Folding of poly-amino acids and intrinsically disordered proteins in overcrowded milieu induced by pH change

pH-induced structural changes of the synthetic homopolypeptides poly-E, poly-K, poly-R, and intrinsically disordered proteins (IDPs) prothymosin alpha (ProT alpha) and linker histone H1, in concentrated PEG solutions simulating macromolecular crowding conditions within the membrane-less organelles, were characterized. The conformational transitions of the studied poly-amino acids in the concentrated PEG solutions depend on the polymerization degree of these homopolypeptides, the size of their side chains, the charge distribution of the side chains, and the crowding agent concentration. The results obtained for poly-amino acids are valid for IDPs having a significant total charge. The overcrowded conditions promote a significant increase in the cooperativity of the pH-induced coil-alpha-helix transition of ProTa and provoke histone H1 aggregation. The most favorable conditions for the pH-induced structural transitions in concentrated PEG solutions are realized when the charged residues are grouped in blocks, and when the distance between the end of the side group carrying charge and the backbone is small. Therefore, the block-wise distribution of charged residues within the IDPs not only plays an important role in the liquid-liquid phase transitions, but may also define the expressivity of structural transitions of these proteins in the overcrowded conditions of the membrane-less organelles. (C) 2018 Elsevier B.V. All rights reserved.Peer reviewe

Generalized nonlinear Schrödinger equations describing the Second Harmonic Generation of femtosecond pulse, containing a few cycles, and their integrals of motion.

An interaction of laser pulse, containing a few cycles, with substance is a modern problem, attracting attention of many researches. The frequency conversion is a key problem for a generation of such pulses in various ranges of frequencies. Adequate description of such pulse interaction with a medium is based on a slowly evolving wave approximation (SEWA), which has been proposed earlier for a description of propagation of the laser pulse, containing a few cycles, in a medium with cubic nonlinear response. Despite widely applicability of the frequency conversion for various nonlinear optics problems solutions, SEWA has not been applied and developed for a theoretical investigation of the frequency doubling process until present time. In this study the set of generalized nonlinear Schrödinger equations describing a second harmonic generation of the super-short femtosecond pulse is derived. The equations set contains terms, describing the pulses self-steepening, and the second order dispersion (SOD) of the pulse, a diffraction of the beam as well as mixed derivatives. We propose the transform of the equations set to a type, which does not contain both the mixed derivatives and time derivatives of the nonlinear terms. This transform allows us to derive the integrals of motion of the problem: energy, spectral invariants and Hamiltonian. We show the existence of two specific frequencies (singularities in the Fourier space) inherent to the problem. They may cause an appearance of non-physical absolute instability of the problem solution if the spectral invariants are not taken into account. Moreover, we claim that the energy preservation at the laser pulses propagation may not occur if these invariants do not preserve. Developed conservation laws, in particular, have to be used for developing of the conservative finite-difference schemes, preserving the conservation laws difference analogues, and for developing of adequate theory of the modulation instability of the laser pulses, containing a few cycles

Development of the Modified Methods to Train a Neural Network to Solve the Task on Recognition of Road Users

Розроблено модифікації простого генетичного алгоритму для розпізнавання образів. У запропонованій модифікації Альфа-Бета на етапі відбору особин до нової популяції особини ранжуються за показником пристосованості, далі випадковим чином визначається кількість пар – певна кількість найпристосованіших особин, та стільки ж найменш пристосованих. Найпристосованіші особини формують підмножину B, найменш пристосовані – підмножину W. Обидві підмножини входять в множину пар V. Число особин, що можуть бути обрані в пари, знаходиться в діапазоні 20–60 % від загальної кількості особин. У модифікації Альфа-Бета фіксована в порівнянні з оригінальною версією простого генетичного алгоритму було додано можливість виникнення двох мутацій, додано фіксовану точку схрещення, а також змінено відбір особин для схрещення. Це дозволяє підвищити показник точності у порівнянні з базовою версією простого генетичного алгоритму. У модифікації Фіксована встановлено фіксовану точку схрещення. В схрещенні приймає участь половина генів – гени що відповідають за кількість нейронів на шарах, значення інших генів завжди передаються нащадкам від однієї з особин. Також, на етапі мутації випадковим чином відбуваються мутації з використанням методу Монте-Карло.Розроблені методи програмно реалізовано для вирішення задачі розпізнавання учасників дорожнього руху (автомобілів, велосипедів, пішоходів, мотоциклів, вантажівок). Також було проведено порівняння показників використання модифікацій простого генетичного алгоритму та визначено кращий підхід вирішення задачі розпізнавання учасників дорожнього руху. Було встановлено, що розроблена модифікація Альфа-Бета показала кращі результати у порівнянні з іншими модифікаціями при вирішенні задачі розпізнавання учасників дорожнього руху. При застосуванні розроблених модифікацій отримано наступні показники точності: Альфа-Бета – 96.90 %, Альфа-Бета фіксована – 95.89 %, фіксована – 85.48 %. Крім того, при застосуванні розроблених модифікацій скорочується час підбору параметрів нейромоделі, зокрема при використанні модифікації Альфа-Бета витрачається лише 73,9 % часу базового методу, при використанні модифікації Фіксована – 91,1 % часу базового генетичного метод

Construction of a Genetic Method to Forecast the Population Health Indicators Based on Neural Network Models

A genetic method has been proposed to forecast the health indicators of population based on neural-network models. The fundamental difference of the proposed genetic method from existing analogs is the use of the diploid set of chromosomes in individuals in a population that is evolving. Such modification makes the dependence of the phenotype of the individual on the genotype less deterministic and, ultimately, helps preserve the diversity of the gene pool of the population and the variability of features of the phenotype during the execution of the algorithm. In addition, a modification of the genetic operator of mutations has been proposed. In addition, a modification genetic operator of mutations is proposed. In contrast to the classical method, those individuals that are exposed to the operator of mutations are selected not randomly but according to their mutation resistance corresponding to the value of the function of an individual adaptability. Thus, individuals with worse values of the target function are mutated, and the genome of the strong individuals remains unchanged. In this case, the likelihood of loss of the function reached during the evolution of the extremum due to the action of the mutation operator decreases, and the transition to the new extremum occurs if enough specific weight of the best attributes in the population is accumulated.A comparative analysis of the models synthesized with the help of the developed genetic method has shown that the best results were achieved in the model based on a neural network of long short-term memory. While creating and training the model based on a long short-term network, the ability to use the particle swarm method to optimize the network settings was investigated. The results of our experimental study have shown that the developed model yields the smallest error in predicting the number of new cases of tuberculosis – the average absolute error is 6.139, which is less compared with models that were built by using other methods).The practical application of the developed methods would make it possible to timely adjust the planned treatment and diagnostic, preventive measures, to determine in advance the necessary resources for localization and elimination of diseases in order to maintain people's health

Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions

The fluorescent dye BADAN (6-bromoacetyl-2-dimetylaminonaphtalene) is widely used in various fields of life sciences, however, the photophysical properties of BADAN are not fully understood. The study of the spectral properties of BADAN attached to a number of mutant forms of GGBP, as well as changes in its spectral characteristics during structural changes in proteins, allowed to shed light on the photophysical properties of BADAN. It was shown that spectral properties of BADAN are determined by at least one non-fluorescent and two fluorescent isomers with overlapping absorbing bands. It was found that BADAN fluorescence is determined by the unsolvated “PICT” (planar intramolecular charge transfer state) and solvated “TICT” (twisted intramolecular charge transfer state) excited states. While “TICT” state can be formed both as a result of the “PICT” state solvation and as a result of light absorption by the solvated ground state of the dye. BADAN fluorescence linked to GGBP/H152C apoform is quenched by Trp 183, but this effect is inhibited by glucose intercalation. New details of the changes in the spectral characteristics of BADAN during the unfolding of the protein apo and holoforms have been obtained

Development of a Genetic Algorithm for Placing Power Supply Sources in a Distributed Electric Network

The problem of substantiation of developing complex distribution systems of electric power supply was considered as a hierarchy of problems at the first stage of which the problem of choosing a rational configuration of the power system was solved. A mathematical model of solution of the problem of optimal placement of several power sources in the power supply system and assigning to them consumers using genetic programming algorithms was developed. The proposed methods make it possible to obtain optimal routes of transmission lines connecting consumers with power sources taking into account the terrain restrictions.A modification of a simple genetic algorithm based on which an information system was implemented was developed. This system solves the problem of combinatorial optimization with respect to the choice of optimal location of power sources in a distributed electrical network.Calculation time was estimated depending on the problem parameters. It was shown that the developed algorithm provides minimum computation time for problems of small and medium dimensionality. The results of solution of the problem for a concrete example demonstrate advantage of the genetic approach over the method of full enumeration. The results obtained can be successfully applied to solve the problem of optimizing placement of power sources in a distributed electrical networ

Hydrogen Production by N-Heterocycle Dehydrogenation over Pd Supported on Aerogel-Prepared Mg-Al Oxides

Tetradecahydrophenazine (14HP) is a nitrogen-containing heterocycle compound with a high content of hydrogen that can be released during its dehydrogenation to phenazine (P). The high stability of the 14HP/P pair and relatively low dehydrogenation temperature make 14HP a promising organic hydrogen carrier. This manuscript is devoted to the investigation of hydrogen production by 14HP dehydrogenation over Pd supported on a series of magnesium-aluminum oxides prepared by the aerogel method. This technique made it possible to synthesize catalyst supports characterized by a high surface area and high concentration of surface active sites where active transition metals could be stabilized in a finely dispersed state. The synthesized aerogels had high specific surface areas and pore volumes. A surface area as high as 600 m2/g after calcination at 500 °C was observed for the mixed aerogel with an Mg:Al ratio of 1:4. An increase in the concentration of acidic electron-acceptor sites determined by EPR on the surface of the mixed magnesium-aluminum oxide supports with a high surface area prepared by the aerogel method was found to result in higher hydrogen production due to the faster dehydrogenation of sterically hindered nitrogen-containing tetradecahydrophenazine heterocycles