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Behavior of the Environment during Ion Diffusion in Liquids
Russian Journal of Physical Chemistry A. 2019. Vol. 93. No. 8. P. 1421–1427.
The coefficient of diffusion of an ion in a liquid is decomposed at a low concentration of ions according to the sum of collective and structural diffusion (the former is the diffusion of an ion and the solvation shell as a whole; the latter is the diffusion of an ion due to exchanges of atoms inside the solvation shell, which alter its configuration). It is established that the range of decomposition applicability corresponds to ions interacting strongly with the solvation shell due to their small size. The results are verified by comparing molecular dynamics calculations of the diffusion of ions in water and liquid xenon. The results are shown to be in good agreement with the available experimental data.
Мальцева В. Е., Ananyev I., Милевская А. В. et al., Теоретические основы химической технологии 2025 Т. 59 № 3 С. 13–22
Проведено квантово-химическое моделирование механизма экстракции Fe(III) из солянокислого раствора с использованием гидрофобных эвтектических растворителей на основе 1-октанола. Установлено, что путь реакции существенно различается в зависимости от того, является ли инертный компонент донором или акцептором водородной связи в димере с октанолом. На основе оценки прочности водородных связей показано, что более слабое взаимодействие между компонентами упрощает протекание ...
Added: May 13, 2026
Mikhail R. Samatov, Liu D., Emir S. Amirov et al., The Journal of Physical Chemistry Letters 2025 Vol. 16 No. 51 P. 13068–13074
Ion migration at grain boundaries (GBs) is a key issue leading to the performance degradation of metal halide perovskites (MHPs). Given the weak lattice interactions, the properties of MHPs are highly sensitive to external strain, which is inevitable in practical applications. Nevertheless, a fundamental understanding of the GB behavior under strain is still lacking. Using ...
Added: December 20, 2025
Babicheva R., Kumar A., Kiran R. et al., Metallurgical and Materials Transactions A: Physical Metallurgy and Materials Science 2025 Vol. 56 P. 5646–5663
In the work, simulations using Monte Carlo (MC) and molecular dynamics (MD) methods are carried out to investigate the Nb–Ta–Hf–Zr system refractory high-entropy alloys (HEAs). In particular, the effects of chemical composition and grain boundary (GB) network on short-range ordering (SRO) during combined MC/MD modeling of relaxation mimicking diffusion process are investigated on single-crystalline and ...
Added: November 27, 2025
Aliper E., Ryzhov I., Obukhova P. et al., Biochimica et Biophysica Acta - Biomembranes 2026 Vol. 1868 No. 1 Article 184472
Antibodies to peptide 1147 (amino acids 1147-61) of the SARS-CoV-2 protein S are highly diagnostic. Peptide 1147, although located in a region that is partly spatially hidden in the intact protein, is not subject to mutations, suggesting therapeutic potential. The aim of this study was to elucidate the architecture of this region and the way ...
Added: October 20, 2025
Volynsky P., Urban A., Pavlov K. et al., International Journal of Molecular Sciences 2025 Vol. 26 No. 2 Article 553
Alzheimer’s disease (AD) pathogenesis is correlated with the membrane content
of various lipid species, including cholesterol, whose interactions with amyloid precursor
protein (APP) have been extensively explored. Amyloid-β peptides triggering AD are
products of APP cleavage by secretases, which differ depending on the APP and secretase location
relative to ordered or disordered membrane microdomains. We used high-resolution
NMR to probe ...
Added: October 12, 2025
Ustinov A., Гузев М. А., Дальневосточный математический журнал 2016 Т. 16 № 1 С. 39–43
We use the number theory methods for explicit calculation of a static stress field in the system of a 1D chain harmonic oscillators. The sums defining stress field are presented in terms of Korobov polynomials for arbitrary number of oscillators and arbitrary averaging scale. ...
Added: October 9, 2025
Nesterova I., Kondratyuk N., Budkov Y. et al., Advances in Colloid and Interface Science 2025 Vol. 346 Article 103623
Room temperature ionic liquids show great promise as electrolytes in various technological applications, such as energy storage or electrotunable lubrication. These applications are particularly intriguing due to the specific behavior of ionic liquids in nanoconfinement. While previous research has been focused on optimizing the required characteristics through the selection of electrolyte properties, the contribution of ...
Added: September 2, 2025
Ahmad Ostovari Moghaddam, Fereidonnejad R., Mikhailov D. et al., Materials Letters 2024 Vol. 359 Article 135968
Interatomic potentials based on the second nearest-neighbor modified embedded-atom method (2NN-MEAM) have been developed for Al-Mn, Ti-Mn and Cu-Mn binary alloys. The potentials were utilized to determine structural, mechanical and thermodynamic properties of intermetallic phases, which were in good agreement with the experimental data or first-principles calculations. The potentials can be utilized to study different properties ...
Added: January 23, 2025
Ostovari Moghaddam A., Fereidonnejad R., Mikhailov D. et al., Calphad: Computer Coupling of Phase Diagrams and Thermochemistry 2024 Vol. 87 Article 102753
Interatomic potentials based on the second nearest-neighbor modified embedded-atom method (2NN-MEAM)
have been developed for Fe-V and Cr-V binary alloys. The structural, mechanical and thermodynamic properties
of various stable and metastable phases in Fe-V and Cr-V binary systems were calculated by molecular dynamic
(MD) simulation using the developed 2NN-MEAM potentials. A good consistency between the MD-calculated
data and the ...
Added: January 12, 2025
Neuberger A., Shalygin A., Trofimov Y. A. et al., Structure 2025 Vol. 33 No. 1 P. 91–103.e5
TRPV6 is a Ca2+ selective channel that mediates calcium uptake in the gut and contributes to the development
and progression of human cancers. TRPV6 is represented by the ancestral and derived haplotypes
that differ by three non-synonymous polymorphisms, located in the N-terminal ankyrin repeat domain
(C157R), S1–S2 extracellular loop (M378V), and C-terminus (M681T). The ancestral and derived haplotypes
were ...
Added: December 9, 2024
Ahmad Ostovari Moghaddam, Fereidonnejad R., Moaddeli M. et al., Computational Materials Science 2025 Vol. 247 Article 113534
The second nearest-neighbor modified embedded-atom method (2NN-MEAM) interatomic potentials were developed for Zr-X (X = Co, Fe, Ni) binary alloys. The structural, mechanical and thermodynamic properties of various stable and metastable phases in Zr-Co, Zr-Fe and Zr-Ni binary systems were calculated by molecular dynamic (MD) simulation using the developed 2NN-MEAM potentials. The results obtained by ...
Added: November 12, 2024
Полянский А. А., Efremov R., Биологические мембраны 2024 Т. 41 № 4 С. 403–421
The paper overviews the results of computational studies of the molecular mechanisms underlying
the adaptation of model cell membranes taking place during their interaction with proteins and peptides. We
discuss changes in the structural and dynamic parameters of the water–lipid environment, the hydrophobic/
hydrophilic organization of the lipid bilayer surface (the so-called “mosaicity”), etc. Taken together,
these effects are ...
Added: September 19, 2024
Veretenenko I. I., Trofimov Y. A., Krylov N. A. et al., Biochimica et Biophysica Acta - Biomembranes 2024 Vol. 1866 No. 7 Article 184376
Lateral heterogeneity, or mosaicity, is a fundamental property inherent to cell membranes that is crucial for their functioning. While microscopic inhomogeneities (e.g. rafts) are easily detected experimentally, lipid domains with nanoscale dimensions (nanoclusters of nanodomains, NDs) resist reliable characterization by instrumental methods. In such a case, important insight can be gained via computer modeling. Here, ...
Added: September 19, 2024
Lohan S., Konshina A. G., Tiwari R. K. et al., European Journal of Pharmaceutical Sciences 2024 Vol. 197 Article 106776
The emergence of multidrug-resistant (MDR) strains causes severe problems in the treatment of microbial infections
owing to limited treatment options. Antimicrobial peptides (AMPs) are drawing considerable attention
as promising antibiotic alternative candidates to combat MDR bacterial and fungal infections. Herein, we present
a series of small amphiphilic membrane-active cyclic peptides composed, in part, of various nongenetically
encoded hydrophilic and ...
Added: September 15, 2024
Polyansky A. A., R. G. Efremov, Russian Journal of Bioorganic Chemistry 2024 Vol. 50 No. 4 P. 1202–1214
This study presents in a systematic manner the key modeling results corroborated by experimental
biophysical data and obtained by the authors during long-term research on bitopic (single-pass) membrane proteins
(BMPs), which are the crucial elements of cell signaling. The manuscript does not claim to be a comprehensive
review of the subject of interest, whereby the authors did not ...
Added: September 15, 2024
El-Mowafi S. A., Konshina A. G., Mohammed E. H. et al., Molecules 2023 Vol. 28 No. 24 Article 8049
In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and their interactions with membranes. The objective was to discern the nature of these interactions and understand how peptide sequence and structure influence antimicrobial activity. We introduced modifications into the established cyclic AMP peptide, ...
Added: September 15, 2024
Fighting Celiac Disease: Improvement of pH Stability of Cathepsin L In Vitro by Computational Design
Chugunov A. O., Dvoryakova E. A., Dyuzheva M. A. et al., International Journal of Molecular Sciences 2023 Vol. 24 No. 15 Article 12369
Roughly 1% of the global population is susceptible to the celiac disease (CD) — inheritable autoimmune inflammation of the small intestine, caused by intolerance to gliadin proteins present in wheat, rye and barley grains, and called gluten in wheat. Classic treatment is a life-long gluten-free diet, which is constraining and costly. Alternative approach is based ...
Added: September 15, 2024
Лукьянчук В. Г., Ланкин А. В., Norman G., Письма в Журнал экспериментальной и теоретической физики 2023 Т. 118 № 8 С. 609–614
An atomistic model of dehydrated Cl-doped double layer aluminum–lithium hydroxide Li⋅Al2(OH)6Cl (DALH-Cl), which is a promising material for the sorption of lithium from weak brines, has been developed. The effective charges of the atoms of the system have been determined using the density derived electrostatic and chemical (DDEC6) methods. A molecular dynamics analysis of DALH-Cl has been ...
Added: April 16, 2024
Лобашев Е. А., Антропов А. С., Stegailov V., Журнал экспериментальной и теоретической физики 2023 Т. 163 № 2 С. 201–213
The formation of gas nanobubbles through the merging of individual fission products of uranium is an important process for the evolution of nuclear fuels. The theoretical description of this process is very difficult because both the dynamics of individual atoms in the lattice and the kinetics of evolution of an ensemble of bubbles should be ...
Added: November 25, 2023
Fominykh N., Nikolskiy V., Stegailov V., Computational Materials Science 2023 Vol. 220 Article 112061
The paper considers a prototype atomistic model of an oxide film with a wüstite structure in contact with a liquid metal coolant containing dissolved iron and oxygen. On the basis of direct molecular dynamics modeling with the Tersoff interatomic potential for Fe–O, we check the correspondence between the formation free energies of defects, determined from ...
Added: November 25, 2023
Backs A., Al-Falou A., Vagov A. et al., Physical Review B: Condensed Matter and Materials Physics 2023 Vol. 107 No. 17 Article 174527
In the vicinity of the type-I/type-II crossover in conventional superconductors, vortices exhibit a nonmonotonic interaction, which leads to exotic vortex matter states. We perform molecular dynamics simulations on a model superconductor in the intertype regime. In a field cooled approach, we examine the transition of a homogeneous vortex lattice (VL) into a structure consisting of ...
Added: November 2, 2023
Pavlov D., Galigerov V., Kolotinskii D. et al., International Journal of High Performance Computing Applications 2024 Vol. 38 No. 1 P. 34–49
Fluid dynamics is a ubiquitous problem that arises in different branches of science and industry. It is usually tackled by numerically solving differential equations on a finite grid. Molecular dynamics was not a feasible tool to approach fluid dynamics until very recently due to its disproportional computational complexity. In this paper we propose a new ...
Added: July 18, 2023