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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.
Maltseva D., Tonevitsky A., Frontiers in Molecular Biosciences 2026 Vol. 13 P. 1–28
MicroRNA (miRNA) genes are frequently located in close proximity within the genome, forming so-called clusters. These clusters are transcribed as polycistronic units, suggesting coordinated transcriptional regulation of the miRNAs they contain. However, individual mature miRNAs from the same cluster often accumulate at varying levels and exhibit distinct tissue-specific expression patterns, indicating the presence of regulatory ...
Added: October 23, 2026
Vasilyev A., Svirin EP, Dubynin I. et al., Cortex 2025 Vol. 189 P. 76–96
Added: October 22, 2026
Karina V. Klycheva, Mariia O. Silkina, Dmitry M. Hushpulian et al., Biochemistry. Biokhimiia 2026 Vol. 91 P. 1842–1858
Involvement of the transcription factor Bach1 in various scenarios of cellular regulation is reviewed herein. To date, the most extensively studied role of Bach1 is that of a repressor of the antioxidant genetic program initiated by the Nrf2 factor. This program counteracts oxidative stress, which triggers both ferroptosis and the intrinsic apoptotic pathway. Bach1 functions unrelated ...
Added: October 22, 2026
Svirin E., Бердышев Д. А., Шишкин С. Л., Вестник Российского государственного медицинского университета 2026 № 3 С. 42–50
Quasi-movements (QMs), which are movement attempts minimized to the point of movement extinction, evoke EEG patterns similar to those of real movement. QMs can model attempted movement in healthy subjects and are therefore of interest as an alternative to motor imagery (MI) in rehabilitation brain–computer interfaces (BCIs), in which the attempted movement of the paralyzed ...
Added: October 22, 2026
Sitdikova K., Tsoy A., Chaprov K. et al., Journal of Neuropathology and Experimental Neurology 2026 Article nlag078
Understanding the earliest pathological changes in Alzheimer disease (AD) is critical for improving early intervention strategies. However, the relationship between amyloid plaque characteristics and early behavioral and molecular alterations remains unclear. We used 6-month-old female APPswe/PS1dE9 mice, a model of early amyloid-dominant pathology, to assess cognition and emotionality across a battery of behavioral tests. Amyloid ...
Added: October 22, 2026
Effects of Wheat Malt Extract on Molecular and Behavioral Markers in Aged APP/PS1 and Wild-Type Mice
Kassenova A., Svirin E., Sitdikova K. et al., International Journal of Molecular Sciences 2026 Vol. 27 No. 11 Article 4994
Added: October 22, 2026
Cespuglio R., Schmitt-Böhrer A., Deykin A. et al., Metabolites 2026 Vol. 16 No. 2 Article 117
Added: October 22, 2026
Obsie E. Y., Zhan Y., Liu Y., Engineering Research Express 2026 Article 7
Maintaining plant health is crucial for crop quality, food security, and agricultural productivity. Although deep learning methods have shown strong potential for species, disease, and severity classification, most existing approaches tackle these tasks separately, failing to exploit shared representations and interdependencies among them. Furthermore, the variability of disease symptoms, such as subtle differences in size, ...
Added: October 22, 2026
Logvenkov S. A., Известия РАН. Механика жидкости и газа 2026 № 3 С. 59–75
The problem of the evolution of cell volume fraction in a spherical aggregate composed of cells,
extracellular matrix, and fluid is considered. The aggregate is surrounded by extracellular matrix. The
problem formulation employs a multiphase model of a biological continuum, previously developed by the
author, consisting of two actively interacting solid phases and a fluid. The propagation of ...
Added: October 20, 2026
Lev Pyatko, Sergey Aksenov, Regular and Chaotic Dynamics 2026 Vol. 31 No. 5 P. 794–813
In the circular restricted three-body problem, families of periodic and quasi-periodic orbits exist in the vicinity of the libration points and are of significant interest for practical applications. This work presents a neural network-based algorithm for orbit construction and station-keeping, applicable to both periodic and quasi-periodic orbits near collinear libration points. The method employs a ...
Added: October 19, 2026
Vorontsova T., М.: Академия, 2025.
The textbook has been prepared in accordance with the requirements of the federal state educational standards for secondary vocational education and is intended for studying the professional modules “Information Security in Information and Telecommunication Systems and Networks Using Software and Hardware‑Software Tools, Including Cryptographic Protection Tools” and “Information Security in Automated Systems Using Software and ...
Added: October 19, 2026
Liaukovich K., Zhurnal Vysshei Nervnoi Deyatelnosti Imeni I.P. Pavlova 2026 Vol. 76 No. 5 P. 587–598
Added: October 19, 2026
Nersisyan A., Frontiers in Molecular Biosciences 2026 Vol. 13 Article 1995001
Antiviral activity is commonly summarized using endpoint measures such as EC50 or EC90, yet these quantities emerge from a dynamic biological system and depend on viral replication kinetics, host-cell properties, experimental design, and the assay used to quantify infection. Infectious-virus titers, viral RNA, infected-cell fractions, viability measurements, and immune readouts capture different components of the ...
Added: October 15, 2026
Aleksei Samarin, Nazarenko A., Nazarenko D. et al., Machine Learning and Knowledge Extraction 2026 Vol. 8 No. 10 Article 330
Automated microscopic image analysis is essential for quantitative microbiology, yet manual acquisition and generic recognition models struggle with morphological variability and scene artifacts. We address both ends of this pipeline. First, we present a low-cost, open-source acquisition system, based on an Arduino UNO R3 microcontroller and NEMA 17 stepper motors, that automates focusing, magnification, and ...
Added: October 14, 2026
Тукачев Н. В., González-Jiménez M., Ramakrishnan G. et al., Physical Chemistry Chemical Physics 2021 Vol. 23 No. 23 P. 13250–13260
Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition. However, understanding the vibrational basis of these mechanisms relies on theoretical models due to the lack of experimental evidence. Here we present the low-frequency vibrational spectra of G-quadruplexes (structures formed by four strands ...
Added: October 14, 2026
Springer, 2026.
This book highlights cutting-edge research in the field of network science, offering scientists, researchers, students and practitioners a unique update on the latest advances in theory and a multitude of applications. It presents the peer-reviewed proceedings of the XIV International Conference on Complex Networks and their Applications (COMPLEX NETWORKS 2025). The carefully selected papers cover ...
Added: October 13, 2026
Springer, 2026.
This book offers a comprehensive overview of the latest research, innovations, and practical applications in the field of sustainability, with a focus on construction materials and their use in building and civil engineering structures. As an outcome of the 3rd International Conference on Sustainability: Developments and Innovations (ICSDI 2026), this book presents a selection of ...
Added: October 13, 2026
Dmitriev A., Kornilov V., Batienkov R., Lecture Notes in Civil Engineering 2026 Vol. 886 P. 249–255
Numerous studies have provided compelling evidence that the probability distribution of avalanche sizes follows a power law, and that 1/f noise is present in the stochastic dynamics of landslides. We present a theoretical explanation of these phenomena within the framework of self-organized criticality theory, proposing a discrete-time model in the form of a sandpile cellular ...
Added: October 13, 2026
Dmitriev A., Shulman I., Lebedev A., Studies in Computational Intelligence 2026 Vol. 1265 P. 266–273
A discrete-time model is presented for the self-organization of the X/Twitter social network to the edge of a phase transition, characterized by avalanche-like propagation of information in the network. The model is based on the analogy between the critical dynamics of the X social network and sandpile cellular automata with Manna rule on the Chung-Lu ...
Added: October 13, 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
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