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Binomial Uncertainty in Molecular Dynamics-Based Reactions Analysis
The Journal of Physical Chemistry Letters. 2024. Vol. 15. No. 7. P. 2105 – 2110.
Chibisov A., Pugachevskii M., Kuzmenko A. et al., Nanotechnology Reviews 2022 Vol. 11 No. 1 P. 620–624
Cerium oxide nanoparticles have unique catalytic and oxygen storage capacity properties. In this work, the morphology and size of cerium oxide nanoparticles were experimentally and theoretically investigated. For the synthesis of nanoparticles, the laser ablation method was used. The analysis of the size and morphological characteristics of nanoparticles was performed using transmission electron microscopy. Using ...
Added: October 11, 2026
Корзникова Е. А., Babicheva R. I., Davletbakov A. A. et al., JOURNAL OF MATERIALS SCIENCE: MATERIALS IN ENGINEERING 2026 Vol. 21 Article 84
The influence of crack position and its size on short-range ordering (SRO) and high-temperature cyclic deformation behavior of refractory high-entropy alloy (RHEA) HfNbTiZr using bicrystal models has been investigated by combined Monte-Carlo (MC) and molecular dynamics (MD) simulations. It was revealed that the SRO process is affected not only by the crack size, namely the ...
Added: September 24, 2026
Khnkoian G., Galigerov V., Grishichkin Y. et al., , in: Parallel Computational Technologies, 19th International Conference, PCT 2025, Moscow, Russia, April 8–10, 2025, Revised Selected Papers. (CCIS, volume 2891)Vol. 2891.: Springer, 2026. P. 532–545.
This work presents atomic-scale modeling of the perturbed flow of a Lennard-Jones fluid in a quasi-two-dimensional system containing one billion atoms. A statistically stationary flow regime corresponding to a Reynolds number of Re ≈ 1000 has been achieved, the flow structure has been analyzed, and the energy spectrum of velocities has been calculated. The results ...
Added: May 19, 2026
Medvedev M., Journal of Chemical Information and Modeling 2025 Vol. 65 No. 12
Added: November 12, 2025
MDProcessing.jl: Julia Programming Language Application for Molecular Dynamics Trajectory Processing
Pisarev V., Panov M., , in: Supercomputing: 9th Russian Supercomputing Days, RuSCDays 2023, Moscow, Russia, September 25–26, 2023, Revised Selected Papers, Part II* 2.: Springer, 2023. P. 209–222.
Molecular simulations and molecular dynamics in particular are among the most performance-demanding computational methods. As the scale of simulations increases, the task of processing the simulation results becomes a computationally-hungry problem as well. The usual approach to build easy-to-use post-processing tools is based on providing an interface to a high-performance library called from a scripting ...
Added: November 11, 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
Smirnov O. M., Pisarev V., Lenev D. Y., Russian Journal of Physical Chemistry A 2024 Vol. 98 No. 14 P. 3384–3388
Vapor–liquid surface tension is calculated on the evaporation curve of n-nonane in the SAFT-γ Mie model. The calculations are made via molecular dynamics for temperatures in the range of 410 to 505 K. The effect the cutoff radius of the interparticle interaction potential in the model has on the coefficient of surface tension and the ...
Added: June 25, 2025
Odintsova E., Darya L. Gurina, Kruchinin S. E. et al., Industrial & Engineering Chemistry Research 2025 Vol. 64 No. 6 P. 3531–3543
The ability to predict transport properties, such as viscosity, through molecular simulation is a valuable advantage. Obtaining reliable estimates for these properties can be more challenging compared to equilibrium properties. Our manuscript focuses on an in-depth discussion of two prominent methods for predicting transport properties: equilibrium molecular dynamics (EMD) using the Green−Kubo approach and nonequilibrium ...
Added: February 5, 2025
Senchikhin I., Urodkova E. K., Minkevich M. M. et al., Biophysical Reviews 2023 Vol. 15 Article 1505
The work is dedicated to the study of the fusion of lipid droplets — organelles consisting of a core of fatty acids, such as triolein, surrounded by a monolayer of phospholipids. In view of the relatively simple implementation and universality of the effect of the lipid composition of the LC membranes on the efficiency of ...
Added: January 21, 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
Kashurin O., Kondratyuk N., Lankin A. et al., Journal of Molecular Liquids 2024 Vol. 416 Article 126347
To accelerate the development of liquid ion-selective barriers based on ethers, we compare the all-atom
force fields GAFF, OPLS-AA with charge correction 1.14*CM1A (OPLS-AA/CM1A), CHARMM version 36
(CHARMM36), and COMPASS for diisopropyl ether (DIPE) to determine the most appropriate model for further
simulations of liquid membranes. Utilizing the selected force fields, we calculate the density and shear viscosity
of ...
Added: November 27, 2024
Lenev D. Y., Zakharov S. A., V. V. Pisarev, Russian Journal of Physical Chemistry A 2024 Vol. 98 No. 12 P. 2816–2822
Molecular dynamics is used to calculate the vapor–liquid equilibrium and liquid–vapor surface
tension for a methane–ethane system. Good agreement of the parachor value for ethane between the molecular
model and experimental data is shown for the 203–253 K range of temperatures and pressures up to
60 atm. The dependence of the surface tension of the mixture on pressure ...
Added: November 15, 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
Yaremenko I., Belyakova Y., Radulov P. et al., Journal of the american chemical society 2022 Vol. 144 No. 16 P. 7264–7282
Added: October 30, 2024
Krivoshchapov N., Medvedev Michael G., Journal of Chemical Information and Modeling 2024 Vol. 64 No. 11 P. 4542–4552
Added: October 29, 2024
Болдырев К. А., Glushak A., Pisarev V. et al., Радиоактивные отходы 2024 № 3 С. 83–95
This article overviews global and Russian atomistic modelling experience in exploring the properties of clay and cement-based materials for the long-term safety assessment of high-level waste (HLW) repositories. It explains the general concept of molecular dynamics simulation providing some case studies solved based on it. It discusses the accuracy of the calculated parameters and coefficients, ...
Added: September 30, 2024
Stanislav I. Bezzubov, Yakushev I., Medvedev A. et al., Crystal Growth & Design 2023 Vol. 23 No. 10 P. 7252–7265
A novel class of crystalline hydrogen peroxide adducts, peroxosolvates of zwitterionic sulfonic acids C2H7NO3S·H2O2 (1), p-C6H7NO3S·H2O2 (2), p-C6H7NO3S·0.5(H2O2) (3), m-C6H7NO3S·H2O2 (4), o-C6H7NO3S·H2O2 (5), C5H5NO3S·H2O2 (6), C12H8N2O3S·H2O2 (7), C8H17NO3S·2(H2O2) (8), C10H9NO4S·1.25(H2O2)·0.25(H2O) (9), C10H9NO4S·H2O2 (10), and C10H9NO4S·0.94(H2O2)·0.06(H2O) (11), were prepared from highly concentrated hydrogen peroxide, and their structures were determined by X-ray crystallography. In all compounds, first ...
Added: September 16, 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