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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.
УРСС, 2005.
Изучается возможность автоматизированного построения математических теорий. Рассматривается дедуктивная система, основанная на языке логики предикатов первого порядка, объектами системы являются математические выражения или формулы, которые описывают математические объекты или их свойства. В дедуктивной системе выводятся математические определения и теоремы. Для доказательства теорем используются методы автоматического доказательства. Разработан алгоритм, выводящий часть формул системы. Для решения задачи используется аппарат математической ...
Added: October 7, 2026
Groshev Maksim, Rybakov Petr, Teterin N. et al., Sensors 2026 Article 6171
Manual assessment of soybean yield components, such as pod number, is laborious, time-consuming, and subjective. Existing computer-vision approaches based on object detection or instance segmentation perform poorly on close-range RGB imagery of soybean canopies due to severe occlusions, ambiguous plant boundaries, and the high cost of bounding-box annotation. To address these challenges, we propose a ...
Added: October 7, 2026
Томск: Издательство Томского государственного университета, 2026.
Материалы сборника Шестнадцатой Международной конференции «Новые информационные
технологии в исследовании сложных структур» (Москва, 21–25 сентября 2026 г.) ориентированы на
широкий круг специалистов, работающих на стыке теории информации, системного анализа и
прикладных предметных областей. В издание вошли результаты исследований, посвящённые
моделированию дискретных и стохастических структур управления и связи, разработке
высокопроизводительных вычислительных и телекоммуникационных систем, а также вопросам
цифровой трансформации образования, архитектурно-градостроительного проектирования,
экологического ...
Added: October 6, 2026
Серебренников Д. А., Belov A. V., Информационные технологии и вычислительные системы 2026 № 3 С. 157–169
В условиях роста стоимости энергоресурсов и необходимости повышения энергоэффективности производственных процессов особую актуальность приобретает задача оптимизации энергопотребления промышленных предприятий. В данной работе рассматривается подход к управлению энергозатратами машиностроительного предприятия на основе методов многокритериальной оптимизации. Постановка задачи включает несколько целевых функций: минимизацию энергопотребления, минимизацию стоимости электроэнергии с учётом тарифных ограничений и максимизацию производственной эффективности. Для решения ...
Added: October 5, 2026
Kuninets A., IEEE Transactions on Information Theory 2026 P. 1–1
In this work we study the applicability of Quasi-Cyclic Subfield Subcodes of Dual Elliptic (QC-SSDE) codes for integration into code-based cryptographic schemes. Detailed algorithms are provided for constructing parity-check matrices as well as block-circulant parity-check matrices for this family of codes, accompanied by empirical results that enable the construction of QC-SSDE codes with predetermined dimensions. ...
Added: October 3, 2026
Zykov S. V., Уфимцев Г. А., Моделирование, оптимизация и информационные технологии 2026 Т. 14 № 8 С. 1–13
Информационные системы формируют большие объёмы событийных журналов, которые используются для анализа работы приложений и сервисов. При этом события могут поступать в аналитический контур позже момента их фактического возникновения и не в исходном порядке. Такая рассинхронизация приводит к ошибкам при построении агрегированных временных показателей, а регулярный полный пересчёт многомерного аналитического куба требует значительных вычислительных затрат. Целью ...
Added: October 2, 2026
Polarization of opinions in the group: a modeling algorithm considering the dynamics of social bonds
Chebotarev V., Andreyuk D., Elizarova Anastasiya et al., Procedia Computer Science 2022 Vol. 213 No. C P. 596–601
The dynamics of opinion in a group are of interest for a number of practical purposes. In particular, consensus helps and polarization of opinions hinders cohesive teamwork. Existing approaches for modeling opinion dynamics mostly do not take into account the dynamism of social relations in a group. This paper proposes an algorithm and a program ...
Added: October 2, 2026
Konstantinov A., Elizarova Anastasiya P., Utkin L., Computing, Telecommunications and Control 2026 Vol. 19 No. 1 P. 16–25
Decision trees and their ensemble extensions, such as random forests, are widely used as classification models due to their simplicity and interpretability. However, in many real-world tasks where class labels overlap in the feature space, standard decision trees rely on hard splits that create fragile decision boundaries. In these regions, small perturbations in the input ...
Added: October 2, 2026
Ekaterina D. Riumina, Klink G. V., Alekseeva E. et al., PNAS, США 2026 Vol. 123 No. 35 P. 1–20
The role of escape from the cytotoxic T cell (CTL) response in SARS-CoV-2 evolution remains controversial. Here, we study the origin and spread of SARS-CoV-2 variants whose mutations reduce presentation by the HLA class I alleles common in human populations. We find that 35% of mutations that are characteristic of the variants of concern, and ...
Added: October 2, 2026
Prokhorov A., Burda M., Journal of Computational and Graphical Statistics 2026 P. 1–13
Bayesian nonparametric density estimation procedures are typically based on single-scale priors, such as Dirichlet process mixtures. Alternative multiscale density priors built on decision trees have many well-known advantages, including the ability to characterize abrupt local changes and to provide an estimate with a desired level of resolution. Despite their theoretical appeal, multiscale methods have typically ...
Added: October 2, 2026
Aly Ismailov, Poptsova M., Plos One 2026 Vol. 21 No. 9 Article e0355902
Added: October 2, 2026
Zlotnik A., Математические заметки 2026 Т. 120 № 6 С. 1005–1009
Численным методам решения систем газодинамических уравнений посвящена обширная литература. Ранее было разработано и успешно апробировано специальное семейство симметричных по пространству консервативных разностных методов, основанных на предварительной кинетической, точнее, квазигазодинамической (КГД), регуляризации этих уравнений. Актуальной задачей является построение численных методов, которые обладают не только свойством консервативности по массе, импульсу и полной энергии, но и удовлетворяют условиям энтропийной ...
Added: October 1, 2026
International Joint Conferences on Artificial Intelligence, 2026.
Added: October 1, 2026
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
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
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