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  1. Article ; Online: Numerical Modelling of High-Speed Loading of Periodic Interpenetrating Heterogeneous Media with Adapted Mesostructure

    Alexander Kraus / Andrey Buzyurkin / Ivan Shabalin / Evgeny Kraus

    Applied Sciences, Vol 13, Iss 7187, p

    2023  Volume 7187

    Abstract: A series of calculations has been conducted to study the high-speed interaction of space debris (SD) particles with screens of finite thickness. For the first time, taking into account the fracture effects, a numerical solution has been obtained for the ... ...

    Abstract A series of calculations has been conducted to study the high-speed interaction of space debris (SD) particles with screens of finite thickness. For the first time, taking into account the fracture effects, a numerical solution has been obtained for the problem of high-velocity interaction between SD particles and a volumetrically reinforced penetrating composite screen. The calculations were performed using the REACTOR 3D software package in a three-dimensional setup. To calibrate the material properties of homogeneous screens made of aluminum alloy A356, stainless steel 316L, and multilayer screens, methodical load calculations were carried out. The properties of materials have been verified based on experimental data through systematic calculations of the load on homogeneous screens made of aluminum alloy A356, stainless steel 316L, and multilayer screens comprising a combination of aluminum and steel plates. Several options for the numerical design of heterogeneous screens based on A356 and 316L were considered, including interpenetrating reinforcement with steel inclusions and a gradient distribution of steel throughout the thickness of an aluminum matrix. The study has revealed that the screens constructed as a two-layer composite of A356/316L, volumetrically reinforced composite screens, and heterogeneous screens with a direct gradient distribution of steel in the aluminum matrix provide protection for devices from both a single SD particle and streams of SD particles moving at speeds of up to 6 km/s. SD particles were modeled as spherical particles with a diameter of 1.9 mm made of the aluminum alloy Al2017-T4 with a mass of 10 mg.
    Keywords heterogeneous material ; reinforcement ; high-speed interaction ; barrier of finite thickness ; space debris ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: The effect of heat flow from friction forces on the surface of the billets

    Shabalin Dmitriy / Kozar Ivan / Kudryavtsev Vladimir / Petrov Anton / Semochkin Egor

    E3S Web of Conferences, Vol 371, p

    2023  Volume 03064

    Abstract: In modern mechanical engineering, technical ceramics is finding increasing use. It has unique anti-corrosion properties and resistance to high temperatures. In most cases, the processing modes and characteristics of abrasive (diamond) wheels are selected ...

    Abstract In modern mechanical engineering, technical ceramics is finding increasing use. It has unique anti-corrosion properties and resistance to high temperatures. In most cases, the processing modes and characteristics of abrasive (diamond) wheels are selected experimentally, since there is no modeling of processing processes in the public domain. The article presents an experimental study of the surface of dissimilar materials under the influence of heat flow from the friction force of grinding wheel grains. The comparison of calculated indicators and the results of laboratory studies is given. It is concluded that the heat flow from the friction forces of the grains on the material does not cause the destruction of the polished surface. It is also shown that the flow density due to varying modes of grinding
    Keywords Environmental sciences ; GE1-350
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Organism-specific differences in the binding of ketoprofen to serum albumin.

    Czub, Mateusz P / Stewart, Alan J / Shabalin, Ivan G / Minor, Wladek

    IUCrJ

    2022  Volume 9, Issue Pt 5, Page(s) 551–561

    Abstract: Serum albumin is a circulatory transport protein that has a highly conserved sequence and structure across mammalian organisms. Its ligand-binding properties are of importance as albumin regulates the pharmacokinetics of many drugs. Due to the high ... ...

    Abstract Serum albumin is a circulatory transport protein that has a highly conserved sequence and structure across mammalian organisms. Its ligand-binding properties are of importance as albumin regulates the pharmacokinetics of many drugs. Due to the high degree of structural conservation between mammalian albumins, nonhuman albumins such as bovine serum albumin or animal models are often used to understand human albumin-drug interactions. Ketoprofen is a popular nonsteroidal anti-inflammatory drug that is transported by albumin. Here, it is revealed that ketoprofen exhibits different binding-site preferences when interacting with human serum albumin compared with other mammalian albumins, despite the conservation of binding sites across species. The reasons for the observed differences were explored, including identifying ketoprofen binding determinants at specific sites and the influence of fatty acids and other ligands on drug binding. The presented results reveal that the drug-binding properties of albumins cannot easily be predicted based only on a complex of albumin from another organism and the conservation of drug sites between species. This work shows that understanding organism-dependent differences is essential for assessing the suitability of particular albumins for structural or biochemical studies.
    Language English
    Publishing date 2022-07-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252522006820
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  4. Article ; Online: Celebrating the 75th birthday of Professor Wladek Minor, one of the most accomplished Polish-American structural biologists.

    Jaskolski, Mariusz / Wlodawer, Alexander / Dauter, Zbigniew / Shabalin, Ivan / Chruszcz, Maksymilian

    Acta biochimica Polonica

    2021  Volume 68, Issue 1, Page(s) 1–4

    Abstract: This paper describes the scientific career and accomplishments of Professor Wladek Minor, who holds an endowed chair at the University of Virginia in Charlottesville, USA. Prof. Minor is a coauthor of data processing software used by macromolecular ... ...

    Abstract This paper describes the scientific career and accomplishments of Professor Wladek Minor, who holds an endowed chair at the University of Virginia in Charlottesville, USA. Prof. Minor is a coauthor of data processing software used by macromolecular crystallographers world-wide, as well as of structural biology servers and of a repository for raw diffraction data. He made major contributions to the validation of biostructural data, with special focus on drug design targets and reproducibility in biomedical research. He is among the most highly cited molecular biologists ever.
    MeSH term(s) Aged ; Crystallography ; Data Mining/methods ; Drug Design ; Faculty/history ; History, 20th Century ; History, 21st Century ; Humans ; Male ; Molecular Biology ; Poland ; Reproducibility of Results ; Software ; United States
    Language English
    Publishing date 2021-01-21
    Publishing country Poland
    Document type Historical Article ; Journal Article ; Portrait
    ZDB-ID 595762-x
    ISSN 1734-154X ; 0001-527X
    ISSN (online) 1734-154X
    ISSN 0001-527X
    DOI 10.18388/abp.2020_5539
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  5. Article: Structural and biochemical characterisation of Co

    Wu, Dongmei / Gucwa, Michal / Czub, Mateusz P / Cooper, David R / Shabalin, Ivan G / Fritzen, Remi / Arya, Swati / Schwarz-Linek, Ulrich / Blindauer, Claudia A / Minor, Wladek / Stewart, Alan J

    Chemical science

    2023  Volume 14, Issue 23, Page(s) 6244–6258

    Abstract: Serum albumin- ... ...

    Abstract Serum albumin-Co
    Language English
    Publishing date 2023-05-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/d3sc01723k
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  6. Article: Angular X-ray cross-correlation analysis applied to the scattering data in 3D reciprocal space from a single crystal.

    Lapkin, Dmitry / Shabalin, Anatoly / Meijer, Janne-Mieke / Kurta, Ruslan / Sprung, Michael / Petukhov, Andrei V / Vartanyants, Ivan A

    IUCrJ

    2022  Volume 9, Issue Pt 4, Page(s) 425–438

    Abstract: An application of angular X-ray cross-correlation analysis (AXCCA) to the scattered intensity distribution measured in 3D reciprocal space from a single-crystalline sample is proposed in this work. Contrary to the conventional application of AXCCA, when ... ...

    Abstract An application of angular X-ray cross-correlation analysis (AXCCA) to the scattered intensity distribution measured in 3D reciprocal space from a single-crystalline sample is proposed in this work. Contrary to the conventional application of AXCCA, when averaging over many 2D diffraction patterns collected from different randomly oriented samples is required, the proposed approach provides an insight into the structure of a single specimen. This is particularly useful in studies of defect-rich samples that are unlikely to have the same structure. The application of the method is shown on an example of a qualitative structure determination of a colloidal crystal from simulated as well as experimentally measured 3D scattered intensity distributions.
    Language English
    Publishing date 2022-05-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252522004250
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  7. Article: Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment.

    Shabalin, Ivan G / Porebski, Przemyslaw J / Minor, Wladek

    Crystallography reviews

    2018  Volume 24, Issue 4, Page(s) 236–262

    Abstract: Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced ... ...

    Abstract Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.
    Language English
    Publishing date 2018-09-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2079077-6
    ISSN 1476-3508 ; 0889-311X
    ISSN (online) 1476-3508
    ISSN 0889-311X
    DOI 10.1080/0889311X.2018.1521805
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  8. Article ; Online: A high-throughput structural system biology approach to increase structure representation of proteins from

    Rosas-Lemus, Monica / Dey, Supratim / Minasov, George / Tan, Kemin / Anderson, Spencer M / Brunzelle, Joseph / Nocadello, Salvatore / Shabalin, Ivan / Filippova, Ekaterina / Halavaty, Andrei / Kim, Youngchang / Maltseva, Natalia / Osipiuk, Jerzy / Minor, Wladek / Joachimiak, Andrzej / Savchenko, Alexei / Anderson, Wayne F / Satchell, Karla J F

    Microbiology resource announcements

    2023  Volume 12, Issue 10, Page(s) e0050723

    Abstract: Clostridioides ... ...

    Abstract Clostridioides difficile
    Language English
    Publishing date 2023-09-25
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00507-23
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  9. Article ; Online: Extracting contrast in an X-ray speckle visibility spectroscopy experiment under imperfect conditions.

    Hua, Nelson / Zaluzhnyy, Ivan A / Hrkac, Stjepan B / Shabalin, Anatoly G / Shpyrko, Oleg G

    Journal of synchrotron radiation

    2020  Volume 27, Issue Pt 6, Page(s) 1626–1632

    Abstract: Pump-probe experiments at synchrotrons and free-electron lasers to study ultrafast dynamics in materials far from equilibrium have been well established, but techniques to investigate equilibrium dynamics on the nano- and pico-second timescales remain ... ...

    Abstract Pump-probe experiments at synchrotrons and free-electron lasers to study ultrafast dynamics in materials far from equilibrium have been well established, but techniques to investigate equilibrium dynamics on the nano- and pico-second timescales remain underdeveloped and experimentally challenging. A promising approach relies on a double-probe X-ray speckle visibility spectroscopy setup at split-and-delay beamlines of X-ray free-electron lasers. However, the logistics in consistently producing two collinear, perfectly overlapping pulses necessary to conduct a faithful experiment is difficult to achieve. In this paper, a method is introduced to extract contrast in the case where an angular misalignment and imperfect overlap exists between the two pulses. Numerical simulations of a dynamical system show that contrast can still be extracted for significant angular misalignments accompanied by partial overlap between the two pulses.
    Language English
    Publishing date 2020-10-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2021413-3
    ISSN 1600-5775 ; 0909-0495
    ISSN (online) 1600-5775
    ISSN 0909-0495
    DOI 10.1107/S1600577520012345
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  10. Article: Crystallographic models of SARS-CoV-2 3CL

    Jaskolski, Mariusz / Dauter, Zbigniew / Shabalin, Ivan G / Gilski, Miroslaw / Brzezinski, Dariusz / Kowiel, Marcin / Rupp, Bernhard / Wlodawer, Alexander

    IUCrJ

    2021  Volume 8, Issue Pt 2, Page(s) 238–256

    Abstract: The appearance at the end of 2019 of the new SARS-CoV-2 coronavirus led to an unprecedented response by the structural biology community, resulting in the rapid determination of many hundreds of structures of proteins encoded by the virus. As part of an ... ...

    Abstract The appearance at the end of 2019 of the new SARS-CoV-2 coronavirus led to an unprecedented response by the structural biology community, resulting in the rapid determination of many hundreds of structures of proteins encoded by the virus. As part of an effort to analyze and, if necessary, remediate these structures as deposited in the Protein Data Bank (PDB), this work presents a detailed analysis of 81 crystal structures of the main protease 3CL
    Language English
    Publishing date 2021-02-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252521001159
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