DFT Modelling of Molecular Structure, Vibrational and UV-Vis Absorption Spectra of T-2 Toxin and 3-Deacetylcalonectrin

This paper discusses the applicability of optical and vibrational spectroscopies for the identification and characterization of the T-2 mycotoxin. Vibrational states and electronic structure of the T-2 toxin molecules are simulated using a density-functional quantum-mechanical approach. A numerical experiment aimed at comparing the predicted structural, vibrational and electronic properties of the T-2 toxin with analogous characteristics of the structurally similar 3-deacetylcalonectrin is performed, and the characteristic spectral features that can be used as fingerprints of the T-2 toxin are determined. It is shown that theoretical studies of the structure and spectroscopic features of trichothecene molecules facilitate the development of methods for the detection and characterization of the metabolites.

Risky interpretations across the length scales: continuum vs. discrete models for soft tissue mechanobiology

Modelling and simulation in mechanobiology play an increasingly important role to unravel the complex mechanisms that allow resident cells to sense and respond to mechanical cues. Many of the in vivo mechanical loads occur on the tissue length scale, thus raising the essential question how the resulting macroscopic strains and stresses are transferred across the scales down to the cellular and subcellular levels. Since cells anchor to the collagen fibres within the extracellular matrix, the reliable representation of fibre deformation is a prerequisite for models that aim at linking tissue biomechanics and cell mechanobiology. In this paper, we consider the two-scale mechanical response of an affine structural model as an example of a continuum mechanical approach and compare it with the results of a discrete fibre network model. In particular, we shed light on the crucially different mechanical properties of the ‘fibres’ in these two approaches. While assessing the capability of the affine structural approach to capture the fibre kinematics in real tissues is beyond the scope of our study, our results clearly show that neither the macroscopic tissue response nor the microscopic fibre orientation statistics can clarify the question of affinity.

Вероятности оже-переходов и сечения эмиссии электронов при распаде вакансии на 2pπ-орбитали в квазимолекуле Ne-=SUP=-+-=/SUP=--Ne

The Auger transition probabilities are calculated while filling a vacancy on 2pπ orbital in a Ne+-Ne quasimolecule, a short-lived system which is formed when ion and atom approach each other and decays when they scatter. For the first time calculations were performed for various degrees of particles ionization in quasimolecule. It was found that with increase of collision energy and decrease of distance of the closest approach of particles the system ionization degree increases very significantly (from 2 to 6). Using of the quantum mechanical approach and taking into account the dynamics of collisions made it possible for the first time to describe quantitatively the experimental spectra of Auge electrons for a complex many-electron quasimolecule. From the whole variety of possible Auger decay channels the dominant contribution of the transition was established, from the initial 3dπ-3dπ state to the 2pπ orbital.

NUMERICAL STUDYING ENERGY PARAMETERS OF MULTIELECTRON ATOM IN A MAGNETIC FIELD: HELIUM

There are presented the results of calculating the energies of the helium atom energy in a homogeneous magnetic field on the basis of the new numerical quantum-mechanical approach. The approach is based on the numerical difference solution of the Schrödinger equation, the model potential method and the operator perturbation theory formalism. The obtained results on energy of the helium atom in dependence upon the magnetic field strength are compared with available theoretical results, obtained on the basis of alternative numerical Hartree-Fock and diagonalization methods.

Proton transfer pathway in anion channelrhodopsin-1

Anion channelrhodopsin from Guillardia theta (GtACR1) has Asp234 (3.2 Å) and Glu68 (5.3 Å) near the protonated Schiff base. Here, we investigate mutant GtACR1s (e.g., E68Q/D234N) expressed in HEK293 cells. The influence of the acidic residues on the absorption wavelengths was also analyzed using a quantum mechanical/molecular mechanical approach. The calculated protonation pattern indicates that Asp234 is deprotonated and Glu68 is protonated in the original crystal structures. The D234E mutation and the E68Q/D234N mutation shorten and lengthen the measured and calculated absorption wavelengths, respectively, which suggests that Asp234 is deprotonated in the wild-type GtACR1. Molecular dynamics simulations show that upon mutation of deprotonated Asp234 to asparagine, deprotonated Glu68 reorients toward the Schiff base and the calculated absorption wavelength remains unchanged. The formation of the proton transfer pathway via Asp234 toward Glu68 and the disconnection of the anion conducting channel are likely a basis of the gating mechanism.

An electron wave packet in the relativistic strophotron FEL

The theory of free electron lasers (FELs) is well developed both in quantum mechanical and classical approaches. In strophotron FEL, in classical approach, resonance frequency and the gain are strongly dependent on initial parameters of electron beam. In the quantum mechanical approach considered by Zaretsky and Nersesov (1983 JETP 57 518), there is no such dependence. The correspondence between the quantum mechanical and classical approaches in a relativistic strophotron FEL is discussed. We study the initial distribution of electrons over vibrational levels determined by the expansion coefficients in relativistic strophotron FEL. It is shown, (presenting electron wave function in the form of Gaussian wave packet), that the number of the vibrational level most efficiently populated at the initial moment of time can be expressed in terms of the initial parameters of the electron beam.

Predicting conductivities of alkali borophosphate glasses based on site energy distributions derived from network former unit concentrations

For ion transport in network glasses, it is a great challenge to predict conductivities specifically based on structural properties. To this end it is necessary to gain an understanding of the energy landscape where the thermally activated hopping motion of the ions takes place. For alkali borophosphate glasses, a statistical mechanical approach was suggested to predict essential characteristics of the distribution of energies at the residence sites of the mobile alkali ions. The corresponding distribution of site energies was derived from the chemical units forming the glassy network. A hopping model based on the site energy landscape allowed to model the change of conductivity activation energies with the borate to phosphate mixing ratio. Here we refine and extend this general approach to cope with minimal local activation barriers and to calculate dc-conductivities without the need of performing extensive Monte-Carlo simulations. This calculation relies on the mapping of the many-body ion dynamics onto a network of local conductances derived from the elementary jump rates of the mobile ions. Application of the theoretical modelling to three series of alkali borophosphate glasses with the compositions 0.33Li2O–0.67[xB2O3–(1 − x)P2O5], 0.35Na2O–0.65[xB2O3–(1 − x)P2O5] and 0.4Na2O–0.6[xB2O3–(1 − x)P2O5] shows good agreement with experimental data.

Hydro-Mechanics Analysis on the Strength Development of Cement-Stabilized Sand

Deep cement mixing is an effective ground stabilization technique to control the ground movement on sand areas, and most of the projects have the problem of seepage. The cement slurry is in a fluid state before the initial setting time, the seepage may affect the diffusion process of cement slurry during this period. A hydro-mechanical approach is proposed to investigate the interaction between the seepage and the strength of cement-stabilized sand. The diffusion of the cement slurry under seepage is considered in this study and the diffusion process is simulated by the finite element method. According to the cement concentration at the end of the diffusion process, the strength of cement-stabilized sand can be predicted by combining an empirical formula. Simulation results examine that the existence of seepage and cracks can enhance the non-uniform diffusion process of cement slurry, and the actual strength distribution of the deep cement-mixed sand is far from the ideal state. This indicates that the influence of seepage on the strength of cement-stabilized sand should be considered in the design of projects.