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Molecular Dynamics Simulations of Nucleosomes Are Coming of Age
Wiley Interdisciplinary Reviews: Computational Molecular Science. 2024. Vol. 14. No. 4. Article e1728.
Fedulova A., Armeev G., Romanova T., Singh-Palchevskaia L., Kosarim N., Motorin N., Komarova G., Shaitan A.
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, including transcription, DNA replication and repair. They mediate genome regulation at the epigenetic level, bridging the discrete nature of the genetic information encoded in DNA with the analog physical nature of the intermolecular interactions required to access that information. Due to their relatively large size and dynamic nature, nucleosomes are difficult objects for experimental characterization. Molecular dynamics (MD) simulations have emerged over the years as a useful tool to complement experimental studies. Particularly in recent years, advances in computing power, refinement of MD force fields and codes have opened up new frontiers in terms of simulation timescales and quality for nucleosomes and related systems. It has become possible to elucidate in atomistic detail their functional dynamics modes such as DNA unwrapping and sliding, to characterize the effects of epigenetic modifications, DNA and protein sequence variation on nucleosome structure and stability, to describe the mechanisms governing nucleosome interactions with chromatin-associated proteins and the formation of supranucleosome structures. In this review, we systematically analyzed all-atom MD simulation studies of nucleosomes and related structures published since 2018 and discussed their relevance in the context of older studies, experimental data, and related coarse-grained and multiscale studies.
Edward R. Rzaev, Aleksandr Y. Romanov, Andrey M. Sukhov, IEEE Access 2026
This work presents a hierarchy of strictly local fault-tolerant routing algorithms for 3D mesh networks-on-chip, culminating in an algorithm that combines a live-neighbor selection rule with a bounded single-hop rollback mechanism. The proposed algorithms operate exclusively on immediate neighbor information, maintain O(1) per hop complexity, and require no global topology knowledge, additional virtual channels, or ...
Added: July 23, 2026
Pislyakov V., Вестник Томского государственного университета. Филология 2026 № 101 С. 175–192
This article examines the use of proverbs in academic texts—specifically, articles published in Russian research journals. For the experiment, ten proverbs were selected as the intersection of two fundamentally different paremiological surveys aimed at compiling lists of popular or common Russian proverbs. One of these surveys was conducted by the classic of paremiology, G.L. Permyakov, ...
Added: July 22, 2026
Korogod D., Shapeev A., Novikov I., Physical Review B: Condensed Matter and Materials Physics 2026 Vol. 114 No. 2 Article 024104
We present two models with explicit long-range electrostatics in the form of Coulomb interactions. Both models include point charges depending on their local atomic environments, and the second model also conserves a total charge of an atomic system. We combine the proposed long-range models with the local moment tensor potential (MTP) and demonstrate that they ...
Added: July 22, 2026
Sozykin K., Rybin N., Chertkov A. et al., Physical Review B: Condensed Matter and Materials Physics 2026 Vol. 113 No. 22 Article 224111
The global optimization of atomic clusters represents a fundamental challenge in computational chemistry and materials science due to the exponential growth of local minima with system size (i.e., the curse of dimensionality). We introduce a framework that overcomes this limitation by exploiting the low-rank structure of potential energy surfaces through tensor train (TT) decomposition. Our ...
Added: July 22, 2026
Михайлов И. А., Machine Learning and Knowledge Extraction 2026 Vol. 8 No. 1 Article 8
Whole-slide histology images (WSIs) can exceed 100 k × 100 k pixels, making direct pixel-level segmentation infeasible and requiring patch-level classification as a practical alternative for downstream WSI segmentation. However, most approaches either treat patches independently, ignoring spatial and biological context, or rely on deep graph models prone to oversmoothing and loss of local tissue ...
Added: July 16, 2026
Kuninets A., Malygina E., Leevik A. G. et al., Journal of Computer Virology and Hacking Techniques 2026 No. 22 Article 62
In this work, we investigate the application of Barnes–Wall lattices in post-quantum cryptographic schemes. We survey and analyze several constructions of Barnes–Wall lattices, including subgroup chains, the generalized k-ing construction, and connections with Reed-Muller codes, highlighting their equivalence over both Z[i] and Z. Building on these structural insights, we introduce a new algorithm for efficient ...
Added: July 16, 2026
Silakov D., Системный администратор 2026 № 5 С. 46–51
В предыдущей статье про Open Source в КНР [1] мы рассказали про Alibaba – крупную корпорацию, занимающую тридцатое место в рейтинге самых значимых мировых брэндов за 2025 год [2]. Место почетное, но не первое среди китайских компаний – на тринадцатом месте расположилась Tencent, разработчик WeChat и ряда других продуктов, широко используемых нашими восточными соседями. Tencent ...
Added: July 14, 2026
IEEE, 2026.
Added: July 13, 2026
Switzerland: Springer, 2026.
This volume contains the refereed proceedings of the 25th International Conference on Mathematical Optimization Theory and Operations Research (MOTOR 2026) 1 held during July 6–11 in a picturesque place near Lake Baikal, Irkutsk, Russia. The MOTOR conference is a direct successor and scientific inheritor of several prominent events on mathematical programming, combinatorial and stochastic optimization, ...
Added: July 12, 2026
Шиманогов И. Н., Vyalyi M., Дискретный анализ и исследование операций 2025 Т. 32 № 4(166) С. 213–230
A well-studied class of algorithmic problems is that of regular realizability: checking the non-emptiness of the intersection of a regular language with a given language. This problem has a natural algebraic interpretation: verifying whether an element of a Boolean algebra belongs to the kernel of a certain homomorphism. This motivates the consideration of an analogous ...
Added: July 12, 2026
Surkov A., Ignatenko V., Koltcov Sergei, Computers, Materials and Continua 2026
Large language models have recently demonstrated promising capabilities in mathematical reasoning; however, their performance on tasks requiring strict symbolic manipulation, such as solving differential equations, remains limited, especially for compact models. In this work, we investigate whether activation steering combined with reinforcement learning can improve the quality of solutions generated by pretrained language models without ...
Added: July 8, 2026
Springer, 2027.
The series Lecture Notes in Computer Science (LNCS), including its subseries Lecture Notes in Artificial Intelligence (LNAI) and Lecture Notes in Bioinformatics (LNBI), has established itself as a medium for the publication of new developments in computer science and information technology research, teaching, and education. LNCS enjoys close cooperation with the computer science R & ...
Added: July 8, 2026
IEEE, 2026.
The purpose of the 2026 IEEE Ural-Siberian Conference on Biomedical Engineering, Radioelectronics and Information Technology (USBEREIT) is to bring together researchers and practitioners from multiple areas of radio science, including biomedical engineering, radioelectronics, microelectronics, information technology, smart energy, information security and others. ...
Added: July 8, 2026
Маликов М. А., Монахова Э. А., Rzaev E. et al., Ученые записки Казанского университета. Серия: Физико-математические науки 2026 Т. 168 № 2 С. 269–286
This article examines series of families of two-dimensional circulant networks with rectangular
L -shapes, optimal in diameter, as network-on-chip topologies with a minimal number of crossings
between the links and a bounded length of the maximum link that does not depend on the network
size. New network-on-chip routing algorithms, which use the coordinates of three adjacent zeros in
the ...
Added: July 8, 2026
Pilé I., Deng Y., Shchur L., Physical Review B: Condensed Matter and Materials Physics 2026 Vol. 114 No. 1 Article 014101
We investigate the spatial overlap of successive spin configurations in Markov chain Monte Carlo simulations using the local Metropolis algorithm and the Swendsen-Wang and Wolff cluster algorithms. We examine the dynamics of these algorithms for models in different universality classes: Ising model, Potts model with three components, and four-state Potts model. The overlap of two ...
Added: July 6, 2026
М.: Наука и технологии, 2026.
«Телекоммуникации» ежемесячный рецензируемый производственный, информационно-аналитический и учебно-методический журнал выходит в свет с июля 2000 г.
Для руководителей и работников промышленности, научно-исследовательских и проектно-конструкторских институтов, высших учебных заведений, аспирантов и студентов, а также для специалистов, разрабатывающих, выпускающих и эксплуатирующих средства телекоммуникаций.
Новости разработок и производства, прогнозы развития, защита информации, Нормативные, справочные, аналитические и учебно-методические материалы.
Переход к глобальному информационному ...
Added: July 4, 2026
МФТИ, 2025.
абота редакции научного журнала «Труды Московского физико-технического института» (кратко «Труды МФТИ»), редакционной коллегии и редакционного совета осуществляется в соответствии с Положением, утвержденным ректором института. В состав редакционной коллегии входят руководители института, факультетов, институтских и факультетских кафедр. Главный редактор журнала —президент МФТИ, член-корр. РАН Кудрявцев Н.Н.
Журнал «Труды МФТИ» входит в базу данных РИНЦ (Российский Индекс Научного Цитирования) и доступен в электронной ...
Added: July 4, 2026
Hualin M., Jie Z., Jerome Y. et al., Journal of Internet Technology 2026 Vol. 27 No. 3 P. 367–382
In open, interference-prone scenarios, the scarcity of precisely annotated signal samples limits the application of deep learning–based modulation identification, which generally relies on extensive labeled data for stability. Relation Networks, as an emerging class of deep learning models, exhibit rapid convergence in few-shot learning tasks. Motivated by the fast convergence property of relation-based learning and ...
Added: July 3, 2026
Osipov D., Информационно-управляющие системы 2026 № 3 С. 49–62
Introduction: In many communication systems under construction and those to be created power control and channel estimation techniques developed for the previous generation communication systems fail to provide desired precision. One way to solve this problem is to use order-statistics-based reception techniques that do not need channel estimation or power control. To ensure the desired ...
Added: July 3, 2026
Окнина Л. Б., Подлепич В. В., Sieber I. et al., Физиология человека 2026 Т. 52 № 3 С. 5–15
The aim of this study was to evaluate the frequency following response (FFR) for the analysis of the intact perception of syllables in humans. For this purpose, event-related potentials (ERPs) in response to isolated Russian syllables were recorded and analyzed in 29 healthy persons in two frequency ranges, standard (1-40 Hz) and high frequency (70-150 ...
Added: June 30, 2026
Springer, 2026.
This book presents established and new research on the close connections between graph games and systems of logic, particularly existing and newly designed modal logics. The volume utilizes two graph games – the sabotage game and the hide-and-seek game – to demonstrate the natural interplay between designing new graph games and exploring new kinds of ...
Added: June 30, 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
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