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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.
Derkacheva A., Sakirkina M., Kraev G. et al., /. 2026.
Comprehensive data on natural hazards and their consequences are crucial for effective for risk assessment, adaptation planning, and emergency response. However, many countries face challenges with fragmented, inconsistent, and inaccessible data, particularly regarding local-scale events. To address this data gap in Russia, we developed an end-to-end processing pipeline that scrapes news from various online sources, ...
Added: April 28, 2026
Domrin V. I., Malova H. V., V. Yu. Popov et al., Cosmic Research 2026 Vol. 64 No. 2 P. 238–252
During magnetospheric perturbations a relatively thin current sheet with thickness about several
proton gyroradii forms in the Earth’s magnetotail. In a framework of the kinetic model describing current
sheet thinning in the magnetotail, the processes of its formation are investigated depending on the normal
magnetic field magnitude which affects both the current sheet structure and particle dynamics within ...
Added: April 27, 2026
Tsareva O. O., Malova H. V., V. Yu. Popov et al., Plasma Physics Reports 2026 Vol. 52 No. 2 P. 179–185
The influence of asymmetry of plasma sources on the structure and spatial localization of a superthin
current sheet (STCS) supported by demagnetized electrons is studied using a self-consistent model. The
simulation takes into account the presence of a single plasma source in the northern hemisphere, which
makes the plasma flow asymmetric. It is demonstrated that the asymmetry of ...
Added: April 27, 2026
NY: Association for Computing Machinery (ACM), 2026.
It is our great pleasure to welcome you to the 35th edition of the Web Conference to be held on June 29 – July 3, 2026, in Dubai, United Arab Emirates.
Following discussions with our partners and key stakeholders, we have taken the decision to postpone the ACM Web Conference 2026, initially planned for April 2026. ...
Added: April 23, 2026
Kashevnik A., Glekler E., Artemenko E. et al., Scientific data 2026 Article 7209
We present a multimodal dataset containing electroencephalography (EEG), electrocardiography (ECG), and video recordings from 49 participants. Each participant completed a single session lasting approximately 45 minutes. During each session they performed five tasks: resting state, inward concentration (focusing on the center of the forehead), outward concentration (visual search), and mind-wandering. EEG data were recorded from ...
Added: April 23, 2026
Kychkin A., Chernitsin I., Прикладная информатика 2026 Т. 21 № 1 С. 40–58
The results of the development of a software microservice embedded in atmospheric air quality monitoring systems to support the identification of industrial pollution sources are presented. The emission and subsequent spread of harmful substances in the lower layers of the atmosphere is dynamic and characterized by high uncertainty due to the specific features of technological ...
Added: April 23, 2026
IEEE, 2026.
Added: April 21, 2026
Kopoleva E., Sergey A. Tsymbal, Kuchur O. et al., Drug Delivery and Translational Research 2026 P. 1–16
Multidrug resistance (MDR) remains one of the principal challenges in cancer chemotherapy, necessitating new strategies to restore drug efficacy. In this study we developed and characterize a redox-responsive nanoplatform based on trithiocyanuric acid and polyethylene glycol (TTCA-PEG NPs) as a potential tool to overcome MDR and provide a biocompatible delivery system for conventional antitumor drugs. ...
Added: April 20, 2026
Wang M., Xiao Y., Braslavski P. et al., Mathematics 2026 Vol. 14 No. 8 Article 1286
Increasingly shaped by heterogeneous on-chain activity rather than a single shared market process, this study investigates 7-day-ahead forecasting using 147 market and on-chain indicators across eight major blockchain ecosystems from October 2023 to April 2025. We benchmark statistical, deep-learning, and foundation-model baselines under multiple feature-selection pipelines using both error metrics and Diebold–Mariano tests. TiRex achieves ...
Added: April 20, 2026
Shchur L., Antonov D., Burovski E., International Journal of Bifurcation and Chaos in Applied Sciences and Engineering 2026 P. 1–9
We present a simple model that simulates the possible influence of one society on another. Specifically, two societies evolve deterministically according to the well-known Nowak-May spatial game with the addition of mutual influence through connections that reflect the current states of the societies. This may be related to the influence of a global information resource ...
Added: April 20, 2026
Ebraheem A., Информационные процессы 2025 Т. 25 № 4 С. 787–798
The article proposes a method for planning the placement of access points and gateways inside buildings for constructing Internet of Things networks. The basis of the method is the use of information from a building information model, which makes it possible to easily take into account both the geometry and the physical and technical characteristics ...
Added: April 19, 2026
Makarov D. M., Kalikin N., Gurikov P. et al., Journal of Supercritical Fluids 2026 Vol. 235 Article 106979
Supercritical CO2 (scCO2 ) is an environmentally friendly solvent, but its low polarity limits the solubility of polar compounds. Cosolvents are commonly used to enhance solvation capability, yet comprehensive datadriven studies are scarce. We compiled the largest dataset to date — 4401 experimental solubility records with 22 cosolvents for 93 nonionic solutes, plus 4855 records ...
Added: April 19, 2026
G.V.Klink, Gulov D. M., Elumeeva T. G. et al., Журнал общей биологии 2024 Т. 85 № 2 С. 83–94
Plant functional traits are important for the formation of plant communities and for the ability of plants to dominate there. The comparison of mean trait values of organisms within community with that for the random samples of the local biota allows estimating the importance of the trait for the formation of the community composition. The ...
Added: April 19, 2026
G.V.Klink, Semenkov I. N., Enchilik P. R., Science of the Total Environment 2025 Vol. 998 Article 180219
Natural regeneration of forest soils affected by agricultural practices is a common phenomenon in many regions worldwide, particularly in boreal ecosystems. Affecting soil quality, the partitioning of extractable fractions of heavy metals and metalloids (HMMs) is not studied during natural regeneration. The following stages of natural regeneration after plowing have been identified in the Smolenskoye ...
Added: April 19, 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
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
Rusina P., Gandalipov E., Abdyusheva Y. et al., Cancers 2023 Vol. 15 No. 15 Article 3766
General toxicity for the organism is a major drawback of anticancer drugs. Development of new generation chemotherapeutics requires the knowledge about macromolecules critical for tumor cell viability. Among these species (called therapeutic targets), the protein kinases are the established enzymes. However, the parts of protein kinases that are supposed to be targeted by drugs can ...
Added: November 1, 2023
Nikita A. Kosarim, Armeev G., Alexey K. Shaytan et al., 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 ...
Added: September 4, 2023
van Tilborg D., Grisoni F., Journal of Chemical Information and Modeling 2022 Vol. 62 No. 23 P. 5938–5951
Machine learning has become a crucial tool in drug discovery and chemistry at large, e.g., to predict molecular properties, such as bioactivity, with high accuracy. However, activity cliffs─pairs of molecules that are highly similar in their structure but exhibit large differences in potency─have received limited attention for their effect on model performance. Not only are these ...
Added: December 22, 2022
Armeev G., Gribkova A., Shaitan A., Frontiers in Molecular Biosciences 2022 Vol. 9 Article 1070489
Twenty-five years have passed since the appearance of the first atomistic model of the nucleosome structure, and since then the number of new structures has gradually increased. With the advent of cryo-microscopy, the rate of accumulation of models has increased significantly. New structures are emerging with different histone variants and a variety of proteins that ...
Added: December 9, 2022
Sivkina A., Karlova M., McCullough L. et al., Communications Biology 2022 Vol. 5 No. 1 Article 2
FACT is a histone chaperone that participates in nucleosome removal and reassembly during transcription and replication. We used electron microscopy to study FACT, FACT:Nhp6 and FACT:Nhp6:nucleosome complexes, and found that all complexes adopt broad ranges of configurations, indicating high flexibility. We found unexpectedly that the DNA binding protein Nhp6 also binds to the C-terminal tails ...
Added: December 9, 2022