Pattern-Based Sensing of Nucleotides in Aqueous Solution with a Multicomponent Indicator Displacement Assay

A multicomponent indicator displacement assay ( MIDA) based on an organometallic receptor and three dyes can be used for the identification and quantification of nucleotides in aqueous solution at neutral pH

Spatial optical solitons supported by mutual focusing

We study composite spatial optical solitons supported by two-wave mutual focusing induced by cross-phase modulation in Kerr-like nonlinear media. We find the families of both single- and two-hump solitons and discuss their properties and stability. We also reveal remarkable similarities between recently predicted holographic solitons in photorefractive media and parametric solitons in quadratic nonlinear crystals.Comment: 3 pages, 3 figure

Multi-component optical solitary waves

We discuss several novel types of multi-component (temporal and spatial) envelope solitary waves that appear in fiber and waveguide nonlinear optics. In particular, we describe multi-channel solitary waves in bit-parallel-wavelength fiber transmission systems for high performance computer networks, multi-colour parametric spatial solitary waves due to cascaded nonlinearities of quadratic materials, and quasiperiodic envelope solitons due to quasi-phase-matching in Fibonacci optical superlattices.Comment: 12 pages, 11 figures; To be published in: Proceedings of the Dynamics Days Asia-Pacific: First International Conference on Nonlinear Science (Hong-Kong, 13-16 July, 1999), Editor: Bambi Hu (Elsevier Publishers, 2000

Approximate solutions and scaling transformations for quadratic solitons

We study quadratic solitons supported by two- and three-wave parametric interactions in chi-2 nonlinear media. Both planar and two-dimensional cases are considered. We obtain very accurate, 'almost exact', explicit analytical solutions, matching the actual bright soliton profiles, with the help of a specially-developed approach, based on analysis of the scaling properties. Additionally, we use these approximations to describe the linear tails of solitary waves which are related to the properties of the soliton bound states.Comment: 11 pages, 9 figures; submitted for publicatio

Two-color nonlinear localized photonic modes

We analyze second-harmonic generation (SHG) at a thin effectively quadratic nonlinear interface between two linear optical media. We predict multistability of SHG for both plane and localized waves, and also describe two-color localized photonic modes composed of a fundamental wave and its second harmonic coupled together by parametric interaction at the interface.Comment: 4 pages, 5 figures (updated references

Metal-based chemosensors for amino acids, peptides, and nucleotides

An organometallic 4d transition metal complex [Cp*RhCl2]2, together with commercially available dyes, was used to construct indicator displacement assays (IDAs) for the detection of peptides, amino acids, and nucleotides. The combination of the Cp*Rh complex with the dye azophloxine was found to form a chemosensing ensemble for the sequence-selective detection of histidine- and methionine-containing peptides in water at neutral pH. A strong interaction of the rhodium complex with peptides bearing histidine or methionine residue in the position 1 or 2 allowed to detect these peptides down to a concentration of 0.3 µM. The same organometallic complex and three commercially available dyes were employed to compose an array of IDA chemosensors for the detection of natural amino acids. We found that the variation of the pH can effectively be used to modulate the selectivity of an IDA sensor. An excellent discrimination of 20 amino acids was achieved. The combination of [Cp*RhCl2]2 with the dyes gallocyanine, evans blue, and mordant yellow 10 forms a multicomponent indicator displacement assay (MIDA), which can be used to sense low millimolar concentrations of nucleotides and the pyrophosphate anion in buffered aqueous solution. Moreover, the MIDA allows to simultaneously determine the concentrations of adenosine triphosphate and pyrophosphate/cyclic adenosine monophosphate with a single UV-Vis measurement. In the second part of our work we investigated whether dynamic combinatorial libraries (DCLs) can be used for sensing purposes. We found that the dyes arsenazo I, methylcalcein blue, and glycine cresol red, in combination with the metal salts CuCl2 and NiCl2, form a DCL of differently colored metal-dye complexes. The addition of an analyte able to interact with a member(s) of such a library, results in a re-equilibraion easily detectable by UV-Vis spectroscopy. Using dipeptides as analytes we demonstrated that this way of sensing is very effective – even closely related peptides such as regio- (Ala-Phe vs. Phe-Ala) and stereo- (Phe-Ala vs. D-Phe-Ala) isomers can easily be discriminated. Additionally, we found that the identity of the best sensor depends on the problem to be addressed

Analysis of Primary Liquid Chromatography Mass Spectrometry Data by Neural Networks for Plant Samples Classification

Plant samples are potential sources of physiologically active secondary metabolites and their classification is an extremely important task in traditional medicine and other fields of research. In the production of herbal drugs, different plant parts of the same or related species can serve as adulterants for primary plant material. The use of highly informative and relatively easily accessible tools, such as liquid chromatography and low-resolution mass spectrometry, helps to solve these tasks by means of fingerprint analysis. In this study, to reveal specific plant part features for 20 species from one family (Apiaceae), and to preserve the maximum information content, two approaches are suggested. In both cases, minimal raw data pretreatment, including rescaling of time and m/z axes and cutting off some uninformative regions, was applied. For the support vector machine (SVM) method, tensor unfolding was required, while neural networks (NNs) were able to work directly with squared heatmaps as input data. Moreover, five data augmentation variants are proposed, to overcome the typical problem of a lack of data. As a result, a comparable F1-score close to 0.75 was achieved by SVM and two employed NN architectures. Eight marker compounds belonging to chlorophylls, lipids, and coumarin apio-glucosides were tentatively identified as characteristic of their corresponding sample groups: roots, stems, leaves, and fruits. The proposed approaches are simple, information-saving and can be applied to a broad type of tasks in metabolomics