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Производительность современных вычислительных платформ в расчетах молекулярной динамики белок - мембранных систем
Труды НИИСИ РАН. 2018. Т. 7. № 4. С. 157–161.
The performance of molecular dynamics software package Gromacs was measured on various
hardware: desktop computers, clusters based on x84_64 processors or many integrated core processors, and
heterogeneous system with gaming graphic cards or general purpose GPU systems. The optimal choice of hardware
for molecular dynamics simulations is discussed.
Priority areas:
IT and mathematics
Language:
Russian
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
Snegirev A., Sychev S., Futures 2026 Vol. 183 P. 1–22
This study addresses the systemic identification and categorization of risks associated with AI development, arising from tensions between technological evolution and institutional, infrastructural, and economic contexts. Drawing on a constructionist methodology, we interpret technological risks as constitutive elements of expert communities' images of the future. Through in-depth interviews with 100 AI experts, proportionally representing corporate, ...
Added: September 23, 2026
Parshakov P., Paklina S., International Journal of Human-Computer Interaction 2026 P. 1–17
This study examines how emotional tone shapes user preference in human–large language model (LLM) interaction. Drawing on the Computers as Social Actors framework, we treat conversational AI as a social communicator whose affective cues influence user judgments. Using large-scale pairwise preference data from LMSYS Chatbot Arena, we model emotional tone through the Valence–Arousal–Dominance framework and ...
Added: September 23, 2026
Andrabi U., Wadood E., Ojha S. K. et al., IEEE Access 2026 Vol. 14 P. 103358–103375
The emergence of 5G networks, aimed at accommodating diverse service requirements such as enhanced Mobile Broadband (eMBB), Ultra-Reliable Low-Latency Communication (URLLC), and massive Machine-Type Communication (mMTC), has presented significant challenges in radio resource management and network slicing. In dynamic heterogeneous network systems, traditional heuristics and mathematical programming methods find it challenging to attain scalable multi-objective ...
Added: September 23, 2026
Paklina S., Parshakov P., Elena Rapoport, Scientometrics 2026 P. 1–26
Generative artificial intelligence has become a routine part of academic writing. While much of the debate has focused on questions of integrity and authorship, less attention has been paid to how AI-assisted writing may affect research evaluation itself. This paper asks a straightforward but important question: does the use of LLMs in academic writing change ...
Added: September 23, 2026
Diachkova E., Nikulin D., Кубкин Я. В. et al., American Journal of Respiratory and Critical Care Medicine 2026 Vol. 212
Accurate classification of a patient with pulmonary hypertension (PH) into one of five groups is fundamental for appropriate disease management strategies. The time from disease onset to correct diagnosis is unacceptably long in many cases. Chronic thromboembolic pulmonary hypertension (CTEPH) develops as a consequence of venous thromboemboli, resulting in a more pronounced hereditary predisposition to ...
Added: September 23, 2026
Xu Y., Ryabov F., Alexandrov I. et al., USA 2026 Vol. 6 No. 8 Article 101324
Центромеры обеспечивают расхождение хромосом, однако организацию их хроматина в пределах повторяющейся альфа-сателлитной ДНК долгое время было трудно изучать. Для решения этой задачи мы создали гаплотип-разрешённые аннотации сателлитной ДНК для полной диплоидной сборки генома человека T2T-HG002. Затем с помощью метода направленного метилирования с секвенированием длинных прочтений (DiMeLo-seq) мы картировали центромерный белок A (CENP-A), модификацию H3K9me3 и ...
Added: September 23, 2026
Hebbar P., Ryabov F., Alexandrov I. et al., Cell 2026 Vol. 189 P. 4891–4908.e12
The common marmoset is a New World monkey widely used to study primate evolution and human disease. We present a telomere-to-telomere (T2T) reference assembly for the species, plus three near-T2T haplotypes. These resolve previously inaccessible regions, including the centromeres, sex chromosomes, subterminal satellites, acrocentric chromosomes, and the major histocompatibility complex (MHC). We find marmoset centromeres ...
Added: September 23, 2026
Kertesz-Farkas A., Acquaye F. L., Journal of Proteome Research 2026 Vol. 25 P. 3764–3768
Ultimately, most tandem mass spectrometry (MS/MS) proteomics experiments aim to not just detect but also quantify the proteins in a given complex sample. Here, we describe an extension to the Crux MS/MS analysis toolkit to enable label-free quantification of peptides. We demonstrate that Crux’s new quantification command, which is modeled after the algorithms implemented in ...
Added: September 23, 2026
Maddalena L., Yildiz B., Del Vecchio Blanco F. et al., Risk Analysis 2026 Vol. 46 No. 4 P. 1–26
Heated tobacco products (HTPs) are marketed as alternatives to conventional cigarettes with a potential reduced risk profile. Yet, their actual impact on cancer and noncancer disease risk remains uncertain and requires rigorous quantitative assessment. In this study, we develop a unified and transparent computational framework for toxicological risk assessment of HTPs, integrating chemical emissions data ...
Added: September 22, 2026
Shabanov N., Kuricheva O., Kurbatova J. et al., / Series Working Papers SSRN "Department of Economics Ca’ Foscari University of Venice". 2026.
The carbon balance of an ecosystem is the difference between Gross Primary Productivity (GPP) and Ecosystem Respiration (Reco) as expressed by Net Ecosystem Exchange (NEE). While remote sensing retrievals of GPP have reached maturity, Reco estimation remains underexplored and ultimately cast bias on NEE. Here we present an end-to-end multi-scale analysis of the mechanism of ...
Added: August 21, 2026
Ponomarenko A., / Series Computer Science "arxiv.org". 2025.
This paper addresses the challenge of merging hierarchical navigable small world (HNSW) graphs, a critical operation for distributed systems, incremental indexing, and database compaction. We propose three algorithms for this task: Naive Graph Merge (NGM), Intra Graph Traversal Merge (IGTM), and Cross Graph Traversal Merge (CGTM). These algorithms differ in their approach to vertex selection ...
Added: July 30, 2026
Piontkovski D., / Series arXiv "math". 2026.
A noncommutative projective variety is defined, following Artin and Zhang, by a graded coherent algebra 𝐴. The category of coherent sheaves is then the quotient qgr(𝐴) of the category of finitely presented graded modules by the subcategory of torsion modules. We consider the categorical and polynomial entropies of the Serre twist, that is, of the ...
Added: June 23, 2026
Piontkovski D., / Series arXiv "math". 2025.
If a symmetric multilinear algebra is weakly nil, then it is Engel. This result may be regarded as an infinite-dimensional analogue of the well-known Jacobian theorem, which states that if a polynomial mapping has a polynomial inverse, then its Jacobian matrix is invertible. This refines a theorem of Gerstenhaber and partially answers a question posed ...
Added: June 23, 2026
Shipilov F., Barnyakov A., Ivanov A. et al., / Series Physics "arxiv.org". 2026.
A fast simulation of the detector response is a vital task in high-energy physics (HEP). Traditional Monte-Carlo methods form the backbone of modern particle physics simulation software but are computationally expensive. We present a machine-learning-based approach to fast simulation of the Focusing Aerogel Ring Imaging Cherenkov (FARICH) detector response. Given a particle track and momentum, ...
Added: May 19, 2026
Khnkoian G., Galigerov V., Grishichkin Y. et al., , in: Parallel Computational Technologies, 19th International Conference, PCT 2025, Moscow, Russia, April 8–10, 2025, Revised Selected Papers. (CCIS, volume 2891)Vol. 2891.: Springer, 2026. P. 532–545.
This work presents atomic-scale modeling of the perturbed flow of a Lennard-Jones fluid in a quasi-two-dimensional system containing one billion atoms. A statistically stationary flow regime corresponding to a Reynolds number of Re ≈ 1000 has been achieved, the flow structure has been analyzed, and the energy spectrum of velocities has been calculated. The results ...
Added: May 19, 2026