Prediction of hot spots in protein interfaces using extreme learning machines with the information of spatial neighbour residues

The identification of hot spots, a small subset of protein interfaces that accounts for the majority of binding free energy, is becoming increasingly important for the research on protein–protein interaction and drug design. For each interface residue or target residue to be predicted, the authors extract hybrid features which incorporate a wide range of information of the target residue and its spatial neighbor residues, that is, the nearest contact residue in the other face (mirror‐contact residue) and the nearest contact residue in the same face (intra‐contact residue). Here, feature selection is performed using random forests to avoid over‐fitting. Thereafter, the extreme learning machine is employed to effectively integrate these hybrid features for predicting hot spots in protein interfaces. By the 5‐fold cross validation in the training set, their method can achieve accuracy (ACC) of 82.1% and Matthew''s correlation coefficient (MCC) of 0.459, and outperforms some alternative machine learning methods in the comparison study. Furthermore, their method achieves ACC of 76.8% and MCC of 0.401 in the independent test set, and is more effective than the major existing hot spot predictors. Their prediction method offers a powerful tool for uncovering candidate residues in the studies of alanine scanning mutagenesis for functional protein interaction sites.Inspec keywords: biochemistry, bioinformatics, correlation methods, drugs, free energy, learning (artificial intelligence), molecular biophysics, proteins, feature selectionOther keywords: hot spot prediction, protein interfaces, extreme learning machines, spatial neighbour residue information, binding free energy, protein‐protein interaction, drug design, interface residue, spatial neighbor residues, nearest contact residue, random forests, alanine scanning energetics database, independent test set, binding interface database, 5‐fold cross validation, correlation coefflcient, alternative machine learning methods, alanine scanning mutagenesis, functional protein interaction sites, feature selection     

Quantitative thermometry of nanoscale hot spots

A method is described to quantify thermal conductance and temperature distributions with nanoscale resolution using scanning thermal microscopy. In the first step, the thermal resistance of the tip-surface contact is measured for each point of a surface. In the second step, the local temperature is determined from the difference between the measured heat flux for heat sources switched on and off. The method is demonstrated using self-heating of silicon nanowires. While a homogeneous nanowire shows a bell-shaped temperature profile, a nanowire diode exhibits a hot spot centered near the junction between two doped segments.     

Geostatistical risk estimation at waste disposal sites in the presence of hot spots

The present paper aims to estimate risk by using geostatistics at the wider coal mining/waste disposal site of Belkovskaya, Tula region, in Russia. In this area the presence of hot spots causes a spatial trend in the mean value of the random field and a non-Gaussian data distribution. Prior to application of geostatistics, subtraction of trend and appropriate smoothing and transformation of the data into a Gaussian form were carried out; risk maps were then generated for the wider study area in order to assess the probability of exceeding risk thresholds. Finally, the present paper discusses the need for homogenization of soil risk thresholds regarding hazardous elements that will enhance reliability of risk estimation and enable application of appropriate rehabilitation actions in contaminated areas.     

工程计算可视化的几个热点问题

随着工程数值模拟的规模和复杂度的提高,可视化研究面临着发展机遇和挑战,结合国内外的技术发展情况,对于工程计算应用中的表达方式、算法优化、集成解决框架等几个热点问题展开讨论,指出可视化技术发展与应用学科结合的重要性.     

Spectral pyrometry of the objects with hot spots

Optical emission spectra of microwave discharges at the powder mixture surface are experimentally recorded, indicating spatial temperature nonuniformity the within the field of vision. Within the field of vision, the maximal and minimal temperature values calculated from the continuous spectrum (wavelength range 380–620 nm) differ by 20–25%. Modeling of the integral emission spectra of a heated surface with hot spots is performed. Spectral pyrometry of the objects with nonuniform temperature, when used within a narrow spectral interval, gives no possbility of determining the exact nature of the measured temperature because the temperature calculated from this spectrum may differ substantially from both averaged and maximal values. To determine the averaged and maximal temperature, it is necessary to significantly widen the recorded spectral interval.     

Fluorescence enhancement in hot spots of AFM-designed gold nanoparticle sandwiches

We observe an enhancement of fluorescence from a single fluorescent sphere, which is sandwiched between two individual gold nanoparticles, forming a hot spot of strong field enhancement. The fluorescence enhancing hot spot is custom-designed by the deliberate assembly of gold nanoparticles with an atomic force microscope cantilever. The fluorescence intensity is monitored while the separation between the two gold nanoparticles is reduced by gradually pushing the gold nanoparticles closer to the fluorescent sphere. The fluorescence enhancement is maximal when the distance between the two gold nanoparticles is smallest, when the excitation polarization is parallel to the axis of the sandwich, and when the fluorescent sphere is positioned exactly on the axis connecting the two gold nanoparticles.     

Tuning temperature and size of hot spots and hot-spot arrays

By using scanning thermal microscopy, it is shown that nanoscale constrictions in metallic microwires deposited on an oxidized silicon substrate can be tuned in terms of temperature and confinement size. High-resolution temperature maps indeed show that submicrometer hot spots and hot-spot arrays are obtained when the SiO(2) layer thickness decreases below 100 nm. When the SiO(2) thickness becomes larger, heat is less confined in the vicinity of the constrictions and laterally spreads all along the microwire. These results are in good agreement with numerical simulations, which provide dependences between silica-layer thickness and nanodot shape and temperature.     

Cell biology at interfaces

A brief review is presented of the significant developments in the understanding of the processes involved in cell adhesion both to other cells and to substrates. The relationship between general cellular behaviour and cell adhesion is a result of the importance of the cytoplasmic cytoskeleton to most cellular processes. Interaction between a substrate and the cell is mediated through intramembranous proteins, such as the integrins. The intramembranous proteins, in turn, influence the assembly of the microfilamentous structures in the cytoplasm. Changes in the state of the microfilaments are accompanied by modifications in the behaviour of both microtubules and intermediate filaments. The expression of different types of cytoskeletal configuration result from differing types of cell-cell or cell-substratum encounters. This leads to significant changes in resultant cellular behaviour. It is argued that an understanding of changes that result from cell-biomaterial interactions, at the ultrastructural level, is necessary in order to assess the biocompatability of implant materials.     

A note on caustics and two-dimensional hot spots in microwave heating

Very recently the problem of microwave heating by millimetric waves has been considered numerically and experimentally. It was found that hot spots are produced around the caustic regions of the wave field. In this note two-dimensional hot-spot solutions to the microwave heating problem are constructed in this range of scales by a combination of geometric optics and layer solutions to nonlinear heat equations. It is shown that hot spots are localized along caustics and simple analytic expressions for their shape are derived. Since the problem solved is local, the scalings obtained apply to general situations that involve caustics and heat layers. This simple analysis explains the shape and positions of high-temperature regions observed in experiments and full numerical calculations.     

Erratum to: Enzyme-amplified SERS immunoassay with Ag-Au bimetallic SERS hot spots

Erratum to Nano Research 2020,13(12):3338-3346 htts://doi.org/00.1007/s12274-020-3014-3 One author name and corresponding affiliation of the original version of this article were unfortunately mislabeled.     

Emergent phenomena at oxide interfaces

Recent technical advances in the atomic-scale synthesis of oxide heterostructures have provided a fertile new ground for creating novel states at their interfaces. Different symmetry constraints can be used to design structures exhibiting phenomena not found in the bulk constituents. A characteristic feature is the reconstruction of the charge, spin and orbital states at interfaces on the nanometre scale. Examples such as interface superconductivity, magneto-electric coupling, and the quantum Hall effect in oxide heterostructures are representative of the scientific and technological opportunities in this rapidly emerging field.     

Intergranular films at Au-sapphire interfaces

The existence of nanometer-thick amorphous equilibrium films at metal-ceramic interfaces has been experimentally verified for the Au–Al₂O₃ system. The films were formed using a novel experimental approach, in which thin sputtered films of Au were dewetted on a sapphire substrate which was previously partially wetted with drops of anorthite glass (CaO–2SiO₂–Al₂O₃). High-resolution transmission electron microscopy and qualitative analytical transmission electron microscopy were used to confirm the existence of the amorphous films. In addition, positive and relatively large Hamaker constants were calculated for the Au-film-Al₂O₃ interface, which indicates the existence of an attractive van der Waals force which stabilizes the film, similar to equilibrium films at grain boundaries in ceramics. A ∼ 1 nm thick surface film was also detected on the (0001) surface of sapphire substrates partially wetted by anorthite glass. The refractive index required to stabilize the surface films, via a positive Hamaker constant, is explored.     

Lattice compatibility at interfaces after recrystallisation

Abstract

The nature, distribution, and implications of local, i.e. intragrain, lattice rotations have been explored in recrystallised nickel using electron backscattered diffraction. The data processing methodology for such methods is discussed in some detail. The results reveal that orientation perturbations with a periodicity of ～1 μm occur frequently within grains, and that there is a strong tendency for two grains which feature either both large perturbations or both small perturbations to be neighbours. The results are interpreted in terms of lattice compatibility, potential sites for instigation of secondary recrystallisation, and the meaningful specification of grain boundary misorientation.     

Supramolecular hydrophobic-hydrophilic nanopatterns at electrified interfaces

We have developed hydrophobic-hydrophilic nanopatterns at electrified surfaces via the self-assembly of amphiphilic molecules. For this purpose, we selected 5-hexadecyloxy isophthalic acid: this neutral amphiphile forms hydrogen-bonded rows that are commensurate with the Au(111) surface. The alkyl chains are interdigitated. The molecular organization of these nanopatterns depends strongly on the substrate potential, which reveals the hierarchical nature of the assembly. The new hydrophobic-hydrophilic nanopatterns are of special interest as templates for the formation of nanostructures of higher complexity.     

Metallic conduction at organic charge-transfer interfaces

The electronic properties of interfaces between two different solids can differ strikingly from those of the constituent materials. For instance, metallic conductivity-and even superconductivity-have recently been discovered at interfaces formed by insulating transition-metal oxides. Here, we investigate interfaces between crystals of conjugated organic molecules, which are large-gap undoped semiconductors, that is, essentially insulators. We find that highly conducting interfaces can be realized with resistivity ranging from 1 to 30 kohms per square, and that, for the best samples, the temperature dependence of the conductivity is metallic. The observed electrical conduction originates from a large transfer of charge between the two crystals that takes place at the interface, on a molecular scale. As the interface assembly process is simple and can be applied to crystals of virtually any conjugated molecule, the conducting interfaces described here represent the first examples of a new class of electronic systems.