Quantum chemistry research is presented in the article, and it concerns the interaction within the complexes formed by the defective graphene clusters and ions of 3d-transition metals V,Cr,Mn, Fe,Co,Ni,Cu. The charges of all regarded ions were +1. All calculations were made at UDFT B3LYP/6-31G level of theory with the BSSE error taken into account. The strongest interaction with the defective clusters is observed in the case of Co+ ion. At the same time, this ion has demonstrated rather weak interaction with the defect-free graphene. Thus, the presence of Co+ in the reaction media increases probability of defect formation with the further forming of short nanotubes and curved carbon clusters with complex topology of their own.
{"title":"Quantum Chemistry Research of Interaction between 3D-Transition Metal Ions and a Defective Graphene on the Supercomputer Base","authors":"N. Khokhriakov, S. Melchor","doi":"10.14529/jsfi180314","DOIUrl":"https://doi.org/10.14529/jsfi180314","url":null,"abstract":"Quantum chemistry research is presented in the article, and it concerns the interaction within the complexes formed by the defective graphene clusters and ions of 3d-transition metals V,Cr,Mn, Fe,Co,Ni,Cu. The charges of all regarded ions were +1. All calculations were made at UDFT B3LYP/6-31G level of theory with the BSSE error taken into account. The strongest interaction with the defective clusters is observed in the case of Co+ ion. At the same time, this ion has demonstrated rather weak interaction with the defect-free graphene. Thus, the presence of Co+ in the reaction media increases probability of defect formation with the further forming of short nanotubes and curved carbon clusters with complex topology of their own.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114831722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A supercomputer simulation of the benchmark MATiS-H problem is considered. A highresolution CABARET code is applied for solving Navier-Stokes equations in the framework of the Monotonically Integrated LES approach for the MATiS-H problem. The code is based on a generalisation of low-dissipative, low-dispersive and non-oscillatory CABARET scheme to hybrid topology meshes in the supercomputing framework. The solutions for the time-averaged fields are reported. These show a relatively small sensitivity to the grid density. Comparison with the experiment data available is provided.
{"title":"Supercomputer Simulation of MATIS-H Problem","authors":"M. A. Zaitsev, V. M. Goloviznin, S. A. Karabasov","doi":"10.14529/JSFI180324","DOIUrl":"https://doi.org/10.14529/JSFI180324","url":null,"abstract":"A supercomputer simulation of the benchmark MATiS-H problem is considered. A highresolution CABARET code is applied for solving Navier-Stokes equations in the framework of the Monotonically Integrated LES approach for the MATiS-H problem. The code is based on a generalisation of low-dissipative, low-dispersive and non-oscillatory CABARET scheme to hybrid topology meshes in the supercomputing framework. The solutions for the time-averaged fields are reported. These show a relatively small sensitivity to the grid density. Comparison with the experiment data available is provided.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"104 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131966240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
It is shown that the global energy minimum of a protein-ligand complex, when the energy is calculated by the PM7 quantum-chemical semiempirical method with the COSMO implicit solvent model, can be determined as follows. First, the low energy minima are found by a docking program when the protein-ligand energy is calculated with the MMFF94 force field in vacuum. Second, energies of all these minima are recalculated with the PM7 method and the COSMO implicit solvent model. Third, among these recalculated energies the minimal energy is determined and the respective minimum is the global energy minimum when the energy is calculated with the PM7 method and the COSMO implicit solvent model. The optimal width of the spectrum of low energy minima found with MMFF94 in vacuum is determined to perform minimal quantity of quantum-chemical recalculations. The proposed approach allows to perform docking in solvent with the quantum-chemical method and to increase the docking positioning accuracy.
{"title":"Supercomputer Docking: Investigation of Low Energy Minima of Protein-Ligand Complexes","authors":"D. Kutov, A. Sulimov, V. Sulimov","doi":"10.14529/JSFI180326","DOIUrl":"https://doi.org/10.14529/JSFI180326","url":null,"abstract":"It is shown that the global energy minimum of a protein-ligand complex, when the energy is calculated by the PM7 quantum-chemical semiempirical method with the COSMO implicit solvent model, can be determined as follows. First, the low energy minima are found by a docking program when the protein-ligand energy is calculated with the MMFF94 force field in vacuum. Second, energies of all these minima are recalculated with the PM7 method and the COSMO implicit solvent model. Third, among these recalculated energies the minimal energy is determined and the respective minimum is the global energy minimum when the energy is calculated with the PM7 method and the COSMO implicit solvent model. The optimal width of the spectrum of low energy minima found with MMFF94 in vacuum is determined to perform minimal quantity of quantum-chemical recalculations. The proposed approach allows to perform docking in solvent with the quantum-chemical method and to increase the docking positioning accuracy.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116574071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Estimation of the recent and future climate changes is the most important challenge in the modern Earth sciences. Numerical climate models are an essential tool in this field of research. However, modelling results are highly sensitive to the spatial resolution of the model. The most of the climate change studies utilize the global atmospheric models with a grid cell size of tens of kilometres or more. High-resolution mesoscale models are much more detailed, but require significantly more computational resources. Applications of such high-resolution models in climate studies are usually limited by regional simulations and by relatively short timespan. In this paper we consider the experience of the long-term regional climate studies based on the mesoscale modelling. On the examples of urban climate studies and extreme wind assessments, we demonstrate the principle advantage of long-term high-resolution simulations, which were carried out on the modern supercomputers.
{"title":"Supercomputer Technologies as a Tool for High-resolution Atmospheric Modelling towards the Climatological Timescales","authors":"V. Platonov, M. Varentsov","doi":"10.14529/jsfi180320","DOIUrl":"https://doi.org/10.14529/jsfi180320","url":null,"abstract":"Estimation of the recent and future climate changes is the most important challenge in the modern Earth sciences. Numerical climate models are an essential tool in this field of research. However, modelling results are highly sensitive to the spatial resolution of the model. The most of the climate change studies utilize the global atmospheric models with a grid cell size of tens of kilometres or more. High-resolution mesoscale models are much more detailed, but require significantly more computational resources. Applications of such high-resolution models in climate studies are usually limited by regional simulations and by relatively short timespan. In this paper we consider the experience of the long-term regional climate studies based on the mesoscale modelling. On the examples of urban climate studies and extreme wind assessments, we demonstrate the principle advantage of long-term high-resolution simulations, which were carried out on the modern supercomputers.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130441177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The paper considers the use of supercomputers in design of medical ultrasound tomography devices. The mathematical models describing the wave propagation in ultrasound tomography should take into account such physical phenomena as diffraction, multiple scattering, and so on. The inverse problem of wave tomography is posed as a coefficient inverse problem with respect to the wave propagation velocity and the absorption factor. Numerous simulations made it possible to determine the optimal parameters of an ultrasound tomograph in order to obtain a spatial resolution of 1.5 mm suitable for early-stage breast cancer diagnosis. The developed methods were tested both on model problems and on real data obtained at the experimental test bench for tomographic studies. The computations were performed on GPU devices of Lomonosov-2 supercomputer at Lomonosov Moscow State University.
{"title":"Supercomputer Simulations in Design of Ultrasound Tomography Devices","authors":"A. Goncharsky, S. Seryozhnikov","doi":"10.14529/jsfi180321","DOIUrl":"https://doi.org/10.14529/jsfi180321","url":null,"abstract":"The paper considers the use of supercomputers in design of medical ultrasound tomography devices. The mathematical models describing the wave propagation in ultrasound tomography should take into account such physical phenomena as diffraction, multiple scattering, and so on. The inverse problem of wave tomography is posed as a coefficient inverse problem with respect to the wave propagation velocity and the absorption factor. Numerous simulations made it possible to determine the optimal parameters of an ultrasound tomograph in order to obtain a spatial resolution of 1.5 mm suitable for early-stage breast cancer diagnosis. The developed methods were tested both on model problems and on real data obtained at the experimental test bench for tomographic studies. The computations were performed on GPU devices of Lomonosov-2 supercomputer at Lomonosov Moscow State University.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122701763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Khrenova, D. Kapusta, I. V. Babchuk, Yulia I. Meteleshko
The progress of supercomputer technologies initiated the development of methods of computational chemistry and their applications, particularly molecular dynamic simulations with ab initio potentials. These new methods allow to solve important problems of chemistry and technology. Particularly, solvent extraction and separation techniques are widely used to decrease the amount of radioactive wastes, especially radioactive caesium isotopes present in liquid phases. We demonstrated that the calculated binding constants between the alkali cation and calix[4]arene differ 10 times for Cs and Na ions, that is in good agreement with the experimental value. We report the results of benchmark calculations of our model system composed of 929 atoms described in the density functional theory approximation with the GGA-type functional PBE with the empirical dispersion correction D3 and combined basis of Gaussian functions and plane waves DZVP with Goedecker-Teter-Hutter pseudopotentials. We demonstrate that efficiency of calculations decrease to about half if the amount of nodes is 16 on the Lomonosov-2 supercomputer.
{"title":"Applications of High Performance Computing: Born-Oppenheimer Molecular Dynamics of Complex Formation in Aqueous Solutions","authors":"M. Khrenova, D. Kapusta, I. V. Babchuk, Yulia I. Meteleshko","doi":"10.14529/jsfi180312","DOIUrl":"https://doi.org/10.14529/jsfi180312","url":null,"abstract":"The progress of supercomputer technologies initiated the development of methods of computational chemistry and their applications, particularly molecular dynamic simulations with ab initio potentials. These new methods allow to solve important problems of chemistry and technology. Particularly, solvent extraction and separation techniques are widely used to decrease the amount of radioactive wastes, especially radioactive caesium isotopes present in liquid phases. We demonstrated that the calculated binding constants between the alkali cation and calix[4]arene differ 10 times for Cs and Na ions, that is in good agreement with the experimental value. We report the results of benchmark calculations of our model system composed of 929 atoms described in the density functional theory approximation with the GGA-type functional PBE with the empirical dispersion correction D3 and combined basis of Gaussian functions and plane waves DZVP with Goedecker-Teter-Hutter pseudopotentials. We demonstrate that efficiency of calculations decrease to about half if the amount of nodes is 16 on the Lomonosov-2 supercomputer.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130915216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We present a polymer modeling approach to generate the ensemble of 3D chromosome conformations at different time points of mitosis-interphase transition. Dynamics of structure during mitosis-G1 transition indicates quick and slow stages of chromosome shape alterations. At intermediate and late time scale the changes in chromosome compaction are small. To assess time dependence of contact map establishment during G1 we calculate contact maps at different times after mitotic decondensation. We demonstrate that the patterns of contacts observed soon after mitotic decondensation remain similar during G1. Whole contact map for mouse chromosome 18 at late G1 time correlates with the experimental chromosome conformation capture data. The simulations reproduce the main experimental findings, contact map persistence during G1 as well as specific pattern of long-range interactions in interphase chromosome. Our results suggest that spatial compartmentalization of an interphase chromosome is driven by interactions between different types of megabase sized chromatin domains during the formation of globular chromosome state at the end of mitotis to G1 transition.
{"title":"High-performance Computational Modeling of Chromosome Structure","authors":"Y. Eidelman, S. Slanina, O. A. Gusev, S. Andreev","doi":"10.14529/jsfi180305","DOIUrl":"https://doi.org/10.14529/jsfi180305","url":null,"abstract":"We present a polymer modeling approach to generate the ensemble of 3D chromosome conformations at different time points of mitosis-interphase transition. Dynamics of structure during mitosis-G1 transition indicates quick and slow stages of chromosome shape alterations. At intermediate and late time scale the changes in chromosome compaction are small. To assess time dependence of contact map establishment during G1 we calculate contact maps at different times after mitotic decondensation. We demonstrate that the patterns of contacts observed soon after mitotic decondensation remain similar during G1. Whole contact map for mouse chromosome 18 at late G1 time correlates with the experimental chromosome conformation capture data. The simulations reproduce the main experimental findings, contact map persistence during G1 as well as specific pattern of long-range interactions in interphase chromosome. Our results suggest that spatial compartmentalization of an interphase chromosome is driven by interactions between different types of megabase sized chromatin domains during the formation of globular chromosome state at the end of mitotis to G1 transition.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"116 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128335105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The experimental study of the dependence of thin film properties on the deposition conditions may be still a great challenge. Today the progress in high performance computing allows one to perform the investigation of these dependencies on the atomistic level using the classical molecular dynamics (MD) simulation. In the present work the computational cost and efficiency of classical full-atomistic simulation of thin film deposition process using the Lonmonosov-2 supercomputer facilities is discussed. It is demonstrated that using 512 computational cores of the Lomonosov-2 supercomputer ensures the simulation of thin film cluster with technologically meaningful thickness of an optical film. Because of a relatively slow growth of the simulation time with the increase of film thickness we guess that simulations clusters with thicknesses that are several times higher than the currently achieved thicknesses about one hundred nanometers is quite realistic if the number of available computational cores will be increased up to several thousands.
{"title":"High-performance Full-atomistic Simulation of Optical Thin Films","authors":"F. Grigoriev, V. Sulimov, A. Tikhonravov","doi":"10.14529/JSFI180325","DOIUrl":"https://doi.org/10.14529/JSFI180325","url":null,"abstract":"The experimental study of the dependence of thin film properties on the deposition conditions may be still a great challenge. Today the progress in high performance computing allows one to perform the investigation of these dependencies on the atomistic level using the classical molecular dynamics (MD) simulation. In the present work the computational cost and efficiency of classical full-atomistic simulation of thin film deposition process using the Lonmonosov-2 supercomputer facilities is discussed. It is demonstrated that using 512 computational cores of the Lomonosov-2 supercomputer ensures the simulation of thin film cluster with technologically meaningful thickness of an optical film. Because of a relatively slow growth of the simulation time with the increase of film thickness we guess that simulations clusters with thicknesses that are several times higher than the currently achieved thicknesses about one hundred nanometers is quite realistic if the number of available computational cores will be increased up to several thousands.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123887133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The origin of dose-response curves for radiation-induced chromosomal instability (CI) is studied using the mechanistic CI model. The model takes into account DNA damage generation and repair in the progeny of irradiated cells and cell passage through mitotic cycle. We consider the formation of DNA double-strand breaks (DSBs) de novo in the S phase, where predominantly chromatid-type aberrations are formed. Among them sister chromatid exchanges of the “isochromatid deletion” type, or “chromatid dicentrics” are of primary interest. When the cell enters mitosis, the fate of chromosomal aberrations depends on their types. Chromosomal and chromatid fragments, having entered mitosis, either are transmitted into one of the daughter cells, or are lost. A chromatid dicentric in mitosis forms an anaphase bridge. These mechanistic assumptions were used to demonstrate that the dose-response curves are closely related to the dynamic curves for CI. The principles underlying this relationship are analyzed.
{"title":"Numerical Simulations of Structural Chromosomal Instability","authors":"Y. Eidelman, S. Slanina, V. Pyatenko, S. Andreev","doi":"10.14529/jsfi180306","DOIUrl":"https://doi.org/10.14529/jsfi180306","url":null,"abstract":"The origin of dose-response curves for radiation-induced chromosomal instability (CI) is studied using the mechanistic CI model. The model takes into account DNA damage generation and repair in the progeny of irradiated cells and cell passage through mitotic cycle. We consider the formation of DNA double-strand breaks (DSBs) de novo in the S phase, where predominantly chromatid-type aberrations are formed. Among them sister chromatid exchanges of the “isochromatid deletion” type, or “chromatid dicentrics” are of primary interest. When the cell enters mitosis, the fate of chromosomal aberrations depends on their types. Chromosomal and chromatid fragments, having entered mitosis, either are transmitted into one of the daughter cells, or are lost. A chromatid dicentric in mitosis forms an anaphase bridge. These mechanistic assumptions were used to demonstrate that the dose-response curves are closely related to the dynamic curves for CI. The principles underlying this relationship are analyzed.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"37 5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128517816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A method of nondestructive ultrasound tomographic imaging employing a rotating transducer system is proposed. The rotating transducer system increases the number of emitters and detectors in a tomographic scheme by several times and makes it possible to neutralize image artifacts resulting from incomplete-data tomography. The inverse problem of tomographic reconstructing the velocity structure inside the inspected object is considered as a nonlinear coefficient inverse problem for a scalar wave equation. Scalable iterative algorithms for reconstructing the longitudinal wave velocity inside the object are discussed. The methods are based on the explicit representation for the gradient of the residual functional. The algorithms employ parallelizing the computations over emitter positions. Numerical simulations performed on the “Lomonosov-2” supercomputer showed that the tomographic methods developed can not only detect boundaries of defects, but also determine the wave velocity distribution inside the defects with high accuracy provided that both reflected and transmitted waves are registered.
{"title":"Supercomputer Simulations of Nondestructive Tomographic Imaging with Rotating Transducers","authors":"S. Romanov","doi":"10.14529/jsfi180318","DOIUrl":"https://doi.org/10.14529/jsfi180318","url":null,"abstract":"A method of nondestructive ultrasound tomographic imaging employing a rotating transducer system is proposed. The rotating transducer system increases the number of emitters and detectors in a tomographic scheme by several times and makes it possible to neutralize image artifacts resulting from incomplete-data tomography. The inverse problem of tomographic reconstructing the velocity structure inside the inspected object is considered as a nonlinear coefficient inverse problem for a scalar wave equation. Scalable iterative algorithms for reconstructing the longitudinal wave velocity inside the object are discussed. The methods are based on the explicit representation for the gradient of the residual functional. The algorithms employ parallelizing the computations over emitter positions. Numerical simulations performed on the “Lomonosov-2” supercomputer showed that the tomographic methods developed can not only detect boundaries of defects, but also determine the wave velocity distribution inside the defects with high accuracy provided that both reflected and transmitted waves are registered.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128979483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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