Methods and Applications of In Silico Aptamer Design and Modeling

Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.     

Macroscopic model for multispecies ion-exchange kinetics

A model for multispecies ion-exchange kinetics based on the Nernst-Planck equation is suggested. It is analyzed in comparison with the “locally-determinate” model described by Hwang and Helfferich [1]. The model makes possible simple computation. The conditions for the occurrence of unusual kinetic curves with a maximum are clarified. The proposed model is developed for different types of kinetic problems and verified by the experimental investigation of a kinetics in ternary systems.     

Pressureless Sintering of Si3N4 Ceramic Using AlN and Rare-Earth Oxides

Using intermediate, liquid-forming compositions in the (Y,La)₂O₃-AlN system as additives, fully dense Si₃N₄ ceramics with high strength at high temperature have been obtained by pressureless sintering. The ceramics contain rod-shaped β-Si₃N₄ with M' or K' solid solutions as grain-boundary phases. The strength of these ceramics is 1150 MPa at 1200°C, and the room-temperature toughness is maintained at }7 MPa·m^1/2. Phase relations that are pertinent to the new additive compositions are delineated to rationalize their beneficial effects on sinterability and mechanical properties.     

SOM‐based projection module for mobile displays

Abstract— The development of a compact, efficient VGA projection module to be embedded in mobile devices is reported. The design incorporates laser/laser diode (LD) light sources, Schlieren optics, and a one‐dimensional diffractive spatial optical modulator (SOM). During development, the optical parameters were determined and the relationships between the parameters to optimize the optical specifications were derived. The resulting optimized specifications enable us to manufacture two types of optical modu les as compact as 13 cc and with as little as 10% speckle contrast ratio.     

SearchFill: A stochastic optimization code for detecting atomic vacancies in crystalline and non-crystalline systems

We present an implementation of a stochastic optimization algorithm applied to location of atomic vacancies. Our method labels an empty point in space as a vacancy site, if the total spatial overlap of a “virtual sphere”, centered around the point, with the surrounding atoms (and other vacancies) falls below a tolerance parameter. A Metropolis-like algorithm displaces the vacancies randomly, using an “overlap temperature” parameter to allow for acceptance of moves into regions with higher overlap, thus avoiding local minima. Once the algorithm has targeted a point with low overlap, the overlap temperature is decreased, and the method works as a steepest descent optimization.Our method, with only two free parameters, is able to detect the correct number and coordinates of vacancies in a wide spectrum of condensed-matter systems, from crystals to amorphous solids, in fact in any given set of atomic coordinates, without any need of comparison with a reference initial structure.     

Large-scale mapping of boreal forest in SIBERIA using ERS tandem coherence and JERS backscatter data

Siberia's boreal forests represent an economically and ecologically precious resource, a significant part of which is not monitored on a regular basis. Synthetic aperture radars (SARs), with their sensitivity to forest biomass, offer mapping capabilities that could provide valuable up-to-date information, for example about fire damage or logging activity. The European Commission SIBERIA project had the aim of mapping an area of approximately 1 million km² in Siberia using SAR data from two satellite sources: the tandem mission of the European Remote Sensing Satellites ERS-1/2 and the Japanese Earth Resource Satellite JERS-1. Mosaics of ERS tandem interferometric coherence and JERS backscattering coefficient show the wealth of information contained in these data but they also show large differences in radar response between neighbouring images. To create one homogeneous forest map, adaptive methods which are able to account for brightness changes due to environmental effects were required. In this paper an adaptive empirical model to determine growing stock volume classes using the ERS tandem coherence and the JERS backscatter data is described. For growing stock volume classes up to 80 m³/ha, accuracies of over 80% are achieved for over a hundred ERS frames at a spatial resolution of 50 m.     

Positional‐Species Composition of Triacylglycerols from the Arils of Mature Euonymus Fruits

Positional‐species composition (PSC) of 1,2,3‐triacyl‐sn‐glycerols (TAG) from the arils of mature fruits of 13 species of Euonymus L. genus was established. The residues of six major fatty acids (FA), palmitic, stearic, hexadecenoic (H), octadecenoic (O), linoleic (L), and linolenic, were present in the TAG. PSC of TAG was determined by their partial lipase hydrolysis. By using hierarchical cluster and principal component analyses, it was definitely demonstrated that separate taxonomic units forming this genus were significantly distinguished as regards PSC of TAG. In particular, the Euonymus subgenus greatly exceeded the Kalonymus subgenus in both total content of L in TAG and in the rate of its incorporation into their mid‐position, while TAG of Kalonymus were marked by a prevalence of O‐TAG and sn‐2‐O isomers. Thus, these subgenera were significantly distinct in the rate of incorporation of O and L residues in the sn‐2 position of TAG molecules. Meanwhile, the TAG from the Euonymus section species were marked by an enhanced concentration of H and the incorporation of H in UUU TAG was much more active than in other TAG types. As for positional‐type composition of TAG, saturated FA were always virtually absent in the sn‐2 position of Euonymus aril TAG.     

Gd-Bi-M-Ce-O (M = Cu,Zr, Ni,Co, Mn) ceria-based solid solutions for low temperature CO oxidation

Ceria based solid solutions doped by Gd, Bi, and the third dopant were synthesized by the co-precipitation method with ultrasonic treatment, followed by calcination at the temperature of 500°С. Characterization of the synthesized nanosystems by XRD, TEM, TG, Raman spectroscopy, FTIR, XPS was carried out. It is shown that all obtained powders of solid solutions crystallized into a cubic structure of the fluorite type, with an average particle size of 5–15 nm. The samples had a mesoporous structure of the pore diameter of 2–5 nm. The catalytic activity of Gd-Bi-M-Ce-O (M = Cu, Zr, Ni, Co, Mn) solid solutions was carried out. The catalyst Gd_0.05Bi_0.15Mn_0.20Ce_0.60O₂ has the lowest oxidation temperature.