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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:
Корзникова Е. А., Babicheva R. I., Davletbakov A. A. et al., JOURNAL OF MATERIALS SCIENCE: MATERIALS IN ENGINEERING 2026 Vol. 21 Article 84
The influence of crack position and its size on short-range ordering (SRO) and high-temperature cyclic deformation behavior of refractory high-entropy alloy (RHEA) HfNbTiZr using bicrystal models has been investigated by combined Monte-Carlo (MC) and molecular dynamics (MD) simulations. It was revealed that the SRO process is affected not only by the crack size, namely the ...
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Alzheimer’s disease (AD) pathogenesis is correlated with the membrane content
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Vapor–liquid surface tension is calculated on the evaporation curve of n-nonane in the SAFT-γ Mie model. The calculations are made via molecular dynamics for temperatures in the range of 410 to 505 K. The effect the cutoff radius of the interparticle interaction potential in the model has on the coefficient of surface tension and the ...
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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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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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Tyukina S., Velmiskina J., Dmitrienko A. et al., The Journal of Physical Chemistry Letters 2024 Vol. 15 No. 7 P. 2105 – 2110
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El-Mowafi S. A., Konshina A. G., Mohammed E. H. et al., Molecules 2023 Vol. 28 No. 24 Article 8049
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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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Added: February 8, 2024