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Analysis of Ion Atmosphere Around Nucleosomes Using Supercomputer MD Simulations
Supercomputing Frontiers and Innovations. 2022. Vol. 9. No. 2. P. 56–67.
The nucleosome is the basic unit of eukaryotic DNA compaction. It consists of about 147 base pairs wrapped around an octamer of histone proteins. Nucleosomal dynamics provides the availability of packaged DNA for various factors that carry out the vital processes associated with chromatin. It is not completely known how the structure and dynamics of the nucleosome depends on the ionic environment. The current researches do not give an unambiguous answer and often contradict each other. In this paper, we demonstrate supercomputer molecular dynamics simulations of nucleosome models surrounded by monovalent sodium and potassium cations. Analyzing the trajectories, we showed the details of the distribution of sodium and potassium ions around the linker DNA, nucleosomal DNA at the sites of nucleosomal opening, and histone residues involved in the process of nucleosomal breathing. We have demonstrated the mobility of DNA linkers and the process of nucleosomal unwrapping in various ionic environments, and also assessed the probable mechanisms of the dependence of nucleosome unwrapping on the type of ions in the system. Our study is intended to emphasize the importance of understanding the role of the ionic environment in the functioning of chromatin.
Beznosikov A., Kormakov G., Grigorievskiy A. et al., Journal of Optimization Theory and Applications 2026 Vol. 209 Article 18
The objective of Vertical Federated Learning (VFL) is to collectively train a model using features available on different devices while sharing the same users. This paper focuses on the saddle point reformulation of the VFL problem via the classical Lagrangian function. We first demonstrate how this formulation can be solved using deterministic methods.More importantly, we explore various stochastic modifications to ...
Added: June 17, 2026
Chertenkov V. I., Shchur L., Lobachevskii Journal of Mathematics 2026 Vol. 47 No. 2 P. 720–727
Supervised machine learning is successfully applied to the study of critical phenomena and allows us to obtain a numerical estimate of the phase transition temperature and the correlation length exponent. We discuss the influence of possible systematic errors, as well as statistical errors, on the accuracy of such numerical estimates. Errors in the training and ...
Added: June 16, 2026
Deeb B., Andrey V. Savchenko, Makarov I., IEEE Access 2026 Vol. 13 P. 56283–56295
Speech Emotion Recognition has gained considerable attention in speech processing and machine learning due to its potential applications in human-computer interaction, mental health monitoring, and customer service. However, state-of-the-art models for speech emotion recognition use many parameters, which leads to computational complexity. In this paper, we introduce a novel deep-learning model to enhance the accuracy ...
Added: June 16, 2026
Makarov N., Savchenko A., Zemtsova I. et al., Scientific Reports 2025 Vol. 15 Article 26641
The grey wolf (Canis lupus) is a pivotal species for ecological studies. As a key participant in ecosystem
processes, it also serves as a model for investigating social structure formation and ecological
adaptation. However, the species’ complex social behavior, spatial dynamics, and expansive habitats
make monitoring and population assessments across large areas particularly challenging. In recent
years, audio traps ...
Added: June 16, 2026
Vasilev R., Savchenko A., Blinov P. et al., Frontiers in Medicine 2026 Vol. 13
Automated disease screening systems face challenges when applied to multi-class medical image analysis, particularly under severe class imbalance inherent in clinical datasets. Retinal fundus imaging enables non-invasive screening for multiple ocular and systemic diseases simultaneously, yet current automated systems typically assess risk for only a single pathology or a limited disease range. We developed a ...
Added: June 16, 2026
Novopoltsev M., Tulenkov A., Murtazin R. et al., IEEE Access 2025 Vol. 13 P. 188170–188181
Video-based Isolated Sign Language Recognition (ISLR) problem presents significant challenges in scaling across diverse languages due to data scarcity and the computational costs associated with training of language-specific models. In this paper, we introduce a novel training pipeline that leverages self-supervised learning on a large-scale sign language dataset. To obtain the foundation model, we utilize ...
Added: June 16, 2026
Stepin A., Mozikov M., Kabanov A. et al., IEEE Access 2026 Vol. 14 P. 48127–48144
The deployment of large language models (LLMs) in interactive roles such as automated negotiators, customer service agents, and strategic partners requires them to handle not only logical tasks but also the socio-emotional dimensions of interaction. In these situations, success often relies on understanding social cues, building trust, and using persuasion effectively. These skills are closely ...
Added: June 16, 2026
Abdullaeva I., Karpukhin I., Filatov A. et al., IEEE Access 2026 Vol. 14 P. 59390–59408
Event sequences, a specialized type of tabular data annotated with timestamps, are prevalent across practical domains such as finance, retail, social networks, and healthcare. Despite the importance of event sequence modeling and analysis, there has been little effort to adapt Large Language Models (LLMs) to this domain. In this paper, we propose a novel solution ...
Added: June 16, 2026
Temereva E., Palaeogeography, Palaeoclimatology, Palaeoecology 2026 Vol. 697 P. 1–11
Unlike most other brachiopods, craniiforms lack a prominent pedicle, cement to a hard substrate by their ventral valve, and thereby can be easily distinguished in paleontological materials. In this study, we describe a new genus and species from the Porkuni Regional Stage of Northeastern Estonia (Baltica), corresponding to the lower part of the Hirnantian Stage ...
Added: June 15, 2026
Temereva E., Zoological Journal of the Linnean Society 2025 Vol. 205 No. 2 P. 1–13
Although Brachiopoda represent a relatively small phylum, they exhibit significant morphological diversity. One of the central issues in understanding the evolution of the ancestral brachiopod body plan pertains to the homologies among body compartments across the different brachiopod subphyla: Craniiformea, Linguliformea, and Rhynchonelliformea. In this context, the pedicle stands out as one of the most ...
Added: June 15, 2026
Association for Computational Linguistics, 2026.
Added: June 14, 2026
Strube M., Braud C., Hardmeier C. et al., Suzhou: Association for Computational Linguistics, 2025.
Added: June 11, 2026
Sorokin D., Kostin A., Savchenko L. et al., Knowledge-Based Systems 2026 Vol. 348 Article 116258
A convenient approach to optimally solving combinatorial optimization tasks is the Branch-and-Bound method.
Its branching heuristic can be learned to solve a large set of similar tasks. The promising results here are
achieved by the recently appeared on-policy reinforcement learning method based on the tree Markov Decision
Process. To overcome its main disadvantages, namely, very large training time ...
Added: June 10, 2026
Namsaraev Z., Nanzatov B., Kozlova A. et al., Scientific Reports 2026 Vol. 16 No. 1 Article 17769
Distilled fermented milk beverages are rare in food technology, despite the global prevalence of plant-based spirits. Currently, the production of distilled strong alcoholic beverages from fermented milk using traditional technologies is known only among Mongolic-speaking peoples and their Siberian neighbors. This study provides the first interdisciplinary analysis of darasun, a traditional Buryat spirit made from fermented ...
Added: June 10, 2026
Butorova A., Bobakov V., Sergeev A. et al., European Physical Journal: Special Topics 2026 P. 1–19
This paper presents a review of artificial intelligence (AI) methods for failure prediction in data center cooling systems, with a focus on the integration of digital twins (DTs), physics-informed learning, and graph-based models. Positioned within complex network science, this review addresses a limitation of conventional graph approaches—their reliance on pairwise connectivity—whereas real-world failures often arise ...
Added: June 10, 2026
Vanhaelen Q., Lin Y., Zhavoronkov A., ACS Medicinal Chemistry Letters 2020 Vol. 11 No. 8 P. 1496–1505
Generative adversarial networks (GANs), first published in 2014, are among the most important concepts in modern artificial intelligence (AI). Bridging deep learning and game theory, GANs are used to generate or “imagine” new objects with desired properties. Since 2016, multiple GANs with reinforcement learning (RL) have been successfully applied in pharmacology for de novo molecular design. Those ...
Added: June 1, 2026
Nikitiuk B., Nikolay Kondratyuk, Pisarev V., Journal of Molecular Liquids 2025 Vol. 440 Article 128894
Understanding how liquids transition into glassy states under varying thermodynamic conditions remains a fundamental challenge in condensed matter physics. While temperature-driven vitrification has been extensively studied, the effects of high pressure on glass formation are comparatively underexplored -- particularly in molecular liquids. In this work, we employ molecular dynamics simulations to investigate the behaviour of ...
Added: November 12, 2025
Konshina A., Bocharov E., Konovalova E. et al., International Journal of Molecular Sciences (Швейцария) 2024 Vol. 25 No. 21 Article 11370
Non-immunoglobulin-based scaffold proteins (SPs) represent one of the key therapeutic
target-specific and high-affinity binders in modern medicine. Among their cellular targets are signaling
receptors, in particular, receptor tyrosine kinases, whose dysfunction leads to the development
of cancer and other serious diseases. Successful applications of SPs have been reported for
HER receptor type 2 (HER2), a member of the human ...
Added: December 9, 2024
Svitanko I. V., Novikov F. N., Medvedev M. G., , in: XXII Mendeleev Congress on General and Applied Chemistry, October 7-12, 2024, Federal Territory “Sirius”, Russia. Book of abstracts in 7 volumesVol. 5.: “Admiral Print” LLC, 2024.
ADD-ONS TO MOLECULAR MODELING METHODS: IMPROVEMENT IN ACTIVITY PREDICTION ...
Added: October 14, 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
Fedulova A., Armeev G., Romanova T. et al., Wiley Interdisciplinary Reviews: Computational Molecular Science 2024 Vol. 14 No. 4 Article e1728
Understanding the function of eukaryotic genomes, including the human genome, is undoubtedly one of the major scientific challenges of the 21st century. The cornerstone of eukaryotic genome organization is nucleosomes—elementary building blocks of chromatin about 10 nm in size that wrap DNA around an octamer of histone proteins. Nucleosomes are integral players in all genomic processes, ...
Added: August 29, 2024
I. V. Svitanko, Pivina T. S., Russian Chemical Bulletin 2024 Vol. 73 No. 5 P. 1093–1108
The review gives a retrospective of methods for molecular modeling of the structures, mechanisms of chemical reactions, and properties of organic compounds. The development and advancement of the ideology of preliminary modeling of the structures and formation mechanisms of reaction products in the planning of any synthesis is a relevant task in this fi eld of science. Some ...
Added: June 21, 2024
Krasavin M., Peshkov A., Lukin A. et al., International Journal of Molecular Sciences 2022 Vol. 23 No. 19 Article 11579
Starting from a screening hit, a set of analogs was synthesized based on a 4-(2-aminoethyl)piperidine core not associated previously with trace amine-associated receptor 1 (TAAR1) modulation in the literature. Several structure–activity relationship generalizations have been drawn from the observed data, some of which were corroborated by molecular modeling against the crystal structure of TAAR1. The ...
Added: February 8, 2024
Yarovaya O., Filimonov A., Baev D. et al., Viruses 2024 Vol. 16 No. 2 Article 215
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (−)-usnic acid and studied their ability to inhibit the main ...
Added: January 31, 2024