scholarly journals PARALLEL OPTIMIZATION TECHNOLOGY FOR ATOMIC-MOLECULAR MORSE CLUSTERS

2022 ◽  
pp. 60-67
Author(s):  
Александр Юрьевич Горнов ◽  
Антон Сергеевич Аникин ◽  
Павел Сергеевич Сороковиков ◽  
Татьяна Сергеевна Зароднюк
Keyword(s):  
Molecular Docking ◽  
Software Package ◽  
Molecular Clusters ◽  
Computational Experiments ◽  
Applied Problem ◽  
Parallel Optimization ◽  
Computing Technology ◽  
Morse Clusters ◽  
New Algorithms

В статье рассматриваются специализированные вычислительные технологии и алгоритмы, используемые для поиска низкопотенциальных атомно-молекулярных кластеров. Проведенные вычислительные эксперименты продемонстрировали достаточно высокую конкурентоспособность новых алгоритмов по сравнению с классическими для функций рассматриваемого типа. С использованием разработанного программного комплекса получены рекордные результаты оптимизации атомно-молекулярных кластеров Морса рекордных размерностей. The paper deals with specialized computing technology and algorithms used for finding low-potential atomic-molecular clusters. The performed computational experiments demonstrated a rather high competitiveness of the new algorithms in comparison with the classical methods for the considerable functions. Using the developed software, the applied problem of molecular docking was solved. Using the developed software package, record results for optimization of atomic-molecular Morse clusters of large dimensions have been obtained.

scholarly journals Problem-oriented software package for the numerical solution and research of structural bioinformatics problems using stochastic optimization methods

2020 ◽  
pp. 37-47
Author(s):  
S. Poluyan ◽  
N. Ershov
Keyword(s):  
Stochastic Optimization ◽  
Open Source Software ◽  
Software Package ◽  
Structure Prediction ◽  
Optimization Methods ◽  
Search Space ◽  
Protein Docking ◽  
Structural Bioinformatics ◽  
Computational Experiments ◽  
Continuous Global Optimization

In this paper presented problem-oriented software package for performing computational experiments in structural bioinformatics problems: protein structure prediction and peptide-protein docking. These problemsare formulated as continuous global optimization tasks. The primary purpose of the presented software package is to provide functionality for performing computational experiments using various stochastic optimization methods. To perform experiments for the selected task the objective function and search space are provided for user. In this work the software packagefunctionality, implementation features and the results of various experimentsare presented. The software is written in C++ and provides the possibility ofusing parallel computing using OpenMP technology. The presented package is open source software that stored in the GitHub repositories.

Development of Computational Experiments’ Database in the TOXI+Risk Software Package for Assessment the Risk and Consequences of Accidents

2020 ◽  
Vol 8 (1) ◽  
pp. 20-29
Author(s):  
Aleksandr Egorov ◽  
Tatiana Savitskaya ◽  
N. Klenina
Keyword(s):  
Risk Analysis ◽  
Software Package ◽  
Oil And Gas ◽  
Oil Products ◽  
Computational Experiments ◽  
Gas Processing ◽  
Accident Statistics

The generalization and analysis of accident statistics on objects of petrochemical, oil and gas processing industries, as well as on oil products supply facilities for the period from 2009 to 2016 has been carried out. Has been performed a brief overview of examples for using the TOXI+Risk software package for emergency simulation and risk analysis. Has been presented the developed database of computational experiments for assessment the risk and consequences of accidents at chemically hazardous objects.

scholarly journals RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes

2020 ◽  
Author(s):  
Clement Agret ◽  
Annie Chateau ◽  
Gaetan Droc ◽  
Gautier Sarah ◽  
Alban Mancheron ◽  
...  
Keyword(s):  
Software Package ◽  
High Throughput Sequencing ◽  
Source Code ◽  
Free Software ◽  
Large Collection ◽  
Sequencing Technologies ◽  
Alignment Free ◽  
The Cost ◽  
New Algorithms ◽  
Extract Information

AbstractBackgroundAs the cost of DNA sequencing decreases, high-throughput sequencing technologies become increasingly accessible to many laboratories. Consequently, new issues emerge that require new algorithms, including tools for indexing and compressing hundred to thousands of complete genomes.ResultsThis paper presents RedOak, a reference-free and alignment-free software package that allows for the indexing of a large collection of similar genomes.RedOak can also be applied to reads from unassembled genomes, and it provides a nucleotide sequence query function. This software is based on a k-mer approach and has been developed to be heavily parallelized and distributed on several nodes of a cluster. The source code of our RedOak algorithm is available at https://gitlab.info-ufr.univ-montp2.fr/DoccY/RedOak.ConclusionsRedOak may be really useful for biologists and bioinformaticians expecting to extract information from large sequence datasets.

scholarly journals Reactivity margin evaluation software for WWR-c reactor

2018 ◽  
Vol 4 (3) ◽  
pp. 197-201
Author(s):  
Ivan Belyavtsev ◽  
Sergey Starkov
Keyword(s):  
Neural Network ◽  
Artificial Neural Network ◽  
Network Architecture ◽  
Software Package ◽  
Web Application ◽  
Approximation Error ◽  
Computational Experiments ◽  
Neuron Network ◽  
Artificial Neural ◽  
Reactivity Margin

The WWR-c reactor reactivity margin can be calculated using a precision reactor model. The precision model based on the Monte Carlo method (Kolesov et al. 2011) is not well suited for operational calculations. The article describes the work on creating a software package for preliminary evaluations of the WWR-c reactor reactivity margin. The research has confirmed the possibility of using an artificial neural network to approximate the reactivity margin based on the reactor core condition. Computational experiments were conducted on training the artificial neural network using the precision model data and real reactor measured data. According to the results of the computational experiments, the maximum relative approximation error ∆k/k for fuel burnup was 3.13 and 3.56%, respectively. The mean computation time was 100 ms. The computational experiments showed it possible to construct the artificial neural network architecture. This architecture became the basis for building a software package for evaluating the WWR-c reactor reactivity margin – REST API based web-application – which has a convenient user interface for entering the core configuration. It is also possible to replenish the training sample with new measurements and train the artificial neuron network once again. The reactivity margin evaluation software is ready to be tested by the WWR-c reactor personnel and to be used as a component of the automated reactor refueling system. With minor modifications, the software package can be used for reactors of other types.

scholarly journals Molecular docking study of oligonucleotides with D-mannitol

2017 ◽  
Vol 15 (1) ◽  
pp. 64-68
Author(s):  
V. Shchodryi ◽  
D. Lozhko ◽  
Z. Tkachuk
Keyword(s):  
Molecular Docking ◽  
Molecular Modeling ◽  
Antiviral Activity ◽  
Software Package ◽  
Virus Entry ◽  
Docking Study ◽  
Binding Energies ◽  
Important Task ◽  
Molecular Docking Study ◽  
Hyperchem Software

Aim. Complex of yeast RNA and D-mannitol has a specific antiviral activity. This complex inhibits the neuraminidase and hemagglutinin activity of viruses such as influenza, parainfluenza and thus it blocks virus entry into the cell and his replication. So, nowadays, study of the interaction of this compound is an important task. Study interaction of the oligoribonucleotides and oligodesoxynucleotides with D mannitol molecule. Methods. Molecular modeling structure of oligoribonucleotides and oligodesoxynucleotides were done by using «Hyperchem» software package. The AutoDock program was used to perform accuracy molecular docking. Results. Were obtained binding energies of D-mannitol molecule with oligoribonucleotides and oligodesoxynucleotides. We have shown the possible connections between atoms of oligonucleotides and D-mannitol molecule. Conclusions. The modeling results should give more detailed information about nature of the oligonucleotides binding with a shugar alcohol D-mannitol.Keywords: molecular docking, oligonucleotides, D-mannitol, binding energies.

MODELS OF A QUANTITATIVE SCALE FOR EVALUATING SEMANTIC INFORMATION

2020 ◽  
Vol 2020 (2) ◽  
pp. 24-32
Author(s):  
Pyotr Shalimov
Keyword(s):  
Mathematical Modeling ◽  
Comparative Analysis ◽  
Software Package ◽  
Semantic Information ◽  
Information Environment ◽  
Computational Experiments ◽  
Simulation Studies ◽  
Evaluation Mode

The problem of mathematical modeling of semantic information is analyzed. A model of the information environment as a carrier of semantic information is developed. The procedure for evaluating semantic information in the simulation of functioning in the accumulation and evaluation mode is presented. A software package for creating an information environment and conducting simulation studies has been developed. We consider the setting of computational experiments in the comparative analysis of the amount of semantic information of a text resource. The most current applications of the model are shown.

scholarly journals Exact and approximate algorithms for the longest induced path problem

2021 ◽  
Author(s):  
Celso C Ribeiro ◽  
Ruslán G. Marzo
Keyword(s):  
Computational Experiments ◽  
Simple Path ◽  
Approximate Algorithms ◽  
Optimal Solutions ◽  
Induced Path ◽  
Enumerative Algorithm ◽  
New Algorithms

The longest induced path problem consists in finding a maximum subset of vertices of a graph such that it induces a simple path. We propose a new exact enumerative algorithm that solves problems with up to 138 vertices and 493 edges and a heuristic for larger problems. Detailed computational experiments compare the results obtained by the new algorithms with other approaches in the literature and investigate the characteristics of the optimal solutions.

scholarly journals MATHEMATICAL MODELING OF THE FUNCTIONING OF A HYDRODYNAMIC SYSTEM WITH DISTRIBUTED PARAMETERS

2021 ◽  
pp. 37-45
Keyword(s):  
Mathematical Modeling ◽  
Mathematical Model ◽  
Dynamic Process ◽  
Computational Experiments ◽  
Applied Problem ◽  
Hydrodynamic System ◽  
Distributed Parameters ◽  
Production Wells ◽  
System States

The work examines the process of functioning of the hydrodynamic system "reservoir-well" taking into account the dynamic process of shutting down and starting a group of production wells. A mathematical model for determining system states, an algorithm for solving an applied problem and the results of computational experiments in the form of graphs are given.

Quanitative aspects of electron diffraction using electron holography

1995 ◽  
Vol 53 ◽  
pp. 616-617
Author(s):  
E. Völkl ◽  
L.F. Allard ◽  
B. Frost ◽  
T.A. Nolan
Keyword(s):  
Electron Beam ◽  
Electron Diffraction ◽  
Software Package ◽  
Spatial Coherence ◽  
Electron Holography ◽  
Image Intensity ◽  
Interference Fringes ◽  
Complex Image ◽  
The Difference ◽  
Recorded Image

Off-axis electron holography has the well known ability to preserve the complex image wave within the final, recorded image. This final image described by I(x,y) = I(r) contains contributions from the image intensity of the elastically scattered electrons IeI (r) = |A(r) exp (iΦ(r)) |, the contributions from the inelastically scattered electrons IineI (r), and the complex image wave Ψ = A(r) exp(iΦ(r)) as:(1) I(r) = IeI (r) + Iinel (r) + μ A(r) cos(2π Δk r + Φ(r))where the constant μ describes the contrast of the interference fringes which are related to the spatial coherence of the electron beam, and Φk is the resulting vector of the difference of the wavefront vectors of the two overlaping beams. Using a software package like HoloWorks, the complex image wave Ψ can be extracted.

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