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arXiv 2018年

作者： Bychkov, I. Demichev, A. Dubenskaya, J. Fedorov, O. Hmelnov, A. Kazarina, Y. Korosteleva, E. Kostunin, D. Kryukov, A. Mikhailov, A. Nguyen, M.D. Postnikov, E. Shigarov, A. Shipilov, D. Zhurov, D. Matrosov Institute for System Dynamics and Control Theory SB RAS Irkutsk Russia Irkutsk State University Irkutsk Russia Skobeltsyn Institute of Nuclear Physics Lomonosov Moscow State University Moscow Russia Applied Physics Institute Irkutsk State University Irkutsk Russia Institute for Nuclear Physics Karlsruhe Institute of Technology Karlsruhe Germany

The paper is devoted to the issues of raw binary data documenting, parsing and verifying in astroparticle data lifecycle. The long-term preservation of raw data of astroparticle experiments as originally generated is essential for re-running analyses and reproducing research results. The selected high-quality raw data should have detailed documentation and accompanied by open software tools for access to them. We consider applicability of binary file format description languages to specify, parse and verify raw data of the Tunka Advanced Instrument for cosmic rays and Gamma Astronomy (TAIGA) experiment. The formal specifications are implemented for five data formats of the experiment and provides automatic generation of source code for data reading libraries in target programming languages (e.g. C++, Java, and Python). These libraries were tested on TAIGA data. They showed a good performance and help us to locate the parts with corrupted data. The format specifications can be used as metadata for exchanging of astroparticle raw data. They can also simplify software development for data aggregation from various sources for the multi-messenger analysis. Copyright © 2018, The Authors. All rights reserved.

关键词： Software design

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Experience in modeling medic-ecological economical systems (Irkutsk region as an example)

Experience in modeling medic-ecological economical systems (...

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Computational Engineering in systems Applications, CESA, IMACS Multiconference on FLAGGED

作者： V. A. Baturin N. V. Efimova N.I. Matorova D.E. Ourbanovich A.B. Stolbov Institute of System Dynamics and Control Theory SB RAS Irkutsk Russia Research Institute of Industrial Medicine and Human Ecology Eastern Siberian Scientific Centre of RAMS Russia

In clause experience of authors on modelling dynamics of parameters of the population health is considered. The model is presented in the form of system of the ordinary differential equations. The major factors influencing chosen parameters are pollution atmospheric air and a fixed capital public health services. On an example of some cities of Irkutsk region results of calculations are presented.

关键词： Biological system modeling Mathematical model Environmental economics Statistics Power generation economics Environmental factors Chemical industry Fuel economy Atmospheric modeling Differential equations

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Conceptual Model of Problem-oriented Heterogeneous Distributed Computing Environment with Multi-agent Management

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Procedia Computer Science 2017年 103卷 162-167页

作者： I. Bychkov G. Oparin A. Tchernykh A. Feoktistov V. Bogdanova S. Gorsky Matrosov Institute for System Dynamics and Control Theory SB RAS Lermontov str. 134 Irkutsk Post Box 292 664033 Russia CICESE Research Center Computer Science Department Carretera Ensenada-Tijuana No. 3918 Zona Playitas Codigo Postal 22860 Apdo. Postal 360 Ensenada B.C. Mexico

One of the promising approaches to the efficient management in a heterogeneous distributed computing environment is the use of multi-agent systems. When researchers want to solve tasks in such an environment, they need utilities for the description of the processing in the specific domain, and knowledge about a software-hardware infrastructure. This multi-component knowledge is used for effective decision-making. Practice and experience of multi-agent systems show that knowledge representation is non-trivial problems. We proposed an approach to the design of the conceptual model of a heterogeneous distributed computing environment based on multi-agent management. An important component of the model is algorithmic knowledge, which provides the support of planning, resources allocation and dynamic decomposition of a problem to subproblems. This knowledge is represented as a semantic network, which describe semantic relations between concepts. Unlike to Semantic Web Services and Semantic Grids, our approach provides advanced planning abilities to support parallelism and scalability. We develop specialized high-level tools for designing and using the conceptual models.

关键词： multi-agent systems knowledge representation distributed computing environment.

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Application of boinc-based volunteer computing for comparison of the geoacoustic inversion algorithms efficiency 8

Application of boinc-based volunteer computing for compariso...

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Selected Papers of the 8th International Conference "Distributed Computing and Grid-Technologies in Science and Education", GRID 2018

作者： Zaikin, O.S. Petrov, P.S. Kurochkin, I.I. ITMO University 49 Kronverkskiy Prospekt Saint Petersburg197101 Russia Matrosov Institute for System Dynamics and Control Theory SB RAS 134 Lermontov Street Irkutsk664033 Russia V.I. Il'ichev Pacific Oceanological Institute FEB RAS Far Eastern Federal University 43 Baltiyskaya Street Vladivostok690041 Russia Far Eastern Federal University 8 Sukhanova Street Vladivostok690090 Russia A.A. Kharkevich Institute for Information Transmission Problems RAS 19 Build 1 Bolshoy Karetny Pereulok Moscow127051 Russia

The BOINC-based volunteer computing project Acoustics@home was employed to study the accuracy of the sound speed profile reconstruction in a shallow-water waveguide using a dispersion-based geoacoustic inversion scheme. This problem was transformed into a problem of black-box minimization of a certain mismatch function. According to the first approach, a sound speed profile is considered a piecewise-linear function with fixed uniformly-spaced nodes. At these nodes the values of sound speed are obtained in the course of inversion. In the second approach the depths of the sound speed profile nodes are also considered inversion parameters, however their number must be smaller than in the first approach due to the computational complexity limitation. Several large-scale computational experiments reveal that for the considered problem the second approach leads to a more accurate sound speed profile estimation. © 2018 Ilya I. Kurochkin, Evgeny A. Gerk.

关键词： Optimization

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Cell-free biosynthesis meets dynamic optimization and control: a fed-batch framework

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IFAC-PapersOnLine 2022年第23期55卷 92-97页

作者： Sebastián Espinel-Ríos Nicolas Huber Edgar Alberto Alcalá-Orozco Bruno Morabito Thomas F.T. Rexer Udo Reichl Steffen Klamt Rolf Findeisen Laboratory for System Theory and Automatic Control Otto von Guericke University Magdeburg Germany Analysis and Redesign of Biological Networks Max Planck Institute for Dynamics of Complex Technical Systems Germany Bioprocess Engineering Max Planck Institute for Dynamics of Complex Technical Systems Germany Control and Cyber-Physical Systems Laboratory TU Darmstadt Germany

Cell-free biosynthesis uses the machinery of cells, such as the metabolic reactions, to carry out conversion processes in vitro. This can be more beneficial than in vivo approaches like fermentations. Some advantages of these synthetic biology processes include higher product yields, rates and titers, and more flexibility in pathway design. Cell-free biosynthesis is still in early stages and, unlike in vivo production, there are very few examples of model-based optimization. Moreover, we encounter static optimizations in most cases, neglecting the dynamic nature of the processes. We present an optimal control framework to maximize the efficiency of cell-free biosynthesis. We focus on fed-batch setups as they allow enhancing the reaction rates via the feeding, extending production processes for longer times, and minimizing the potential negative effects of enzyme kinetics with substrate inhibition. Our framework can in principle handle several cost functions and exploit both static and dynamic degrees of freedom. An aspect that can hinder model-based optimization is model uncertainty, which can arise due to uncertain parameters, oversimplified model assumptions or unknown reaction mechanisms. To counteract this, we propose the use of model predictive control during the process operation. In addition, we outline the use of moving horizon estimation as an observer in the case of unmeasured states. We consider the de novo cell-free synthesis of uridine diphosphate-N-acetylglucosamine as a biomedical relevant case study, where we were able to maximize the volumetric productivity in simulations, and indirectly also the titer and enzyme efficiency use.

关键词： Cell-free fed-batch optimization control state estimation UDP-GlcNAc

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Soft sensor for monitoring dynamic changes in cell composition

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IFAC-PapersOnLine 2022年第23期55卷 98-103页

作者： Sebastián Espinel-Ríos Bruno Morabito Katja Bettenbrock Steffen Klamt Rolf Findeisen Laboratory for System Theory and Automatic Control Otto von Guericke University Magdeburg Germany Analysis and Redesign of Biological Networks Max Planck Institute for Dynamics of Complex Technical Systems Germany Bioprocess Engineering Max Planck Institute for Dynamics of Complex Technical Systems Germany Control and Cyber-Physical Systems Laboratory TU Darmstadt Germany

Precise and accurate online monitoring methods are needed to enable smart biomanufacturing and automation. Most of the sensors available focus on process parameters such as metabolite and dissolved gas concentrations, cell density or viability, among other variables like pH, temperature, etc. In this work, we develop a soft sensor algorithm to estimate the cell composition online, a very important aspect often overlooked in the bioprocess monitoring literature. Our strategy is based on full information estimation, an optimization-based estimator that takes into account the dynamics of the cell metabolism and considers all the available measurements from the beginning of the process, thus it has a memory effect. Being able to track dynamic changes in cell composition can open the door to promising applications, e.g., predictive control and automation of biosystems. As a case study, we consider the Escherichia co li’ s metabolism growing on glycerol under different levels of oxygen supply. We compare the performance of our soft sensor method against resource balance analysis, a previously proposed estimator based on steady-state assumptions. Overall, the presented full information estimator was able to track the dynamic changes in cell composition significantly more accurately. We also discuss how our estimation strategy can be transformed into a moving horizon estimation, where only the available measurements in a fixed and moving window are considered, thereby reducing possible computational burdens.

关键词： Cell composition soft sensor full information estimation resource balance analysis dynamic enzyme-cost flux balance analysis

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Preface

Communications in Computer and Information Science

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Communications in Computer and Information Science 2020年 1275 CCIS卷 v-vii页

作者： Kochetov, Yury Gruzdeva, Tatiana Bykadorov, Igor Sobolev Institute of Mathematics Novosibirsk Russia Matrosov Institute for System Dynamics and Control Theory Irkutsk Russia

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Fermion propagator diagonalization and eigenvalue problem

arXiv

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arXiv 2021年

作者： Dolzhikov, D.A. Kaloshin, A.E. Lomov, Vladimir P. Joint Institute for Nuclear Research Dubna141980 Russia Irkutsk State University Irkutsk664003 Russia Institute for System Dynamics and Control Theory RAS Irkutsk664033 Russia

We discuss diagonalization of propagator for mixing fermions system based on the eigenvalue problem. The similarity transformation converting matrix propagator into diagonal form is obtained. The suggested diagonalization has simple algebraic properties for on-shell fermions and can be used in renormalization of fermion mixing matrix. Copyright © 2021, The Authors. All rights reserved.

关键词： Mixing

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QCD Phase Diagram at NICA energies: K+/π+ horn effect and light clusters in THESEUS

arXiv

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arXiv 2020年

作者： Blaschke, D. Friesen, A.V. Ivanov, Yu.B. Kalinovsky, Yu.L. Kozhevnikova, M. Liebing, S. Radzhabov, A. Röpke, G. JINR Dubna Dubna141980 Russia Moscow115409 Russia University of Wroclaw Wroclaw50-204 Poland Matrosov Institute System Dynamics & Control Theory Irkutsk664003 Russia Irkutsk State University Irkutsk664003 Russia University of Rostock RostockD-18051 Germany

We discuss recent progress in the development of the three-fluid hydrodynamics-based program THESEUS towards an event generator suitable for applications to heavy-ion collisions at the intermediate energies of the planned NICA and FAIR experiments. We follow the strategy that modifications of particle distributions at the freeze-out surface in the QCD phase diagram may be mapped directly to the observable ones within a sudden freeze-out scheme. We report first results of these investigations for the production of light clusters (deuterons and tritons) which can be compared to experimental data from the HADES and the NA49 experiment and for the interpretation of the"horn" effect observed in the collision energy dependence of the K+/π+ ratio. Medium effects on light cluster production in the QCD phase diagram are negligible at the highest NICA energies but shall play a dominant role at the lowest energies. A sharp"horn"-type signal in the K+/π+ ratio can be obtained when the onset of Bose condensation modelled by a pion chemical potential results in an enhancement of pions at low momenta (which is seen at LHC energies) and would occur already in the NICA energy range. Copyright © 2020, The Authors. All rights reserved.

关键词： Heavy ions

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Optimal control and dynamic modulation of the ATPase gene expression for enforced ATP wasting in batch fermentations

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IFAC-PapersOnLine 2022年第7期55卷 174-180页

作者： Sebastián Espinel-Ríos Bruno Morabito Johannes Pohlodek Katja Bettenbrock Steffen Klamt Rolf Findeisen Analysis and Redesign of Biological Networks Max Planck Institute for Dynamics of Complex Technical Systems Germany Laboratory for System Theory and Automatic Control Otto von Guericke University Magdeburg Germany Control and Cyber-Physical Systems Laboratory TU Darmstadt Germany

Competitive biotechnological processes need to operate over various conditions and adapt to changing economic contexts. Dynamic ATP turnover allows trading off declines in biomass formation and volumetric productivity for enhancements of product yields in fermentations where the product pathway is linked to ATP synthesis. To facilitate its practical implementation, we propose to dynamically manipulate the cellular ATP turnover by putting the ATPase enzyme, which hydrolyzes ATP into ADP, under the control of an optogenetic gene expression system. This allows achieving dynamic control of the ATP wasting online via a tunable external input. While light as control input is promising because it is easily tunable, generally non-invasive/non-toxic, and more affordable than classical chemical inducers, it makes the overall control task challenging. Thus, we derive an expanded version of dynamic enzyme-cost flux balance analysis that takes into account the dynamics of the optogenetic actuator. We then formulate a suitable optimal control problem to find optimal inputs for achieving the desired process performance. We test our approach in simulations using the batch anaerobic lactate fermentation of glucose by Escherichia coli as a case study.

关键词： ATP wasting ATPase optimal control gene expression optogenetics batch fermentation

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