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MDProcessing.jl: Julia Programming Language Application for Molecular Dynamics Trajectory Processing
P. 209–222.
Pisarev V., Panov M.
Molecular simulations and molecular dynamics in particular are among the most performance-demanding computational methods. As the scale of simulations increases, the task of processing the simulation results becomes a computationally-hungry problem as well. The usual approach to build easy-to-use post-processing tools is based on providing an interface to a high-performance library called from a scripting language such as Python. We overview the advantages of using Julia programming language for building such tools, due to its easy surface syntax close to that of scripting languages and JIT compilation enabling high runtime performance. Then, we overview the package MDProcessing.jl written in Julia, regarding its customizability, abstractions for common processing workflows and performance characteristics.
Publication based on the results of:
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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 ...
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Alzheimer’s disease (AD) pathogenesis is correlated with the membrane content
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The ability to predict transport properties, such as viscosity, through molecular simulation is a valuable advantage. Obtaining reliable estimates for these properties can be more challenging compared to equilibrium properties. Our manuscript focuses on an in-depth discussion of two prominent methods for predicting transport properties: equilibrium molecular dynamics (EMD) using the Green−Kubo approach and nonequilibrium ...
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The work is dedicated to the study of the fusion of lipid droplets — organelles consisting of a core of fatty acids, such as triolein, surrounded by a monolayer of phospholipids. In view of the relatively simple implementation and universality of the effect of the lipid composition of the LC membranes on the efficiency of ...
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Two-dimensional C60 carbon allotropes have gained much attention since their first synthesis in 2022, but many of their thermophysical and mechanical properties remain unreported in the literature. In this article, we performed a high-temperature molecular dynamics study of quasi-hexagonal (qHP) and quasi-tetragonal (qTP) C60 phases using the modern machine-learning interatomic potential GAP-20. We show that, contrary to ...
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To accelerate the development of liquid ion-selective barriers based on ethers, we compare the all-atom
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Lenev D. Y., Zakharov S. A., V. V. Pisarev, Russian Journal of Physical Chemistry A 2024 Vol. 98 No. 12 P. 2816–2822
Molecular dynamics is used to calculate the vapor–liquid equilibrium and liquid–vapor surface
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Ahmad Ostovari Moghaddam, Fereidonnejad R., Moaddeli M. et al., Computational Materials Science 2025 Vol. 247 Article 113534
The second nearest-neighbor modified embedded-atom method (2NN-MEAM) interatomic potentials were developed for Zr-X (X = Co, Fe, Ni) binary alloys. The structural, mechanical and thermodynamic properties of various stable and metastable phases in Zr-Co, Zr-Fe and Zr-Ni binary systems were calculated by molecular dynamic (MD) simulation using the developed 2NN-MEAM potentials. The results obtained by ...
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This study presents in a systematic manner the key modeling results corroborated by experimental
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In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and their interactions with membranes. The objective was to discern the nature of these interactions and understand how peptide sequence and structure influence antimicrobial activity. We introduced modifications into the established cyclic AMP peptide, ...
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Fighting Celiac Disease: Improvement of pH Stability of Cathepsin L In Vitro by Computational Design
Chugunov A. O., Dvoryakova E. A., Dyuzheva M. A. et al., International Journal of Molecular Sciences 2023 Vol. 24 No. 15 Article 12369
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M. A. Gureev, Danilkina N. A., Khlebnikov A. F. et al., Russian Journal of General Chemistry 2024 Vol. 94 No. 1 P. S100–S119
Enediyne antibiotics are a class of potent DNA-cleaving antitumor agents. Searching for promising analogs of enediyne antibiotics, the features of interaction with the DNA of enediynes fused with heterocycles have been studied using molecular modeling methods. Depending on their structure, 10-membered heteroenediynes can exhibit both intercalator properties and bind to the minor groove of DNA. ...
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Hydrocalumite, is a hydration product of aluminum-rich cements, and is known in cement chemistry as an AFm phase. Structurally, it belongs to the family of layered double hydroxides, or “anionic clays”, where positively charged crystal layers require the presence of negatively charged ions in the interlayer space. Therefore, AFm phases can serve as potential adsorbents ...
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Лукьянчук В. Г., Ланкин А. В., Norman G., Письма в Журнал экспериментальной и теоретической физики 2023 Т. 118 № 8 С. 609–614
An atomistic model of dehydrated Cl-doped double layer aluminum–lithium hydroxide Li⋅Al2(OH)6Cl (DALH-Cl), which is a promising material for the sorption of lithium from weak brines, has been developed. The effective charges of the atoms of the system have been determined using the density derived electrostatic and chemical (DDEC6) methods. A molecular dynamics analysis of DALH-Cl has been ...
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Borisevich S., Khamitov E., Maxim A. Gureev et al., Viruses 2022 Vol. 14 No. 1 Article 119
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Borisevich S. S., Maxim A. Gureev, Yarovaya O. I. et al., Journal of Biomolecular Structure and Dynamics 2022 Vol. 40 No. 12 P. 5481–5492
The development of new anti-influenza drugs remains an active area, and efforts in this direction will likely continue far into the future. In this paper, we present the results of a theoretical study explaining the mechanisms behind the antiviral activity of camphor derivatives. These include camphecene and a number of its analogues. The compounds tested ...
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Yarovaya O., Shcherbakov D., Borisevich S. et al., Viruses 2022 Vol. 14 No. 6 Article 1295
In the present work we studied the antiviral activity of the home library of monoterpenoid derivatives using the pseudoviral systems of our development, which have glycoproteins of the SARS-CoV-2 virus strains Wuhan and Delta on their surface. We found that borneol derivatives with a tertiary nitrogen atom can exhibit activity at the early stages of ...
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