial quantitative d-dimer measurements, after the discontinuation of anticoagulation for VTE, are of use in identifying patients at higher risk of VTE recurrence. We followed an unselected group of patients attending a hospital based Thrombosis Clinic in whom anticoagulation for VTE was stopped. Over a 2 year period from July 2005 to July 2007, anticoagulation was discontinued in 216 patients (112 females, 104 males) after a median period of 6 months’ treatment (range 2–324 months). The patients ranged in age from 16–88 years, with a mean age of 54 years. Of the group, 146 had been anticoagulated for a deep vein thrombosis (DVT), 59 for pulmonary embolism (PE) +/− DVT, and 11 had been anticoagulated for VTE at other sites. Major risk factors for VTE (recent surgical procedure, malignancy, pregnancy) were present at diagnosis in 80 patients. Minor risk factors (minor trauma, prolonged travel or immobility, hormone therapy) were present in 61 patients, while no risk factors were identified in 69 patients. Presence of risk factors was unknown in the remaining 6 patients. After discontinuation of their anticoagulation, patients were followed up in the Thrombosis Clinic for a median of 14.5 months (range 0–41 months). D-dimer measurements were recorded at the point of stopping anticoagulation, 4 weeks later, and then on subsequent clinic visits. Quantitative d-dimer results were obtained using an automated latex immunoassay (Instrumentation Laboratories, d-dimers HS) on an ACL TOP CTS analyser. Recurrence of VTE occurred in 23 of the 216 (10.7%) patients. D-dimer results off anticoagulation were available in 207 patients. Forty six patients had repeatedly high d-dimer measurements (> 300ng/ml) off anticoagulation. D-dimers remained within the normal range in 112 patients. In 33 patients, d-dimers were initially normal, but subsequently became high, while the opposite was true in 16 patients, where initially high d-dimers later fell into the normal range. Of the recurrences, 8 occurred in the group who had repeatedly high d-dimers after anticoagulation was stopped (17.4%), whilst only 3 recurrences occurred in patients whose d-dimers were consistently normal (2.7%). In the group whose d-dimers were initially normal, but subsequently became high during follow up, there were 6 recurrences (18.2%). There was 1 recurrence in the group whose d-dimers were initially high, but then became normal. In the 9 patients in whom serial d-dimer results were not available, 5 recurrent VTE were observed: 4 of these occurred within 4 weeks of the patient stopping anticoagulation. After statistical analysis of the data, taking into account the nature of the original event, age, gender and d-dimer measurements, a high d-dimer off anticoagulation was the only significant independent variable predicting for recurrence of VTE (Chi-square 13.1 p<0.00001). This data supports a role for monitoring d-dimer measurements in identifying patients at increased risk of VTE recurrence. Further investigation is needed to establish the benefits of reanticoagulation in these patients.
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Blum, Thorsten B., Alexander Hahn, Thomas Meier, Karen M. Davies, and Werner Kühlbrandt. "Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows." Proceedings of the National Academy of Sciences 116, no. 10 (February 13, 2019): 4250–55. http://dx.doi.org/10.1073/pnas.1816556116.
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Mitochondrial ATP synthases form dimers, which assemble into long ribbons at the rims of the inner membrane cristae. We reconstituted detergent-purified mitochondrial ATP synthase dimers from the green algaePolytomellasp. and the yeastYarrowia lipolyticainto liposomes and examined them by electron cryotomography. Tomographic volumes revealed that ATP synthase dimers from both species self-assemble into rows and bend the lipid bilayer locally. The dimer rows and the induced degree of membrane curvature closely resemble those in the inner membrane cristae. Monomers of mitochondrial ATP synthase reconstituted into liposomes do not bend membrane visibly and do not form rows. No specific lipids or proteins other than ATP synthase dimers are required for row formation and membrane remodelling. Long rows of ATP synthase dimers are a conserved feature of mitochondrial inner membranes. They are required for cristae formation and a main factor in mitochondrial morphogenesis.
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Carter-Brzezinski, Luke, Scott Houston, and Jecko Thachil. "D-dimers: a most misunderstood test." British Journal of Hospital Medicine 82, no. 8 (August 2, 2021): 1–5. http://dx.doi.org/10.12968/hmed.2021.0279.
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The role of D-dimers in the management of venous thromboembolism is well established and testing for D-dimers has become common in most acute settings. Although it has been validated for the purpose of excluding venous thromboembolism, the test is increasingly ordered to ‘diagnose’ venous thromboembolism. Furthermore, in the COVID-19 pandemic, heavy reliance has been put on this test with the inclusion of D-dimers to guide treatment pathways. This review summarises the appropriateness of D-dimer tests in these different clinical settings.
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Strzałka, Alicja, Piotr Hogendorf, Aleksander Skulimowski, Michał Spychalski, Janusz Strzelczyk, and Adam Durczynski. "Thyroid hormones concentration in portal and peripheral blood in patients with pancreatic cancer: Preliminary study." Cancer Biomarkers 29, no. 3 (October 28, 2020): 301–6. http://dx.doi.org/10.3233/cbm-201595.
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BACKGROUND: The prognostic value of D-dimers concentration in portal blood in patients with pancreatic cancer has been established in several studies. Thyroid hormones and their receptors, especially T3 also seems to have a specific role in process of neoplasia and metastatic spread. OBJECTIVE: The aim of the study was to look for changes of thyroid hormones concentration between portal and peripheral blood. METHODS: We included prospectively 8 patients with pancreatic cancer, without liver dysfunction, qualified to surgical treatment. D-dimers, THS, fT3, fT4 concentration was determined in blood samples from portal and peripheral vein taken intraoperatively. RESULTS: The difference and quotient of portal and peripheral concentration of D-dimers, THS, fT3 and fT4 was calculated (D-dimer-; THS-; fT3-; fT4-d and -q). The level of D-dimers measured in portal blood was > 2700 ng/mL in 3 patients. The peripheral fT3 level was significantly higher In high portal D-dimers group. FT3 change coefficients showed strong statistically significant negative correlation with portal D-dimer concentration level. CONCLUSIONS: We suggest that fT3 or its receptors can influence progression of pancreatic malignancies. The results of this study are also a new evidence that both fT3 and portal D-dimers are biologically linked to intensity of local neoplastic process. Nevertheless, deeper knowledge about portal circulation probably constitute missing part in understanding nature of pancreatic neoplasia. Investigations both on larger group and in the field of basic sciences are needed.
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Kristensen, K., T. Cui, H. Zhang, A. Gold, M. Glasius, and J. D. Surratt. "Dimers in α-pinene secondary organic aerosol: effect of hydroxyl radical, ozone, relative humidity and aerosol acidity." Atmospheric Chemistry and Physics 14, no. 8 (April 28, 2014): 4201–18. http://dx.doi.org/10.5194/acp-14-4201-2014.
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Abstract. The formation of secondary organic aerosol (SOA) from both ozonolysis and hydroxyl radical (OH)-initiated oxidation of α-pinene under conditions of high nitric oxide (NO) concentrations with varying relative humidity (RH) and aerosol acidity was investigated in the University of North Carolina dual outdoor smog chamber facility. SOA formation from ozonolysis of α-pinene was enhanced relative to that from OH-initiated oxidation in the presence of initially high-NO conditions. However, no effect of RH on SOA mass was evident. Ozone (O3)-initiated oxidation of α-pinene in the presence of ammonium sulfate (AS) seed coated with organic aerosol from OH-initiated oxidation of α-pinene showed reduced nucleation compared to ozonolysis in the presence of pure AS seed aerosol. The chemical composition of α-pinene SOA was investigated by ultra-performance liquid chromatography/electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry (UPLC/ESI-HR-Q-TOFMS), with a focus on the formation of carboxylic acids and high-molecular weight dimers. A total of eight carboxylic acids and four dimers were identified, constituting between 8 and 12% of the total α-pinene SOA mass. OH-initiated oxidation of α-pinene in the presence of nitrogen oxides (NOx) resulted in the formation of highly oxidized carboxylic acids, such as 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA) and diaterpenylic acid acetate (DTAA). The formation of dimers was observed only in SOA produced from the ozonolysis of α-pinene in the absence of NOx, with increased concentrations by a factor of two at higher RH (50–90%) relative to lower RH (30–50%). The increased formation of dimers correlates with an observed increase in new particle formation at higher RH due to nucleation. Increased aerosol acidity was found to have a negligible effect on the formation of the dimers. SOA mass yield did not influence the chemical composition of SOA formed from α-pinene ozonolysis with respect to carboxylic acids and dimers. The results support the formation of the high-molecular weight dimers through gas-phase reactions of the stabilized Criegee Intermediate (sCI) formed from the ozonolysis of α-pinene. The high molecular weight and polar nature of dimers formed in the gas phase may explain increased particle number concentration as a result of homogenous nucleation. Since three of these dimers (i.e. pinyl-diaterpenyl dimer (MW 358), pinyl-diaterebyl dimer (MW 344) and pinonyl-pinyl dimer (MW 368)) have been observed in both laboratory-generated and ambient fine organic aerosol samples, we conclude that the dimers observed in this study can be used as tracers for the O3-initiated oxidation of α-pinene, and are therefore indicative of enhanced anthropogenic activities, and that the high molecular weight and low volatility dimers result in homogenous nucleation under laboratory conditions, increasing the particle number concentration.
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Dyr, Jan E., Jana Stikarova, Jiri Suttnar, Katerina Kuzelova, Pavel Sacha, Ondrej Kucerka, Jan Louzil, et al. "Measurable Amount of Active Thrombin Is Bound to Circulating D-Dimers. Is There Any Impact on Diagnosis and Pathophysiology of Thrombosis?" Blood 128, no. 22 (December 2, 2016): 2570. http://dx.doi.org/10.1182/blood.v128.22.2570.2570.
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Abstract Introduction Thrombosis is a common pathology underlying ischemic heart disease, stroke, and venous thromboembolism. D-dimer is a global indicator of blood coagulation activation and fibrinolysis and, therefore, an indirect marker of thrombotic activity. D-dimers half-life is 48 hours. D-dimer determination is the standard procedure in the treatment of thrombosis. Serine protease thrombin plays pivotal roles in thrombosis and hemostasis, blood coagulation and platelet activation. Thrombin has a short half-life and naturally occurring inhibitors, such as antithrombin, rapidly bind thrombin, which makes the direct measurements of in vivo active thrombin difficult. Thrombin binds to fibrin where it is quite efficiently protected from inhibition by heparin-antithrombin but susceptible to inactivation by different antithrombin-independent inhibitors. There are two low affinity non-substrate thrombin binding sites, one in each half of the dimeric fibrinogen E region, and one high affinity thrombin non-substrate binding site on fibrinogen gamma' chains inside the D region (Meh DA, Siebenlist KR, Mosesson MW, J Biol Chem. 1996, 23121-5). We have shown that thrombin bound to fibrin promotes further fibrin growth in the presence of fibrinogen and absence of free thrombin in solution (Riedel T, Brynda E, Dyr JE, Houska, M, J. Biomed. Mater. Res. Part A 2009, 437-447). The aim of this project was to look for any thrombin activity on isolated D-dimers using several commercial D-dimer kits in groups of patients with elevated D-dimers. Methods Three D-dimers kits were used (ELISA kits CEA506Hu, USCN and D-Dimer (D2D), BioAssay™; and immunoturbidimetric assay D-Dimer KAI-090, K-ASSAY). To detect thrombin activity on captured D-dimers one chromogenic (S-2238, Chromogenix) and two fluorogenic (SN-59, Haematologic Technologies, Inc.; (p-tosyl-Gly-Pro-Arg)2-R110, Thermo Fisher Scientific, Inc.) specific substrates and specific inhibitors (hirudine and PPACK) were used. Independently, bound proteins were removed from immobilized antibodies in 8 M urea and after treatment with trypsin analyzed by mass spectrometry (TripleTOF 5600, Sciex). 34 patients with high, moderate, and low levels of D-dimers and with different diagnosis were analyzed. Results Out of 18 patients with main diagnosis linked with thrombosis 61 % exhibited active thrombin on D-dimers. In these patients we found active thrombin bound to D-dimers captured by antibodies in all applied D-dimer kits. Using mass spectrometry thrombin bound to isolated D-dimers was detected. Specificity of thrombin activity related to D-dimers was determined by combination of several specific thrombin substrates and inhibitors. The activity of bound thrombin was remarkably stable over the period of more than 24 hours. It showed that precise measurement of even very low activity of thrombin was possible. In the group of 16 non-thrombotic patients with elevated D-dimers only 19 % exhibited thrombin activity. Interestingly, differences in values of thrombin activity were up to five orders of magnitude and differences in the activities related to the value of captured D-dimers were even greater. Conclusion This, to our knowledge, is the first report showing the presence of active thrombin bound to circulating D-dimers. Although the group of patients we were so far able to evaluate is too small to being statistically tested, the results are highly encouraging. The amount of bound active thrombin on fibrin degradation products reflects the way of thrombus formation and its degradation (times, durations and rates of relevant reactions and especially the rate of thrombin generation). The thrombin concentration present at the time of fibrin gelation plays an important role in formation of fibrin clot structure, including its mechanical and fibrinolytic stability. It remains to be seen in further studies with much larger cohorts of patients if the presence of active thrombin has any impact on pathophysiology of thrombosis and if its determination may be of importance for the improvement of diagnosis of thrombotic events. Supported by the project of the Ministry of Health of the Czech Republic for conceptual development of the research organization 00023736, by Grant from the Academy of Sciences, Czech Republic (P205/12/G118), and by ERDF OPPK CZ.2.1.16/3.1.00/28007. Disclosures No relevant conflicts of interest to declare.
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Blaby, I. K., and D. K. Summers. "The role of FIS in the Rcd checkpoint and stable maintenance of plasmid ColE1." Microbiology 155, no. 8 (August 1, 2009): 2676–82. http://dx.doi.org/10.1099/mic.0.029777-0.
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Escherichia coli plasmid ColE1 lacks active partitioning, and copies are distributed randomly to daughter cells at division. The plasmid is maintained stably in the bacterial population as long as its copy number remains high. The accumulation of plasmid dimers and higher multimers depresses copy number, and is an important cause of multicopy plasmid instability. ColE1 dimers are restored to the monomeric state by site-specific recombination, which requires the host-encoded proteins XerCD, ArgR and PepA acting at the plasmid cer site. In addition, a 70 nt RNA expressed from the cer site of plasmid dimers delays the division of dimer-containing cells. Here, we report that the global regulator FIS binds to cer in a sequence-specific manner, close to the Rcd promoter (P cer ). FIS is not required for plasmid dimer resolution, but is essential for repression of P cer in plasmid monomers. Repression also requires the XerCD recombinase, but not ArgR or PepA. We propose a model for monomer–dimer control of P cer in which the promoter is repressed in plasmid monomers by the concerted action of FIS and XerCD. Rcd transcription is triggered in plasmid dimers by the lifting of XerCD-mediated repression in the synaptic complex.
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Ren, Shi Wei. "The Spin Transport of the Coblt Dimers with Different Directions." Applied Mechanics and Materials 543-547 (March 2014): 3947–50. http://dx.doi.org/10.4028/www.scientific.net/amm.543-547.3947.
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In this paper, the spin transport properties of the coblt dimers parrallel to the transport direction and perpendicular to ransprot direction are investigated by using the first principle analysis. Calculation shows that both the coblt dimers parrallel to the transport direction and perpendicular to ransprot direction give obvious spin polarized density of states and current. It is found that the dimer parrallel to the transport direction have larger spin polarization current.The spin polarized efficiency for the parrallel dimer increase steadily with the increase of the bias voltage. But the the spin polarization for the transverse dimer changes greatly.
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Liang, Xu, Li Xu, Minzhi Li, John Mack, Justin Stone, Tebello Nyokong, Yu Jiang, Nagao Kobayashi, and Weihua Zhu. "Facile synthesis, spectroscopic and electrochemical properties, and theoretical calculations of porphyrin dimers with a bridging amide-bonded xanthene moiety." Journal of Porphyrins and Phthalocyanines 19, no. 07 (July 2015): 819–29. http://dx.doi.org/10.1142/s1088424615500492.
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A free base porphyrin dimer bridged by a flexible amide-bonded xanthene moiety and its binuclear zinc(II) complex zinc(II) complex were synthesized and characterized. Structural characterization by MS and 1 H NMR spectroscopy confirmed the bridged porphyrin dimer structure. The properties of the dimers were characterized by IR, UV-visible absorption, fluorescence and magnetic circular dichroism (MCD) spectroscopy, and electrochemistry studies. Theoretical calculations were carried out to analyze the electronic structures of porphyrin dimers with a bridging amide-bonded xanthene moiety.
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Mayorquín-Torres, Martha C., Gerardo I. Santiago-Sampedro, Marcos Flores-Álamo, and Martín A. Iglesias-Arteaga. "Synthesis of Symmetrical and Hybrid Dimeric Steroids by Double Suzuki–Miyaura Cross Coupling of 4-Bromo-3-oxo Steroids and Benzene-1,4-diboronic Acid." Synthesis 51, no. 15 (April 10, 2019): 2909–14. http://dx.doi.org/10.1055/s-0037-1611484.
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Two symmetrical dimers and one hybrid dimer in which the steroid cores are connected by a 1,4-phenylene moiety were obtained by double Suzuki–Miyaura cross coupling of benzene-1,4-diboronic acid with 4-bromo-4-en-3-oxosteroids derived from cholesterol and diosgenin. Detailed NMR characterization of the obtained dimers is described.
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Kong, Xianqi, and T. Bruce Grindley. "Control of regioselectivity in reactions of dialkylstannylene acetals. Part II. NMR results and mechanistic analysis." Canadian Journal of Chemistry 72, no. 12 (December 1, 1994): 2405–15. http://dx.doi.org/10.1139/v94-307.
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The 119Sn NMR spectra of dialkylstannylene acetals derived from a number of carbohydrate-based terminal 1,2-diols have been recorded. The spectra of chloroform-d solutions at room temperature of most of these dialkylstannylene acetals were consistent with the presence of single symmetric dimers only although some did contain small proportions of higher oligomers. A general mechanistic scheme is presented that explains the regioselectivity of p-toluenesulfonation reactions of dialkylstannylene acetals presented in the preceding paper. In the scheme, the reaction intermediates are the dialkylstannylene acetal dimers. For p-toluenesulfonation reactions, equilibration between the three possible dimers is faster than reaction with p-toluenesulfonyl chloride. Reaction regioselectivity depends both on the position of the dimer equilibrium and on the rates of reaction of individual dicoordinate oxygen atoms in the dimers. The general scheme was also used to explain the regioselectivity obtained for the very fast oxidation reactions of dialkylstannylene acetals with bromine or N-bromosuccinimide. In these kinetically controlled reactions, regiochemistry is determined by the initial reaction of dicoordinate oxygen atoms in the most populated dimer(s) with the electrophilic oxidizing reagent.
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Tholen, Inger, Christiane Weingart, and Barbara Kohn. "Concentration of D-dimers in healthy cats and sick cats with and without disseminated intravascular coagulation (DIC)." Journal of Feline Medicine and Surgery 11, no. 10 (October 2009): 842–46. http://dx.doi.org/10.1016/j.jfms.2009.04.008.
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The objective of this prospective study was to measure concentrations of D-dimers in 48 cats with various diseases and in 20 healthy cats to evaluate the sensitivity and specificity for D-dimers to diagnose disseminated intravascular coagulation (DIC). The cats were classified as having DIC if an underlying disease and at least three of the following criteria were present: thrombocytopenia, prolonged activated partial thromboplastin time, prothrombin time or thrombin time, schistocytes and/or a reduced antithrombin activity. D-dimer concentrations were measured using a semi-quantitative latex agglutination (LA) test (Accuclot D-Dimer, Sigma Diagnostics). The D-dimer test was positive for 8/12 cats with DIC and for 16/36 sick cats without DIC. D-dimers were negative for all healthy control cats. The comparison of the sick cats with DIC and those without DIC revealed a specificity and sensitivity of the D-dimer test of 56% and 67%; a comparison of the results for healthy cats and cats with DIC revealed a specificity and sensitivity of 100% and 67%, respectively. The D-dimer LA test is only of limited value for the diagnosis of DIC in cats.
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Huang, Dengchao, Shilin Liu, and Kang Yang. "Highly Unidirectional Radiation Enhancement Based on a Hybrid Multilayer Dimer." Nanomaterials 12, no. 4 (February 21, 2022): 710. http://dx.doi.org/10.3390/nano12040710.
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Dimers made of plasmonic particles support strong field enhancements but suffer from large absorption losses, while low-loss dielectric dimers are limited by relatively weak optical confinement. Hybrid dimers could utilize the advantages of both worlds. Here, we propose a hybrid nanoantenna that contains a dimer of core-dual shell nanoparticles known as the metal–dielectric–metal (MDM) structure. We discovered that the hybrid dimer sustained unidirectional forward scattering, which resulted in a nearly ideal Kerker condition in the frequency close to the resonance peak of the dimer due to enhancing the amplitude of the induced high-order electric multiples in the gap and effectively superimposing them with magnetic ones, which respond to the excitation of the plane wave in the dielectric layer of the dimer. Furthermore, when an electric quantum emitter is coupled to the dimer, our study shows that the optimal hybrid dimer simultaneously possesses high radiation directivity and low-loss features, which illustrates a back-to-front ratio of radiation 53 times higher than that of the pure dielectric dimer and an average radiation efficiency 80% higher than that of the pure metallic dimer. In addition, the unique structures of the hybrid hexamer direct almost decrease 75% of the radiation beamwidth, hence heightening the directivity of the nanoantenna based on a hybrid dimer.
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Troyanovsky, Regina B., Eugene Sokolov, and Sergey M. Troyanovsky. "Adhesive and Lateral E-Cadherin Dimers Are Mediated by the Same Interface." Molecular and Cellular Biology 23, no. 22 (November 15, 2003): 7965–72. http://dx.doi.org/10.1128/mcb.23.22.7965-7972.2003.
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ABSTRACT E-cadherin is a transmembrane protein that mediates Ca2+-dependent cell-cell adhesion. To study cadherin-cadherin interactions that may underlie the adhesive process, a recombinant E-cadherin lacking free sulfhydryl groups and its mutants with novel cysteines were expressed in epithelial A-431 cells. These cysteine mutants, designed according to various structural models of cadherin dimers, were constructed to reveal cadherin dimerization by the bifunctional sulfhydryl-specific cross-linker BM[PE0]3. Cross-linking experiments with the mutants containing a cysteine at strand B of their EC1 domains did show cadherin dimerization. By their properties these dimers correspond to those which have been characterized by coimmunoprecipitation assay. Under standard culture conditions the adhesive dimer is a dominant form. Calcium depletion dissociates adhesive dimers and promotes the formation of lateral dimers. Our data show that both dimers are mediated by the amino-terminal cadherin domain. Furthermore, the interfaces involved in both adhesive and lateral dimerization appear to be the same. The coexistence of the structurally identical adhesive and lateral dimers suggests some flexibility of the extracellular cadherin region.
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Syahrul, Maya Sari, Iswan Rina, and Nurweni Putri. "KONTRUKSI PT-Symmetry MULTI DIMER PADA DOMAIN TAK HINGGA." Jurnal Lebesgue : Jurnal Ilmiah Pendidikan Matematika, Matematika dan Statistika 4, no. 3 (December 30, 2023): 1988–94. http://dx.doi.org/10.46306/lb.v4i3.528.
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Parity-Time Symmetry, or abbreviated as -Symmetry, can be explained as the propagation of an optical beam in two bound waveguides, where one waveguide experiences strengthening and the other waveguide experiences weakening, with each intensity having the same value. Then, the two waveguides are known as dimers, so the phenomenon is called dimer -Symmetry. Furthermore, the -Symmetry dimer is expanded into a system consisting of a collection of -Symmetry Dimers, where each dimer is bound by a binding constant. The result of this expansion is called the multi dimer -Symmetry system. Research on the propagation of optical rays in waveguides plays an important role in the development of optical-based communication technology in the future
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Dong, Jinyi, Yihao Zhou, Jiahao Pan, Chao Zhou, and Qiangbin Wang. "Assembling gold nanobipyramids into chiral plasmonic nanostructures with DNA origami." Chemical Communications 57, no. 50 (2021): 6201–4. http://dx.doi.org/10.1039/d1cc01925b.
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