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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.
Mysin I. E., Dubrovin S. V., Cognitive Neurodynamics 2026 Vol. 20 No. 191 P. 1–30
The hippocampal theta rhythm is crucial for memory and navigation. It is paced by parvalbumin-expressing GABAergic neurons in the medial septum. These neurons segregate into two subpopulations—Teevra and Komal cells—which fire in anti-phase bursts at theta frequency, with a stable phase shift of approximately 150 degrees, and exhibit mutual inhibition. While essential, the network mechanism ...
Added: November 14, 2026
Мысин И. Е., Журнал высшей нервной деятельности им. И.П. Павлова 2024 Т. 74 № 5 С. 517–537
Information in the brain is encoded by large populations of neurons, i.e., neural ensembles. Place cells in hippocampal the CA1 field have become an experimental model for studying neural ensembles in the brain, as they provide a convenient research system. This review addresses the latest research on place cells in the CA1 field. The principles ...
Added: November 13, 2026
Ефимов К. Д., Журнал Новой экономической ассоциации 2026 № 72 С. 105–114
This study proposes a method for automatic detection of collusive behavior in electronic public procurement auctions based on analysis of the full bid trajectory. The empirical dataset comprises 508 auction histories from 2016–2020 collected from the RTS tender e-procurement platform; the positive class is labeled using case materials of the Federal Antimonopoly Service (FAS Russia), ...
Added: November 13, 2026
Sergey N. Koltcov, Budkovaia M., Surkov A. et al., IEEE Journal of Biomedical and Health Informatics 2026 P. 1–10
Large language models (LLMs) show promise for clinical decision support, but privacy constraints and unreliable free-text decisions limit deployment. We present Medotor, a locally deployed system for screening patients with chronic rhinosinusitis with nasal polyps (CRSwNP) for biologic therapy, and evaluate prompt design on 163 retrospective cases (132 eligible and 31 ineligible). Five models were ...
Added: November 13, 2026
Колодеева Ок. Е., Колодеева Ол. Е., Razumovskaya A. et al., Доклады российской академии наук. Науки о жизни 2026 Т. 530 № 1 С. 614–620
Targeted delivery of therapeutic agents using lipid vesicles is an important area of modern biomedicine. However, the intrinsic biological effects of such carriers on cells require further investigation. Nanoarchaeosomes represent one promising class of delivery vehicles. In the present study, we investigated the response of Caco-2 intestinal epithelial cells to unloaded nanoarchaeosomes. Their exposure was ...
Added: November 13, 2026
Физулин А. В., Stepanyants V., Amerikanov A. et al., FUTURE TRANSPORTATION 2026 Vol. 6 No. 6 Article 264
Cooperative warning functions depend on whether V2X information becomes available in time to influence vehicle control. This article presents an event-based co-simulation framework coupling SUMO, ns-3 (ms-van3t), 5G-LENA NR sidelink and application records, with Sionna RT enabled for the intersection scenario. In 140 emergency-vehicle-warning runs, reducing mean packet reception ratio (PRR) from 0.9412 to 0.0675 ...
Added: November 12, 2026
Stoianova A. D., Trofimets V. Y., Matrokhina K. V., International Journal of Engineering, Transactions A: Basics 2025 Vol. 38 No. 4 P. 701–709
The article considers the issue of managerial decision-making in an oil and gas company, which is related to the class of multi-criteria choice problems. To improve the validity of decisions in the context of companies’ sustainable development it is proposed to implement a Decision Support System (DSS). A brief review of the existing methods of ...
Added: November 10, 2026
Sergei Koltcov, Ryumin D., Alexandr Axyonov et al., PeerJ Computer Science 2026 Article 12:e4141
Educational institutions face increasing pressure to adapt their curricula to the rapidly evolving demands of the job market, and recommender systems can be important tools to guide students in selecting courses that align with their career goals. We present EdFitter, a hybrid course recommendation system that combines pretrained text embeddings for retrieval with large language ...
Added: November 10, 2026
Guskov T., Gerke K., Kondratyuk N. et al., Molecular Simulation 2026 Vol. 52 No. 7 P. 546 – 555
Equilibration is often assumed rather than tested in molecular dynamics studies of confined liquid–liquid interfaces, even though different physical properties may relax on different time scales. In this work, equilibration is examined using an automated truncation method based on the marginal standard error rule. Interfacial geometry, wetting behaviour, and density-related properties are analysed for liquid–liquid ...
Added: November 10, 2026
Lukyanchuk V., Norman G., Kondratyuk N. et al., Scientific Reports 2026 Vol. 16 No. 1 Article 16435
Previously, it has been effectively shown that nuclear quantum effects (NQE) considerably influence the prediction of the warm dense hydrogen phase diagram. Here, we study the influence of NQE on the parameters of the conducting state formation in warm dense hydrogen using path integral molecular dynamics (PIMD) within the framework of the finite temperature density ...
Added: November 10, 2026
Cham: Springer, 2027.
This volume is Part VIII of the refereed proceedings of the European Conference on Machine Learning and Knowledge Discovery in Databases, ECML PKDD 2026, held in Naples, Italy, September 7–11, 2026. It contains 40 papers from the Research Track and the Applied Data Science Track and is published as volume 16948 of Lecture Notes in ...
Added: November 9, 2026
Avdoshin S.M., Pesotskaya E.Y., Proceedings of the Institute for System Programming of the RAS 2026 Vol. 38 No. 6, part 2 P. 133–146
Artificial intelligence has significantly reshaped contemporary software engineering practice,
changing how software systems are designed, implemented, tested, and maintained. Recent advances in large
language models and AI-assisted development tools have expanded the role of AI from supporting isolated
tasks to participating in multiple stages of the software lifecycle. In many development settings, software is
now created from high-level specifications ...
Added: November 8, 2026
Aleksei Samarin, Belous F., Торопов А. Г. et al., Technologies 2026 Vol. 14 No. 11 P. 1–21
Abstract
Automated interpretation of magnetic flux leakage (MFL) data is central to condition assessment of long-distance oil and gas pipelines. Yet, full-resolution panoramas are difficult to process without either suppressing small anomalies through resizing or fragmenting elongated objects at sliding-window boundaries. We propose MFL-ScrollNet, a recurrent sliding-window detector that formulates panoramic analysis as an ordered sequence ...
Added: November 8, 2026
IEEE Computer Society (Conference Publishing Services, CPS), 2026.
Added: November 7, 2026
Popkova D., Menshov A., Sintsova O. et al., International Journal of Biological Macromolecules (Нидерланды) 2026 Vol. 376 No. 1 P. 1–19
Reducing polysaccharide degradation through inhibition of α-amylases and α-glucosidases is one of the strategies
for glycemic control in the treatment of diabetes mellitus. Here we report the identification and characterization
of a new β-defensin-like miniprotein magnificamide-2 (Mgf-2), one of the most potent inhibitors of mammalian
α-amylases with subnanomolar binding affinity (Ki of recombinant Mgf-2 is 0.029 nM against ...
Added: November 7, 2026
Bagaeva D. I., Demina G. R., Panina I. S. et al., International Journal of Biological Macromolecules (Нидерланды) 2026 Vol. 358 No. 1 P. 1–19
It was shown previously that mycobacteria (Mycobacterium smegmatis and Mycobacterium tuberculosis) accumulate
tetramethyl ether of coproporphyrin III (TMC) during transition to dormant state. However, the enzymes
involved in TMC synthesis remained unknown. Here we have identified a new M. smegmatis methyltransferase
MSMEG_0614 (CPmtA) that catalyzes the S-adenosyl-L-methionine-dependent conversion of coproporphyrin
(CP) into TMC through sequential methylation of its carboxyl ...
Added: November 7, 2026
Sergey Avdoshin, Elena Pesotskaya, Saleh H. et al., Procedia Computer Science 2026 Vol. 292 P. 1332–1341
The rapid development of generative large language models (LLMs) has intensified the need for reliable methods capable of distinguishing AI-generated text from human writing, especially in academic and professional settings. This paper presents the results of a systematic benchmarking study evaluating the performance and limitations of contemporary LLM-text detectors
applied to Russian-language academic content. We introduce ...
Added: November 7, 2026
Neuberger A., Veretenenko I. I., Shalygin A. et al., Nature Communications 2026 Vol. 17 No. 1 P. 1–13
Polyamines are organic cations that are present at sub-millimolar concentrations
in the cytoplasm and extracellular fluids and serve as versatile modulators
of TRP channels, fine-tuning their functions in physiological and
pathological contexts, including pain, inflammation and cancer. Despite
extensive functional studies, the structural basis by which polyamines regulate
TRP channels remains unclear. Here, we combine calcium imaging, electrophysiology,
cryo-electron microscopy, mutagenesis ...
Added: November 7, 2026
Neuberger A., Shalygin A., Veretenenko I. I. et al., Nature Communications 2025 Vol. 16 No. 1 P. 1–16
TRPV6 is a member of the vanilloid subfamily of transient receptor potential
channels, which serves as the master regulator of Ca2+ homeostasis. TRPV6
functions as a constitutively active Ca2+ channel, and emerging evidence
indicates that its overactivity underpins the progression of several human
diseases, including cancer. Hence, there is a pressing need to identify TRPV6
inhibitors in conjunction with a ...
Added: November 7, 2026
Zhang Z., Ilvovsky D., Neurocomputing 2027 Vol. 710
Efficient management of the Key-Value (KV) cache is essential for deploying large language models (LLMs) in long-context scenarios, where memory requirements often exceed the capacity of resource-constrained hardware. Many existing training-free compression algorithms typically rely on attention-driven heuristics, but exhibit two key limitations. First, they require explicit attention score computation, which is difficult to reconcile ...
Added: November 5, 2026
Water confined in heterogeneous clay–quartz pores: Structure and dynamics from atomistic simulations
Glushak A., Tararushkin E., Smirnov G., Colloids and Surfaces A: Physicochemical and Engineering Aspects 2027 Vol. 752 Article 141756
The molecular-scale behavior of water in heterogeneous clay–quartz systems is critical for understanding cementation processes in natural soils and compacted bentonite, which is crucial for oil recovery and nuclear waste disposal barriers construction. Here we investigate how heterogeneity of mixed Na-montmorillonite and α-quartz surfaces affect water structure and dynamics in nanopores of 2.5 to 60 Å ...
Added: September 15, 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