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  1. Article: SARS-CoV-2 proteins structural studies using synchrotron radiation.

    Kosenko, Maksim / Onkhonova, Galina / Susloparov, Ivan / Ryzhikov, Alexander

    Biophysical reviews

    2023  Volume 15, Issue 5, Page(s) 1185–1194

    Abstract: In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of ... ...

    Abstract In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of biological macromolecules has expanded. Significant progress in the development of structural biology methods has been largely achieved through the use of synchrotron radiation. Modern sources of synchrotron radiation allow to conduct high-performance structural studies with high temporal and spatial resolution. Thus, modern techniques make it possible to obtain not only static structures, but also to study dynamic processes, which play a key role in understanding biological mechanisms. One of the key directions in the development of structural research is the drug design based on the structures of biomolecules. Synchrotron radiation offers insights into the three-dimensional time-resolved structure of individual viral proteins and their complexes at atomic resolution. The rapid and accurate determination of protein structures is crucial for understanding viral pathogenicity and designing targeted therapeutics. Through the application of experimental techniques, including X-ray crystallography and small-angle X-ray scattering (SAXS), it is possible to elucidate the structural details of SARS-CoV-2 virion containing 4 structural, 16 nonstructural proteins (nsp), and several accessory proteins. The most studied potential targets for vaccines and drugs are the structural spike (S) protein, which is responsible for entering the host cell, as well as nonstructural proteins essential for replication and transcription, such as main protease (M
    Language English
    Publishing date 2023-09-29
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-023-01153-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Traversing automata with current state uncertainty under LTL$_f$ constraints

    Ryzhikov, Andrew / Wolf, Petra

    2023  

    Abstract: In this paper, we consider a problem which we call LTL$_f$ model checking on paths: given a DFA $\mathcal{A}$ and a formula $\phi$ in LTL on finite traces, does there exist a word $w$ such that every path starting in a state of $\mathcal{A}$ and labeled ... ...

    Abstract In this paper, we consider a problem which we call LTL$_f$ model checking on paths: given a DFA $\mathcal{A}$ and a formula $\phi$ in LTL on finite traces, does there exist a word $w$ such that every path starting in a state of $\mathcal{A}$ and labeled by $w$ satisfies $\phi$? The original motivation for this problem comes from the constrained parts orienting problem, introduced in [Petra Wolf, "Synchronization Under Dynamic Constraints", FSTTCS 2020], where the input constraints restrict the order in which certain states are visited for the first or the last time while reading a word $w$ which is also required to synchronize $\mathcal{A}$. We identify very general conditions under which LTL$_f$ model checking on paths is solvable in polynomial space. For the particular constraints in the parts orienting problem, we consider PSPACE-complete cases and one NP-complete case. The former provide very strong lower bound for LTL$_f$ model checking on paths. The latter is related to (classical) LTL$_f$ model checking for formulas with the until modality only and with no nesting of operators. We also consider LTL$_f$ model checking of the power-set automaton of a given DFA, and get similar results for this setting. For all our problems, we consider the case where the required word must also be synchronizing, and prove that if the problem does not become trivial, then this additional constraint does not change the complexity.
    Keywords Computer Science - Formal Languages and Automata Theory ; Computer Science - Logic in Computer Science
    Subject code 004
    Publishing date 2023-11-29
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Quantitative measurement of influenza virus transmission in animal model: an overview of current state.

    Onkhonova, Galina / Gudymo, Andrei / Kosenko, Maksim / Marchenko, Vasiliy / Ryzhikov, Alexander

    Biophysical reviews

    2023  Volume 15, Issue 5, Page(s) 1359–1366

    Abstract: Influenza virus transmission is a crucial factor in understanding the spread of the virus within populations and developing effective control strategies. Studying the transmission patterns of influenza virus allows for better risk assessment and ... ...

    Abstract Influenza virus transmission is a crucial factor in understanding the spread of the virus within populations and developing effective control strategies. Studying the transmission patterns of influenza virus allows for better risk assessment and prediction of disease outbreaks. By monitoring the spread of the virus and identifying high-risk populations and geographic areas, it is possible to allocate resources more effectively, implement timely interventions, and provide targeted healthcare interventions to diminish the burden of influenza virus on vulnerable populations. Theoretical models of virus transmission are used to study and simulate of influenza virus spread within populations. These models aim to capture the complex dynamics of transmission, including factors such as population size, contact patterns, infectiousness, and susceptibility. Animal models serve as valuable tools for studying the dynamics of influenza virus transmission. This article presents a brief overview of existing research on the qualitative and quantitative study of influenza virus transmission in animal models. We discuss the methodologies employed, key insights gained from these studies, and their relevance.
    Language English
    Publishing date 2023-09-07
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-023-01113-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: NFAD: fixing anomaly detection using normalizing flows.

    Ryzhikov, Artem / Borisyak, Maxim / Ustyuzhanin, Andrey / Derkach, Denis

    PeerJ. Computer science

    2021  Volume 7, Page(s) e757

    Abstract: Anomaly detection is a challenging task that frequently arises in practically all areas of industry and science, from fraud detection and data quality monitoring to finding rare cases of diseases and searching for new physics. Most of the conventional ... ...

    Abstract Anomaly detection is a challenging task that frequently arises in practically all areas of industry and science, from fraud detection and data quality monitoring to finding rare cases of diseases and searching for new physics. Most of the conventional approaches to anomaly detection, such as one-class SVM and Robust Auto-Encoder, are one-class classification methods,
    Language English
    Publishing date 2021-11-18
    Publishing country United States
    Document type Journal Article
    ISSN 2376-5992
    ISSN (online) 2376-5992
    DOI 10.7717/peerj-cs.757
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Calorimetric Heats of Intrusion of LiCl Aqueous Solutions in Hydrophobic MFI-Type Zeosil: Influence of the Concentration.

    Ryzhikov, Andrey / Dirand, Céline / Astafan, Amir / Nouali, Habiba / Daou, T Jean / Bezverkhyy, Igor / Chaplais, Gérald / Bellat, Jean-Pierre

    Langmuir : the ACS journal of surfaces and colloids

    2024  Volume 40, Issue 17, Page(s) 8827–8835

    Abstract: For the first time, we report calorimetric measurements of intrusion of aqueous LiCl solutions in a hydrophobic pure siliceous MFI zeolite (silicalite-1) under high pressure. Our results show that the intrusion heats are strongly dependent on the LiCl ... ...

    Abstract For the first time, we report calorimetric measurements of intrusion of aqueous LiCl solutions in a hydrophobic pure siliceous MFI zeolite (silicalite-1) under high pressure. Our results show that the intrusion heats are strongly dependent on the LiCl concentration. The intrusion process is endothermic for diluted solutions (molar H
    Language English
    Publishing date 2024-04-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2005937-1
    ISSN 1520-5827 ; 0743-7463
    ISSN (online) 1520-5827
    ISSN 0743-7463
    DOI 10.1021/acs.langmuir.3c03931
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: The degree of a finite set of words

    Perrin, Dominique / Ryzhikov, Andrew

    2021  

    Abstract: We prove several results concerning finitely generated submonoids of the free monoid. These results generalize those known for free submonoids. We prove in particular that if $X=Y\circ Z$ is a composition of finite sets of words with $Y$ complete, then $ ... ...

    Abstract We prove several results concerning finitely generated submonoids of the free monoid. These results generalize those known for free submonoids. We prove in particular that if $X=Y\circ Z$ is a composition of finite sets of words with $Y$ complete, then $d(X)\le d(Y)d(Z)$.
    Keywords Computer Science - Formal Languages and Automata Theory
    Publishing date 2021-06-28
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Book ; Online: Performance Modeling of Data Storage Systems using Generative Models

    Al-Maeeni, Abdalaziz Rashid / Temirkhanov, Aziz / Ryzhikov, Artem / Hushchyn, Mikhail

    2023  

    Abstract: High-precision modeling of systems is one of the main areas of industrial data analysis. Models of systems, their digital twins, are used to predict their behavior under various conditions. We have developed several models of a storage system using ... ...

    Abstract High-precision modeling of systems is one of the main areas of industrial data analysis. Models of systems, their digital twins, are used to predict their behavior under various conditions. We have developed several models of a storage system using machine learning-based generative models. The system consists of several components: hard disk drive (HDD) and solid-state drive (SSD) storage pools with different RAID schemes and cache. Each storage component is represented by a probabilistic model that describes the probability distribution of the component performance in terms of IOPS and latency, depending on their configuration and external data load parameters. The results of the experiments demonstrate the errors of 4-10 % for IOPS and 3-16 % for latency predictions depending on the components and models of the system. The predictions show up to 0.99 Pearson correlation with Little's law, which can be used for unsupervised reliability checks of the models. In addition, we present novel data sets that can be used for benchmarking regression algorithms, conditional generative models, and uncertainty estimation methods in machine learning.
    Keywords Computer Science - Machine Learning ; Computer Science - Artificial Intelligence ; Computer Science - Performance
    Subject code 006
    Publishing date 2023-07-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Book ; Online: Latent Neural Stochastic Differential Equations for Change Point Detection

    Ryzhikov, Artem / Hushchyn, Mikhail / Derkach, Denis

    2022  

    Abstract: Automated analysis of complex systems based on multiple readouts remains a challenge. Change point detection algorithms are aimed to locating abrupt changes in the time series behaviour of a process. In this paper, we present a novel change point ... ...

    Abstract Automated analysis of complex systems based on multiple readouts remains a challenge. Change point detection algorithms are aimed to locating abrupt changes in the time series behaviour of a process. In this paper, we present a novel change point detection algorithm based on Latent Neural Stochastic Differential Equations (SDE). Our method learns a non-linear deep learning transformation of the process into a latent space and estimates a SDE that describes its evolution over time. The algorithm uses the likelihood ratio of the learned stochastic processes in different timestamps to find change points of the process. We demonstrate the detection capabilities and performance of our algorithm on synthetic and real-world datasets. The proposed method outperforms the state-of-the-art algorithms on the majority of our experiments.
    Keywords Computer Science - Machine Learning
    Publishing date 2022-08-22
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: A drastic influence of the anion nature and concentration on high pressure intrusion-extrusion of electrolyte solutions in Silicalite-1.

    Ryzhikov, A / Nouali, H / Daou, T J / Patarin, J

    Physical chemistry chemical physics : PCCP

    2018  Volume 20, Issue 9, Page(s) 6462–6468

    Abstract: High pressure intrusion-extrusion of concentrated solutions of sodium salts in a pure-silica MFI-type zeolite (Silicalite-1) was studied for potential applications in mechanical energy absorption and storage. It was discovered that the anion nature has a ...

    Abstract High pressure intrusion-extrusion of concentrated solutions of sodium salts in a pure-silica MFI-type zeolite (Silicalite-1) was studied for potential applications in mechanical energy absorption and storage. It was discovered that the anion nature has a drastic influence on the behavior and the energetic performances of "Silicalite-1 - concentrated Na
    Language English
    Publishing date 2018-02-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c7cp06520e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: Synchronizing Strongly Connected Partial DFAs

    Berlinkov, Mikhail V. / Ferens, Robert / Ryzhikov, Andrew / Szykuła, Marek

    2021  

    Abstract: We study synchronizing partial DFAs, which extend the classical concept of synchronizing complete DFAs and are a special case of synchronizing unambiguous NFAs. A partial DFA is called synchronizing if it has a word (called a reset word) whose action ... ...

    Abstract We study synchronizing partial DFAs, which extend the classical concept of synchronizing complete DFAs and are a special case of synchronizing unambiguous NFAs. A partial DFA is called synchronizing if it has a word (called a reset word) whose action brings a non-empty subset of states to a unique state and is undefined for all other states. While in the general case the problem of checking whether a partial DFA is synchronizing is PSPACE-complete, we show that in the strongly connected case this problem can be efficiently reduced to the same problem for a complete DFA. Using combinatorial, algebraic, and formal languages methods, we develop techniques that relate main synchronization problems for strongly connected partial DFAs with the same problems for complete DFAs. In particular, this includes the \v{C}ern\'{y} and the rank conjectures, the problem of finding a reset word, and upper bounds on the length of the shortest reset words of literal automata of finite prefix codes. We conclude that solving fundamental synchronization problems is equally hard in both models, as an essential improvement of the results for one model implies an improvement for the other.

    Comment: Full version of the paper at STACS 2021
    Keywords Computer Science - Formal Languages and Automata Theory ; Mathematics - Combinatorics
    Subject code 511
    Publishing date 2021-01-13
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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