Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins

Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.

Average minimum distances of periodic point sets – foundational invariants for mapping periodic crystals

The fundamental model of any solid crystalline material (crystal) at the atomic scale is a periodic point set. The strongest natural equivalence of crystals is rigid motion or isometry that preserves all inter-atomic distances. Past comparisons of periodic structures often used manual thresholds, symmetry groups and reduced cells, which are discontinuous under perturbations or thermal vibrations of atoms. This work defines the infinite sequence of continuous isometry invariants (Average Minimum Distances) to progressively capture distances between neighbors. The asymptotic behaviour of the new invariants is theoretically proved in all dimensions for a wide class of sets including non-periodic. The proposed near linear time algorithm identified all different crystals in the world's largest Cambridge Structural Database within a few hours on a modest desktop. The ultra fast speed and proved continuity provide rigorous foundations to continuously parameterise the space of all periodic crystals as a high-dimensional extension of Mendeleev's table of elements.

Use of a 4-circle goniometer for neutron and X-ray diffractometer in the study of single crystals

Objectives. This study described the 4-circle goniometer Syntex P1N and its possible applications in X-ray and neutron structure analysis of single crystals.Methods. The 4-circle goniometer Syntex P1N, due to its high-precision mechanical characteristics and individual components from domestic equipment (sets of DRON type X-ray diffractometers), formed the basis for developing an instrument complex for X-ray and neutron-structure studies.Results. The neutron diffractometer was upgraded based on the Syntex P1N goniometer. Therefore, the 10BF3-based end neutron counter, included in the diffractometer kit, was replaced by the 3He-based domestic side counter, SNM-16. Such a significant reduction in the linear dimensions of the detector allowed us to expand the range of measured angles of 2θ from 90° to 140° and increase the accuracy of the measured interplanar distances accordingly. The goniometer was adjusted relative to the primary neutron beam by placing it on a specially designed plate. Highly accurate measured parameters of the unit cell and the intensity of the reflexes were achieved by optimizing the installation geometry and the protection of the goniometer and detector. Based on the Syntex P1N goniometer, an instrument complex for X-ray diffraction studies has also been developed. Both the developed X-ray and the upgraded neutronography facilities were used to perform experiments to measure the unit cell parameters, the coordinates of atoms, and the parameters of their thermal vibrations on several crystals of domestic synthetic samples: diamond C, silicon Si, halite, or rock salt NaCl, and corundum α-Al2O3. An excellent correlation was achieved by comparing the data obtained with the corresponding chemical crystals’ parameters and reference samples recommended by the International Union of Crystallographers.Conclusions. This paper described a neutron installation and a Syntex P1N neutron diffractometer for the study of single crystals. Based on the latter, an instrument complex for X-ray diffraction studies has also been developed. Experiments on standard samples have shown a high level of accuracy in measuring the lattice parameters, the coordinates of atoms, and the parameters of their thermal vibrations on both the X-ray and neutron diffractometers.

Some electrophysical properties of polycrystalline silicon obtained in a solar oven

The article describes the results of the study of the microstructure and some electrophysical properties of silicon obtained by re-melting in a solar oven. It was found that the granularity of polycrystalline silicon consists of Si atoms with a size of 10–15 µm, the roughness of its surface. Decrease in specific resistance at T≤600 K, increase in concentration of ionized input atoms and concentration of charge carriers, the position at Т∼600 ÷ 700 K is based on the decrease in the free path of the charge carriers as a result of thermal vibrations of the crystal lattice, the situation at T ≥ 700 K K was explained by the emergence of new recombination centers specific to localized traps. Polycrystalline silicon heated by sunlight does not create a barrier effect of traps localized in the grain boundary regions from polycrystalline silicon obtained by other methods. This can expand the possibilities of creating highly efficient semiconductor devices, solar cells, thermoelectric materials for micro- and nanoelectronics, photovoltaics.

Intelligent Life Prediction of Thermal Barrier Coating for Aero Engine Blades

The existing methods for thermal barrier coating (TBC) life prediction rely mainly on experience and formula derivation and are inefficient and inaccurate. By introducing deep learning into TBC life analyses, a convolutional neural network (CNN) is used to extract the TBC interface morphology and analyze its life information, which can achieve a high-efficiency accurate judgment of the TBC life. In this thesis, an Adap–Alex algorithm is proposed to overcome the problems related to the large training time, over-fitting, and low accuracy in the existing CNN training of TBC images with complex tissue morphologies. The method adjusts the receptive field size, stride length, and other parameter settings and combines training epochs with a sigmoid function to realize adaptive pooling. TBC data are obtained by thermal vibration experiments, a TBC dataset is constructed, and then the Adap–Alex algorithm is used to analyze the generated TBC dataset. The average training time of the Adap–Alex method is significantly smaller than those of VGG-Net and Alex-Net by 125 and 685 s, respectively. For a fixed number of thermal vibrations, the test accuracy of the Adap–Alex algorithm is higher than those of Alex-Net and VGG-Net, which facilitates the TBC identification. When the number of thermal vibrations is 300, the accuracy reaches 93%, and the performance is highest.

Термофорез углеродных наночастиц (нанолент и нанотрубок) на плоской многослойной подложке гексагонального нитрида бора (h-BN)

Using the method of molecular dynamics and a 2D chain model, it is shown that thermophoresis of carbon nanoparticles (nanoribbons and nanotubes) on a flat multilayer substrate (on a flat surface of a hexagonal boron nitride crystal) has high efficiency. Placing a nanoparticle on a flat surface of a substrate involved in heat transfer leads to its movement in the direction of the heat flow. The heat flow along the substrate leads to the formation of constant forces acting on the nanoparticle nodes (thermophoresis forces). The main effect of the force is exerted on the edges of graphene nanoribbons, exactly where the main interaction of the nanoribbon with the bending phonons of the substrate occurs. These phonons have a long free path, so the effective transfer of nanoparticles using thermophoresis can occur at sufficiently large distances. The motion of carbon nanoparticles under the action of a heat flow has the form of particle motion in a viscous medium under the action of a constant force. Over time, the nanoparticles always enter the mode of movement at a constant speed. The velocity of the stationary motion is almost the same for all sizes and types of carbon nanoparticles, which is explained by the fact that the thermophoresis force and effective friction have the same source – the interaction of the nanoparticle with the bending thermal vibrations of the substrate layers.

About rms amplitude of zero oscillations of atoms in crystal

It is shown that the values of the energy and amplitude of zero-point vibrations of atoms in a crystal, due to the uncertainty principle, depend on the dynamic characteristics of atoms in the crystal. It was found that the root-mean-square amplitude of thermal and zero-point vibrations of atoms, like other properties, has a periodic dependence on the ordinal number of elements in the Mendeleev's Periodic Table. It is shown that the value of the root-mean-square amplitude of thermal vibrations of atoms in a lattice of elements with a high value of the Debye temperature at room temperature does not differ much from the value of the amplitude of zero-point vibrations of atoms (at T = 0 K). This is explained by the small number of excited vibrations with the maximum frequency in these crystals at room temperature, since the room temperature is much lower than their Debye temperature, at which the entire spectrum of thermal vibrations of atoms in the crystal is excited. The results can be used in materials science and technology to assess the strength and thermo physical characteristics of materials at cryogenic temperatures, without resorting to measuring them directly at absolute zero.