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Copyright of Proceedings of the YSU B: Chemical & Biological Sciences / Gitakan Teghekagir. K'imia, Kensabanut'yun is the property of Publishing House of Yerevan State University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Frataxin (FXN) is a protein involved in storage and delivery of iron in the mitochondria. Single-point mutations in the FXN gene lead to reduced production of functional frataxin, with the consequent dyshomeostasis of iron. FXN variants are at the basis of neurological impairment (the Friedreich's ataxia) and several types of cancer. By using altruistic metadynamics in conjunction with the maximal constrained entropy principle, we estimate the change of free energy in the protein unfolding of frataxin and of some of its pathological mutants. The sampled configurations highlight differences between the wild-type and mutated sequences in the stability of the folded state. In partial agreement with thermodynamic experiments, where most of the analyzed variants are characterized by lower thermal stability compared to wild type, the D104G variant is found with a stability comparable to the wild-type sequence and a lower water-accessible surface area. These observations, obtained with the new approach we propose in our work, point to a functional switch, affected by single-point mutations, of frataxin from iron storage to iron release. The method is suitable to investigate wide structural changes in proteins in general, after a proper tuning of the chosen collective variable used to perform the transition. [ABSTRACT FROM AUTHOR]

Frataxin (FXN) is a protein involved in storage and delivery of iron in the mitochondria. Single-point mutations in the FXN gene lead to reduced production of functional frataxin, with the consequent dyshomeostasis of iron. FXN variants are at the basis of neurological impairment (the Friedreich’s ataxia) and several types of cancer. By using altruistic metadynamics in conjunction with the maximal constrained entropy principle, we estimate the change of free energy in the protein unfolding of frataxin and of some of its pathological mutants. The sampled configurations highlight differences between the wild-type and mutated sequences in the stability of the folded state. In partial agreement with thermodynamic experiments, where most of the analyzed variants are characterized by lower thermal stability compared to wild type, the D104G variant is found with a stability comparable to the wild-type sequence and a lower water-accessible surface area. These observations, obtained with the new approach we propose in our work, point to a functional switch, affected by single-point mutations, of frataxin from iron storage to iron release. The method is suitable to investigate wide structural changes in proteins in general, after a proper tuning of the chosen collective variable used to perform the transition.

A computer simulation of the structure and energy of 〈110〉 symmetric tilt boundaries has been performed for polycrystalline tungsten. Calculations have been made using an embedded atom potential implemented in the LAMMPS software. It has been shown that structure of the 〈110〉 symmetric tilt boundaries can consist of a limited number of structural elements. The energy and width of grain boundaries for different misorientations, as well as energies of vacancy formation have been determined via molecular statistics simulation of grain boundaries. The correlation between the energy of vacancy formation in grain boundaries and changes in the boundary structure has been analyzed. [ABSTRACT FROM AUTHOR]

In this paper, a novel simulation method of turbulence by solving filtered Navier-Stokes equations based on LES methodology and calculating the sub-grid scale stress with D-IP method is developed. Compared to the sub-grid scale models used in LES method with Boussinesq assumption, the sub-gird scale stress of the LES-DIP method is directly estimated based on statistics of molecule motions. To validate the LES-DIP method, turbulent channel flow at different Reynolds numbers of Re r =180, 390 and 590 are simulated. The results are found to be in agreement with those of DNS with much smaller computational cost. [ABSTRACT FROM AUTHOR]

Three fundamental problems of molecular statistics can be identified using the shape of a nanoparticle and the curvature of a λ-layer surrounding it, which correspond to the polar, axial, and plane symmetry. Within the framework of a single-velocity approximation, solutions to these problems are constructed and formulas for coefficients of average resistance to motion of variously-shaped particles are found. [ABSTRACT FROM AUTHOR]

The molecular statistical method for evaluating the distribution of active sites of various adsorbents relative to their energies has been improved. This method is used not only for the treatment of experimental data on the adsorption of hydrocarbons on various adsorbents, which is the usual procedure, but also data on the adsorption of polar water and methanol molecules on the active sites of adsorbent surfaces. Two types of active sites differing in energy have been shown to exist on the surface of graphitized carbon black, the complex shungite carbon/mineral adsorbent, and modified Silochrom. Chromatographic, calorimetric, and structural adsorption data were used to establish the relationship between the observed maxima of the energy distribution function of the adsorption sites with concrete adsorption sites or pores of the surface, on which the molecules are adsorbed. [ABSTRACT FROM AUTHOR]

A complex theoretical-experimental investigation has been carried out on the interaction of water with hydrophilic centers-phenolic and carboxyl groups-on the surface of graphite and graphitized thermal carbon black in low surface occupation range. It is shown that microclusters, formed by the absorption on such centers, have a cyclic structure of 4–5 molecules similar to those observed in liquid water and on the surface of silver iodide. The formation of such structures is shown to be energetically advantageous. It is shown that the generalized Langmuir equation, derived from molecular-statistical considerations, is considerably better over a wide range of relative pressure for the description of the experimental isotherm for the adsorption of water on graphitized thermal carbon black and allows for a better interpretation of structural and energetic characteristics of adsorbed systems obtained by a complex of methods. [ABSTRACT FROM AUTHOR]