SCREENING OF POTENTIAL LIGANDS FOR THE MAIN PROTEASE OF THE SARS-COV-2 CORONAVIRUS BY USING MOLECULAR DOCKING

An RNA virus from the Coronaviridae family, a subgroup of Coronavirinae, was first identified in late 2019 as the cause of severe acute respiratory infection in China.1 Despite the fact that clinical guidelines have been developed for the treatment of a new coronavirus infection, there are currently no specific medicine of preventing and treating a new coronavirus infection

Single and molecular ion irradiation-induced effects in GaN : experiment and cumulative MD simulations

An investigation of mechanisms of enhancement of irradiation-induced damage formation in GaN under molecular in comparison to monatomic ion bombardment is presented. Ion-implantation-induced effects in wurtzite GaN bombarded with 0.6 keV amu(-1) F, P, PF2, PF4, and Ag ions at room temperature are studied experimentally and by cumulative MD simulation in the correct irradiation conditions. In the low dose regime, damage formation is correlated with a reduction in photoluminescence decay time, whereas in the high dose regime, it is associated with the thickness of the amorphous/disordered layer formed at the sample surface. In all the cases studied, a shift to molecular ion irradiation from bombardment by its monatomic constituents enhances the damage accumulation rate. Implantation of a heavy Ag ion, having approximately the same mass as the PF4 molecule, is less effective in surface damage formation, but leads to noticeably higher damage accumulation in the bulk. The cumulative MD simulations do not reveal any significant difference in the total amount of both point defects and small defect clusters produced by light monatomic and molecular ions. On the other hand, increased production of large defect clusters by molecular PF4 ions is clearly seen in the vicinity of the surface. Ag ions produce almost the same number of small, but more large defect clusters compared to the others. These findings show that the higher probability of formation of large defect clusters is important mechanism of the enhancement of stable damage formation in GaN under molecular, as well as under heavy monatomic ion irradiation.Peer reviewe

Nonlinear electrochemical relaxation around conductors

We analyze the simplest problem of electrochemical relaxation in more than one dimension - the response of an uncharged, ideally polarizable metallic sphere (or cylinder) in a symmetric, binary electrolyte to a uniform electric field. In order to go beyond the circuit approximation for thin double layers, our analysis is based on the Poisson-Nernst-Planck (PNP) equations of dilute solution theory. Unlike most previous studies, however, we focus on the nonlinear regime, where the applied voltage across the conductor is larger than the thermal voltage. In such strong electric fields, the classical model predicts that the double layer adsorbs enough ions to produce bulk concentration gradients and surface conduction. Our analysis begins with a general derivation of surface conservation laws in the thin double-layer limit, which provide effective boundary conditions on the quasi-neutral bulk. We solve the resulting nonlinear partial differential equations numerically for strong fields and also perform a time-dependent asymptotic analysis for weaker fields, where bulk diffusion and surface conduction arise as first-order corrections. We also derive various dimensionless parameters comparing surface to bulk transport processes, which generalize the Bikerman-Dukhin number. Our results have basic relevance for double-layer charging dynamics and nonlinear electrokinetics in the ubiquitous PNP approximation.Comment: 25 pages, 17 figures, 4 table

Temperature- and pressure-dependent metallic states in (BEDT-TTF)8[Hg4Br12(C6H5Br)2]

Temperature-driven metal-insulator and pressure-driven insulator-metal transitions observed in(BEDT-TTF)8[Hg4X12(C6H5Y)2]] with X = Y = Br are studied through band structure calculations based on X-ray crystal structure determination and Shubnikov-de Haas (SdH) oscillations spectra, respectively. In connection with chemical pressure effect, the transition, which is not observed for X = Cl, is due to gap opening linked to structural changes as the temperature decreases. Even though many body interactions can be inferred from the pressure dependence of the SdH oscillations spectra, all the data can be described within a Fermi liquid picture

Luminescence in anion-deficient hafnia nanotubes

Hafnia-based nanostructures and other high-k dielectrics are promising wide-gap materials for developing new opto- and nanoelectronics devices. They possess a unique combination of physical and chemical properties such as insensitivity to electrical and optical degradation, radiation damage stability, a high specific surface area, and an increased concentration of the appropriate active electron-hole centers. The present paper aims to investigate the structural, optical, and luminescent properties of anodized non-stoichiometric $HfO_2$ nanotubes. As-grown amorphous hafnia nanotubes and nanotubes annealed at 700{\deg}C with a monoclinic crystal lattice served as samples. It has been shown that the bandgap $E_g$ for direct allowed transitions amounts to $5.65\pm0.05$ eV for amorphous and $5.51\pm0.05$ eV for monoclinic nanotubes. For the first time, we have studied the features of the intrinsic cathodoluminescence and photoluminescence of the obtained nanotubular $HfO_2$ structures with an atomic deficiency in the anion sublattice at temperatures of 10 and 300 K. A broad emission band with a maximum of 2.3-2.4 eV has been revealed. We have also conducted an analysis of the kinetic dependencies of the observed photoluminescence for synthesized $HfO_2$ samples in the millisecond range at room temperature. It showed that there are several types of optically active capture and emission centers based on vacancy states in the $O_{3f}$ and $O_{4f}$ positions with different coordination numbers and a varied number of localized charge carriers ($V^0$, $V^-$, and $V^{2-}$). The uncovered regularities can be used to optimize the functional characteristics of developed-surface luminescent media based on nanotubular and nanoporous modifications of hafnia.Comment: 15 pages, 6 figures, 3 tables, 50 reference

High frequency magnetic oscillations of the organic metal θ\theta-(ET)4_4ZnBr4_4(C6_6H4_4Cl2_2) in pulsed magnetic field of up to 81 T

De Haas-van Alphen oscillations of the organic metal $\theta$-(ET)$_4$ZnBr$_4$(C$_6$H$_4$Cl$_2$) are studied in pulsed magnetic fields up to 81 T. The long decay time of the pulse allows determining reliable field-dependent amplitudes of Fourier components with frequencies up to several kiloteslas. The Fourier spectrum is in agreement with the model of a linear chain of coupled orbits. In this model, all the observed frequencies are linear combinations of the frequency linked to the basic orbit $\alpha$ and to the magnetic-breakdown orbit $\beta$.Comment: 6 pages, 4 figure

Crystal structure, Fermi surface calculations and Shubnikov-de Haas oscillations spectrum of the organic metal θ\theta-(BETS)4_4HgBr4_4(C6_6H5_5Cl) at low temperature

The organic metal \theta$-(BETS)$_4$HgBr$_4$(C$_6$H$_5$Cl) is known to undergo a phase transition as the temperature is lowered down to about 240 K. X-ray data obtained at 200 K indicate a corresponding modification of the crystal structure, the symmetry of which is lowered from quadratic to monoclinic. In addition, two different types of cation layers are observed in the unit cell. The Fermi surface (FS), which can be regarded as a network of compensated electron and hole orbits according to band structure calculations at room temperature, turns to a set of two alternating linear chains of orbits at low temperature. The field and temperature dependence of the Shubnikov-de Haas oscillations spectrum have been studied up to 54 T. Eight frequencies are observed which, in any case, points to a FS much more complex than predicted by band structure calculations at room temperature, even though some of the observed Fourier components might be ascribed to magnetic breakdown or frequency mixing. The obtained spectrum could result from either an interaction between the FS's linked to each of the two cation layers or to an eventual additional phase transition in the temperature range below 200 K.Comment: accepted for publication in Solid State Science

Diffuse-Charge Dynamics in Electrochemical Systems

The response of a model micro-electrochemical system to a time-dependent applied voltage is analyzed. The article begins with a fresh historical review including electrochemistry, colloidal science, and microfluidics. The model problem consists of a symmetric binary electrolyte between parallel-plate, blocking electrodes which suddenly apply a voltage. Compact Stern layers on the electrodes are also taken into account. The Nernst-Planck-Poisson equations are first linearized and solved by Laplace transforms for small voltages, and numerical solutions are obtained for large voltages. The ``weakly nonlinear'' limit of thin double layers is then analyzed by matched asymptotic expansions in the small parameter $\epsilon = \lambda_D/L$, where $\lambda_D$ is the screening length and $L$ the electrode separation. At leading order, the system initially behaves like an RC circuit with a response time of $\lambda_D L / D$ (not $\lambda_D^2/D$), where $D$ is the ionic diffusivity, but nonlinearity violates this common picture and introduce multiple time scales. The charging process slows down, and neutral-salt adsorption by the diffuse part of the double layer couples to bulk diffusion at the time scale, $L^2/D$. In the ``strongly nonlinear'' regime (controlled by a dimensionless parameter resembling the Dukhin number), this effect produces bulk concentration gradients, and, at very large voltages, transient space charge. The article concludes with an overview of more general situations involving surface conduction, multi-component electrolytes, and Faradaic processes.Comment: 10 figs, 26 pages (double-column), 141 reference

RESEARCH OF THE DYNAMICS OF NON-DIFFRACTION AIRY SECTION PULSES IN THE ENVIRONMENT OF CARBON NANOTUBES

The problem of the propagation dynamics of optical pulses (light bullets) with an Airy profile in an inhomogeneous medium of carbon nanotubes is considered. It is shown numeri-cally that the proposed type of beam exhibits a steady and stable propagation