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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.
Ryumina E., Aksenov A., Сысоев Д. С. et al., IEEE Computer Society, 2026.
Ambivalence/hesitancy recognition in unconstrained videos is a challenging problem due to the subtle, multimodal, and context-dependent nature of this behavioral state. In this paper, a multimodal approach for video-level ambivalence/hesitancy recognition is presented for the 10th ABAW Competition. The proposed approach integrates four complementary modalities: scene, face, audio, and text. Scene dynamics are captured with ...
Added: September 30, 2026
Knyazev E., Чеботарева О. Е., М.: Издательский дом НИУ ВШЭ, 2026.
This teaching and learning guide provides a concise overview of the theoretical and practical aspects of the basic skills required to work in a biological laboratory. It also includes protocols for practical classes conducted as part of the introductory professional training placement for first-year students in the Bachelor’s programme in Cell and Molecular Biotechnology at ...
Added: September 30, 2026
Ivanov F., Kotov F., IEEE Access 2026 Vol. 14 P. 104662–104679
U-UV codes, based on the Plotkin (U, U + V) construction, provide a unified framework that includes polar and Reed–Muller codes and enables flexible design through the choice of component codes. While modern capacity-approaching codes achieve excellent performance at large block lengths, their efficiency at short and moderate lengths remains limited, especially under low-latency constraints. ...
Added: September 30, 2026
Djambong Tenkeu H., Institute for System Programming of the RAS, 2026.
Added: September 29, 2026
Ryskina H., Knyazev E., Вопросы биологической, медицинской и фармацевтической химии 2026 Т. 29 № 9 С. 84–91
Introduction. The active integration of rapidly developing omics and computer technologies in the 21st century has led to a breakthrough in understanding the principles of the functioning of living systems. One of the dynamically developing integrative areas in biology is biological modeling. The fundamental paradigm has been the methodology that allows for the prediction of ...
Added: September 29, 2026
Ivanashev Y., Доклады Российской академии наук. Математика, информатика, процессы управления (ранее - Доклады Академии Наук. Математика) 2026 Т. 529 С. 93–101
Язык L является нижним для релятивизируемого сложностного класса C, если CL=C. Для классов #P, GapP и SpanP известны точные нижние классы языков: Low(#P) = UP ∩ coUP, Low(GapP) = SPP и Low(SpanP) = NP ∩ coNP. В этой статье мы доказываем, что Low(TotP) = P, и приводим характеризации нижних классов функций для #P, GapP, TotP ...
Added: September 28, 2026
Piliugin L., Antropov A., Lobashev E. et al., Journal of Nuclear Materials 2026 Vol. 632 Article 156876
The effects of dislocations on the mobility of gas nanobubbles pinned to them are considered as novel unex- plored mechanisms of accelerated fission gas release and investigated using classical molecular dynamics of helium bubbles in FCC aluminum. Non-equilibrium methods are developed to calculate the mobility of a pinned bubble both along and across the dislocation ...
Added: September 28, 2026
Kashpurovich I., Oleynichenko A., Stegailov V., Supercomputing Frontiers and Innovations 2026 Vol. 13 No. 1 P. 52–73
We report a high-performance implementation of the resolution-of-the-identity Hartree–Fock method that fully exploits the permutational symmetry of three-center electron repulsion integrals (ERI). The present implementation adopts a hybrid MPI+OpenMP parallelization strategy. Two different algorithmic approaches (with and without the pre-transformation of ERIs) are compared. A custom data layout introduced previously is employed. Designed to efficiently ...
Added: September 28, 2026
Teregulov T., Loubenets E. R., / Series Quantum Physics "arXiv". 2026. No. 2609.31472.
We develop a new three-party quantum secret-sharing (QSS) protocol based on a three-qubit W state. This protocol encodes the secret-sequence bits using X gates and employs randomly selected Hadamard operations and measurement bases to generate information and security-test rounds. We evaluate the efficiency of the proposed protocol and analyze its security against an internal adversary ...
Added: September 28, 2026
Silakov D., Системный администратор 2026 С. 84–89
Social media users rarely think about what lies behind the beautiful facade of activity feeds, teeming with photos and video stories. However, the widespread popularity of such platforms generates a huge amount of all sorts of content that needs to be stored, processed quickly, and displayed, and in the era of AI, it also needs ...
Added: September 28, 2026
Prokhorov A., Wei Z., Sang H. et al., Journal of Productivity Analysis 2026 Vol. 65 P. 1–16
The stochastic frontier model (SFM) is widely employed in the analysis of productivity and efficiency, yet strict parametric forms, such as the Cobb-Douglas and Translog functions, are often assumed for modeling production, leading to potential misspecification issues. While semi- and nonparametric SFMs offer greater flexibility, they face challenges in imposing monotonicity and concavity to maintain ...
Added: September 28, 2026
Qian X., Guan X., Zhang B. et al., Journal of Global Optimization 2026
Inverse quickest path problem on networks ...
Added: September 27, 2026
Gureev M., Advanced Science 2026 P. 1–13
Targeted protein degradation represents a promising therapeutic strategy, yet its broader application is often limited by the scarcity of usable E3 ligases. Glutathione peroxidase 4 (GPX4) is a key target for inducing ferroptosis, but achieving sustained and potent inhibition remains challenging with conventional enzymatic inhibitors. Herein, we report the first small‐molecule GPX4 degraders that incorporate ...
Added: September 26, 2026
Switzerland: Springer Cham, 2026.
This volume gathers selected, peer-reviewed contributions presented at the 19th Conference of the International Federation of Classification Societies (IFCS 2026), held on 14–16 July 2026 in Milan, Italy. Reflecting the volume’s motto, Navigating Complexity – Statistical Methods, Data Analysis, and Machine Learning for Actionable Insights, the papers showcase modern methodologies and real-world applications designed to extract ...
Added: September 25, 2026
Kraevskiy A., Sokolovskiy E., Prokhorov A., Emerging Markets Review 2026 No. 74 P. 1–19
Financial markets of emerging economies are vulnerable to extreme and cascading information spillovers, surges, sudden stops and reversals. With this in mind, we develop a new online early warning system (EWS) to detect what is referred to as ‘concept drift’ in machine learning, as a ‘regime shift’ in economics and as a ‘change-point’ in statistics. ...
Added: September 25, 2026
Дубич Е. В., Schagin D., Славянский форум 2026 № 2 (52) С. 560–565
The paper compares HTTP/2 and HTTP/3 for static resource transfer under software-simulated network degradation. The experiment shows that HTTP/3 is not universally faster, but it is more stable as latency and packet loss increase. ...
Added: September 25, 2026
Joulitov A.K., Lomazova I.A., Proceedings of the Institute for System Programming of the RAS 2026 Vol. 38 No. 4(2) P. 215–224
In process mining, DFG (Directly-Follows Graph) models are popular due to their simplicity and clarity. However, if a process is acyclic but contains concurrent events, standard algorithms for discovering DFG models can generate "fake" cycles that do not actually exist in the event log. These cycles hinder the analysis of information processes, significantly reducing the ...
Added: September 24, 2026
Добрина Д. Н., Nesterenko A., Прикладная дискретная математика. Приложение 2026 № 19 С. 151–159
Работа содержит результаты формального анализа криптографических механизмов, входящих в состав проекта методических рекомендаций «Защищенный универсальный протокол передачи данных и управления микросхемой интеллектуальной карты» (протокол SECUNDA). Получена формальная модель и перечень трудноразрешимых математических задач, трудоёмкостью решения которых можно оценить стойкость используемых криптографических механизмов. ...
Added: September 24, 2026
I.I. Sergeev, I.A. Lomazova, Modeling and Analysis of Information Systems 2026 Vol. 33 No. 3 P. 394–419
Object-centric process mining has emerged as a powerful paradigm for analyzing event data involving multiple interacting business objects. Existing discovery techniques often rely on object-centric Petri nets with fixed arc multiplicities, limiting their ability to represent parametric resource consumption and production patterns and to capture quantitative dependencies between interacting object types. In this paper, we ...
Added: September 24, 2026
Ivan Bulychev, Savchenko A., AI 2026 Vol. 7 No. 9 Article 380
Recent advances in large language model (LLM) agents have shown promise for autonomous decision-making in recommender systems. However, existing approaches suffer from two fundamental limitations: flat agent memories that conflate different information modalities and prohibitive computational costs that prevent scaling beyond a few hundred users. We propose Hybrid-GraphRAG, a recommender system that integrates hierarchical agent ...
Added: September 24, 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