DOCKING PROBLEMS: PROTEIN-LIGAND LOW ENERGY MINIMA ANALYSIS-

17-1

On possibility of using of measurements of random polarization of radio reflections from meteor trails for generating shared encryption keys

© 2017 IEEE. Meteor burst channel is formed by a scattering of radio waves from the ionized trails left by fast meteor particles. Meteor phenomena make the channel to be stochastic. Using this randomness along with approximate reciprocity of radio propagation, two communication points are able to generate a purely random shared encryption key by joint observation on the channel parameters. In previous studies, it was shown that the randomness of carrier phase and propagation time of detected meteor radio reflections can be used for the key generation purposes. However, a polarization of the radio reflections is also random, and it might be used to generate the keys too. In this study, the first ever attempt on examining a possibility of generating of purely random encryption keys using the samples of random polarization of meteor radio reflections is made. By computer simulation based on a rigorous solution to the problem of oblique diffraction of radio waves on meteor trails, statistical properties of the polarization of meteor radio reflections are studied. The estimates of the cross-correlation between the values of polarization measured synchronously at both sides of a radio link and differing due to non-perfect reciprocity of meteor burst channel are presented. Some preliminary results on the testing generation of a random key are also presented in the end of the paper

Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused more by different parameterization and less by methods and indicates the need for further improvement of implicit solvent models parameterization. Within the same parameterization, various implicit methods give practically the same correlation with results obtained in explicit solvent model for ligands and proteins: e.g. correlation values of polar ligand solvation energies and the corresponding energies in the frame of explicit solvent were 0.953-0.966 for the APBS program, the GBNSR6 program and all models used in the DISOLV program. The DISOLV program proved to be on a par with the other used programs in the case of proteins and ligands solvation energy calculation. However, the solution of the Poisson-Boltzmann equation (APBS program) and Generalized Born method (implemented in the GBNSR6 program) proved to be the most accurate in calculating the desolvation energies of complexes

Secure key distribution based on meteor burst communications

The paper discusses possibility of secure encryption keys distribution based on stochastic properties of meteor burst radio propagation. Unlike wireless key distribution, this method provides much greater channel length and key distribution distances, which is up to 2000 km. Another important advantage is an ability of meteor burst communications to operate in severe climate, under conditions of polar and other remote areas. The paper also considers various physical factors ensuring stochastic variations in characteristics of received radio signal, which are applicable for the secret key generation. The simulation results revealing the most important randomizing factors within meteor burst channel are presented

On the dynamics of nonreciprocal properties of radio reflections from ionized meteor trails

© 2017 IEEE. Meteor burst propagation is based on scattering of radio waves of the meter range from the ionized trails left by fast meteor particles burning at the altitudes of 80-110 km. An interaction between radio wave and the meteor trail is a complex non-stationary process, which is determined by the polarization phenomena at the transmission, propagation, diffraction on the trail, and reception of the wave. These phenomena lead to non-Absolute reciprocity of the radio link both on amplitude and carrier phase. Scattering properties of the meteor trail and associated level of channel nonreciprocity have strong time dependence due to active expansion of the trail. The knowledge of such dependence would be crucial in predicting the moment of minimum channel nonreciprocity. This is particularly important for the implementation of meteor synchronization systems of nanosecond precision and meteor key distribution systems as all these systems rely on reciprocal properties of the channel. Based on a rigorous solution to the problem of oblique diffraction of radio wave on meteor trail, we simulate typical profiles of the dynamics of amplitude and phase nonreciprocity during a single meteor radio reflection. The results on correlation between the dynamics of amplitude nonreciprocity and dynamics of phase nonreciprocity of meteor burst channel are also presented

Comparison of frequency-selective properties of meteor burst channel at the beginning and at the end of radio reflections from meteor trails

© 2017 IEEE. Meteor burst propagation is based on scattering of radio waves from the ionized trails left by fast meteor particles. One of the promising applications of meteor radio propagation is development of Meteor Synchronization Systems (MSSs) for synchronizing two remote stations with potentially subnanosecond accuracy. Frequency-selective properties of meteor burst channel limit potential accuracy of coherent multi-carrier MSS systems. To adapt to frequency distortions of timing signals, a frequency response of the channel should be appropriately considered. Continuous expansion of the meteor trail plasma due to ambipolar diffusion provokes significant changes in frequency-selective properties of the channel at the end of detection of radio reflections. This should be taken into account to assess a minimum channel bandwidth correctly. On the basis of rigorous solution to the problem of diffraction of radio waves on a meteor trail, we perform a numerical simulation of the amplitude-frequency and phase-frequency responses of meteor burst channel. A comparison of the frequency-selective properties of the channel at the beginning and at the end of the signal detection is presented for the cases of radio reflections from underdense and overdense meteor trails. The frequency responses obtained with the diffraction approach are compared with the results of the classical (approximate) theory of a radio reflection from meteor trail

Tyumen District in 1920s: Settlement Numbers and Development Features

The subject of this study is the rural settlements of the Tyumen district in the first quarter of the 20th century. It is noted that during this period, the Tyumen district was situated at the heart of the Tyumen region, ranking first in terms of population size (44,545 people) and the area of territory covered (5.4 thousand square kilometers). The paper examines changes in the number and typology of settlements within the Tyumen district through the lens of its rural localities. It has been established that the district’s settlement network consisted of 177 localities, falling into 11 types, with villages making up a significant proportion — over 50%. This fact indicates that in long-settled regions, settlement networks have existed in virtually unchanged forms despite various external and internal factors. Fifteen villages were identified as creating the framework of the Tyumen district’s settlement network, demonstrating resilience and successfully adapting to new conditions. For instance, data from 1912 and 1926 show that population numbers in these localities were growing, especially in those settlements occupying advantageous (central) positions within the existing network. Many villages in the Tyumen district attained this status during the Soviet period, even though at the beginning of the 20th century they were mere villages. Successful new connections between settlements were facilitated by transportation factors (the presence of railways, tract roads, and a navigable water artery — the Tura River)