Natalia Nikitina

Natalia Nikitina
Karelian Research Centre of the Russian Academy of Sciences | Karelian Research Centre of RAS · Institute of Applied Mathematical Research

PhD

About

39
Publications
2,014
Reads
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91
Citations
Citations since 2016
25 Research Items
90 Citations
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Introduction
Natalia N. Nikitina currently works at the Institute of Applied Mathematical Research, Karelian Research Centre of the Russian Academy of Sciences. Natalia does research in Applied Mathematics and Distributed Computing. Co-admin and co-founder of the volunteer computing projects SiDock@home and RakeSearch based on BOINC middleware.
Additional affiliations
June 2018 - present
Karelian Research Centre of the Russian Academy of Sciences
Position
  • Researcher
September 2016 - September 2016
Ensenada Center for Scientific Research and Higher Education
Position
  • Visiting researcher
October 2013 - July 2014
Universität zu Lübeck
Position
  • Visiting researcher
Education
September 2004 - June 2010
Petrozavodsk State University
Field of study
  • Applied mathematics and informatics

Publications

Publications (39)
Chapter
Network models are widely employed in many areas of science and technology. Mathematical analysis of their properties includes various methods to characterize, rank and compare network nodes. A key concept here is centrality, a numerical value of node importance in the whole network. As the links in a network represent interactions between the node...
Chapter
This paper addresses the performance evaluation of a heterogeneous distributed computing environment (Desktop Grid) for large-scale medicinal chemistry experiments in silico. Dynamic change of the set of computational nodes, their heterogeneity and unreliability impose difficulties on task scheduling and algorithm scaling. We analyze the performanc...
Chapter
In this paper, we describe a volunteer computing project SiDock@home aimed at high-throughput virtual screening of a specially developed library of small compounds against a set of targets playing important roles in the life-cycle of the virus. The originality of the screening library and the molecular docking software allows us to obtain new knowl...
Chapter
COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 pathogen. Although a number of new vaccines are available to combat this threat, a high prevalence of novel mutant viral variants is observed in all world regions affected by this infection. Among viral proteomes, the highly glycosylated spike protein (Spr...
Chapter
Full-text available
This study focuses on searching for pairs of orthogonal diagonal Latin squares of order 10. Consider a cells mapping in accordance to which one diagonal Latin square is mapped to another one. Given a certain cells mapping schema, the problem is to find a pair of orthogonal diagonal Latin squares of order 10 such that they match the schema (or to pr...
Chapter
In this paper, we describe the experience of setting up a computational infrastructure based on BOINC middleware and running a volunteer computing project on its basis. We characterize the first series of computational experiments and review the project’s development in its first six months. The gathered experience shows that BOINC-based Desktop Gr...
Chapter
The paper addresses the problem of accelerating the “tail” stage of a computational experiment in a Desktop Grid. We provide the mathematical model of a “tail” stage, describe the setting of simulation experiments and provide their results. Task replication in “tail” phase proves to be efficient in decreasing the duration of “tail” by orders of mag...
Chapter
The paper describes a discrete event simulation model of a Desktop Grid system. Firstly, we present a stochastic model of a volunteer computing project. We then employ the event simulation approach based on the generalized semi-Markov processes to develop a discrete event simulation model. Finally, using the simulation model, we describe a performa...
Conference Paper
Full-text available
The paper discusses the reduction of problems based on Latin squares to the exact cover problem aiming at its subsequent solution using the dancing links algorithm. The former problems include generation of Latin squares and diagonal Latin squares of a general form/with a given normalization, generation of orthogonal Latin and diagonal Latin square...
Chapter
The article describes a number of simple transformations (rotation of intercalates, loops, Latin subrectangles, replacement of transversals) in the problem of constructing a collection of orthogonal diagonal Latin squares (ODLS) of order 10 aiming to try to find a triple of pairwise orthogonal diagonal Latin squares of order 10. The averaged time s...
Chapter
In this paper, we propose an efficient computational scheme for virtual drug screening using a Desktop Grid. The scheme is based on a game-theoretical mathematical model, more precisely a crowding game. The proposed scheme provides needed balance between the results quality and the search scope.
Chapter
In this paper we describe the experience of setting up a computational infrastructure based on BOINC middleware and running a volunteer computing project on its basis. The project is aimed at characterizing the space of diagonal Latin squares of order 9 in the form of an ensemble of orthogonality graphs, previously not addressed. We implement the s...
Chapter
Full-text available
The paper is devoted to discovering new features of diagonal Latin squares of small order. We present an algorithm, based on a special kind of transformations, that constructs a canonical form of a given diagonal Latin square. Each canonical form corresponds to one isotopy class of diagonal Latin squares. The algorithm was implemented and used to e...
Chapter
This work describes BOINC-based Desktop Grid implementation of adaptive task scheduling algorithm for virtual drug screening. The algorithm bases on a game-theoretical mathematical model where computing nodes act as players. The model allows to adjust the balance between the results retrieval rate and the search space coverage. We present the devel...
Article
Full-text available
В работе рассматривается задача идентификации параметров модели разложения гидридов металлов методом параллельного сканирования пространства параметров. Задача является вычислительно емкой, но при этом хорошо подходит для выполнения в среде Desktop Grid. Выбор заданий рассматривается как математическая игра. В работе показано, что процесс поиска мо...
Article
Full-text available
We consider parameter identification of a hydride decomposition model by scanning the parameter space in parallel. Such problem is resource demanding, but suits best for Desktop Grid computing. Considering task retrieval as a game, we show that the search process can be improved to produce solutions faster in comparison with random search, with no...
Article
The paper surveys the state of the art of task scheduling in Desktop Grid computing systems. We describe the general architecture of a Desktop Grid system and the computing model adopted by the BOINC middleware. We summarize research papers to bring together and examine the optimization criteria and methods proposed by researchers so far for improv...
Article
Full-text available
In virtual drug screening, the chemical diversity of hits is an important factor, along with their predicted activity. Moreover, interim results are of interest for directing the further research, and their diversity is also desirable. In this paper, we consider a problem of obtaining a diverse set of virtual screening hits in a short time. To this...
Article
The community detection in social and communication networks is an important problem in many applied fields: biology, sociology, social networks. This is especially true for networks that are represented by large graphs. In this paper, we propose a method for community detection based on the maximum likelihood method for the random formation of a n...
Article
Full-text available
In this paper we propose a mathematical model and implement an algorithm to detect commu�nities structure in networks presented by either non-oriented simple graphs or multigraphs and belonging to various subject areas. The base of the mathematical model is the maximum likelihood method for random generation of a network with given parameters of li...
Article
Full-text available
We survey the areas of Desktop Grid task scheduling that seem to be insufficiently studied so far and are promising for efficiency, reliability, and quality of Desktop Grid computing. These topics include optimal task grouping, “needle in a haystack” paradigm, game-theoretical scheduling, domain-imposed approaches, special optimization of the final...
Conference Paper
Full-text available
Virtual drug screening is one of the most common applications of high-throughput computing. As virtual screening is time consuming, a problem of obtaining a diverse set of hits in a short time is very important. We propose a mathematical model based on game theory. Task scheduling for virtual drug screening in high-performance computational systems...
Conference Paper
Desktop Grids utilize computational resources of desktop computers in their idle time. The BOINC middleware for organizing Desktop Grids has an architecture developed to unite a large number of computing nodes. However, a large flow of server requests may limit the Desktop Grid performance. In the paper we present a game-theoretical model of task s...
Conference Paper
Full-text available
We propose a mathematical model of a desktop grid computing system that solves tasks with two possible answers. Replication is used in order to reduce the error risk: wrong answers are returned with some known probabilities and penalty is added to the calculation cost in case of an error. We solve the optimization problems to determine the optimal...
Article
Full-text available
Desktop grids utilize idle computational resources within a research organization. Task scheduling is a very important issue for a desktop grid due to its significant impact on computational performance. In the paper we propose a game-theoretical model of task scheduling in a desktop grid. The model allows to consider the trade-off between the serv...
Article
Full-text available
We consider a reliable desktop grid solving multiple tasks with answers from a given set. Wrong answer can be obtained with some small probability p: reliability means that p is small with respect to 1−p. Penalty is added to the computation cost if a wrong answer is believed to. We consider the optimization problem of choosing the quorum in case of...
Article
Full-text available
In the paper, the problem of determination of the moment of intrusion into a computing system and subsequent change of the service protocol for the input stream of tasks is considered. To determine the moment of the intrusion, a method of cumulative sums is used. Analytical expressions for the method characteristics in the case of the Bernoulli dis...
Chapter
The annual international workshop Networking Games and Management (NGM-2013) http://mathem.krc.karelia.ru/ event.php?id=184&plang=rand. was held June 23-25, 2013 at a recreation camp in Urozero on the shore of one of the cleanest lakes in Europe. With nature as a backdrop, participants gathered to discuss the latest trends and advances of game-theo...
Article
Full-text available
In the paper we consider the inverse problem of evaluating kinetic parameters of the model of dehydriding of metal powder using experimental data. The «blind search» in the space of parameters revealed multiple physically reasonable solutions. The solutions were obtained using high-performance computational modeling based on BOINC-grid.
Chapter
The Sixth International Conference on Game Theory and Management held June 27-29 at Graduate School of Management in St. Petersburg, Russia attracted over 100 researchers interested in game-theoretic and management models and applications. Participants had an opportunity to attend the presentations on a wide range of game-theoretic models. Among ot...
Chapter
The Networking Games and Management (NGM-2012) workshop gathered over 30 scientists and PhD students from 5 countries from June 30 to July 2 to discuss current advances in networking games and management at Petrozavodsk. Russia’s North with its many lakes, forests and flowers enhanced the warm, friendly atmosphere that permeated the whole event. Th...
Article
Full-text available
In this work we present the new results obtained during the implementation of the research devoted to development of the system to prevent large-scale copying of documents from digital libraries. The system is based on user's behavior modeling applying with the Markov model. We present main results of experiments aimed at selection of the best valu...
Chapter
There are many issues concerning information security of digital libraries. Apart from traditional information security problems there are some specific ones for digital libraries. In this work we consider a behavioral modeling approach to discover unauthorized copying of a large amount of documents from a digital library. Supposing the regular use...
Conference Paper
In the paper we describe a web service of access to computing resources of a desktop grid built in the High-performance Data Center of Karelian Research Centre of the RAS. The grid is based on lightweight, highly scalable BOINC platform. We present the architecture of the system, the current results of implementation and plans for the future. We al...

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Projects

Projects (4)
Project
Special Issue of MDPI Mathematics (Q1 WoS, IF 2.258) to gather papers on mathematical research of rare and novel diseases. Deadline for manuscript submissions: 31 March 2022. https://www.mdpi.com/journal/mathematics/special_issues/mathematical_advances_studying_rare_novel_diseases
Project
This project is aimed at developing a job scheduling algorithm to screen large databases so as to ensure high number and diversity of useful results at early steps already.