{"id":12100,"date":"2023-07-06T16:02:09","date_gmt":"2023-07-06T14:02:09","guid":{"rendered":"https:\/\/new.sano.science\/?post_type=people&p=12100"},"modified":"2024-02-05T16:31:58","modified_gmt":"2024-02-05T15:31:58","slug":"krzysztof-gadek","status":"publish","type":"people","link":"https:\/\/sano.science\/people\/krzysztof-gadek\/","title":{"rendered":"Krzysztof G\u0105dek"},"excerpt":{"rendered":"

Scientific Programmer<\/p>\n","protected":false},"featured_media":12086,"template":"","people_teams":[19,34,37],"class_list":["post-12100","people","type-people","status-publish","has-post-thumbnail","hentry","people_teams-research","people_teams-extreme-scale-data-and-computing","people_teams-scientific-programmers"],"yoast_head":"\nKrzysztof G\u0105dek - Centre for Computational Personalized Medicine<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sano.science\/people\/krzysztof-gadek\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Krzysztof G\u0105dek\" \/>\n<meta property=\"og:description\" content=\"Scientific Programmer\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sano.science\/people\/krzysztof-gadek\/\" \/>\n<meta property=\"og:site_name\" content=\"Centre for Computational Personalized Medicine\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/sano.science\/\" \/>\n<meta property=\"article:modified_time\" content=\"2024-02-05T15:31:58+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/krzysztof_gadek.png\" \/>\n\t<meta property=\"og:image:width\" content=\"350\" \/>\n\t<meta property=\"og:image:height\" content=\"350\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@sanoscience\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/krzysztof-gadek\\\/\",\"url\":\"https:\\\/\\\/sano.science\\\/people\\\/krzysztof-gadek\\\/\",\"name\":\"Krzysztof G\u0105dek - 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Programming since he was 12 years old, it’s one his biggest passion. In Sano started as intern on the HPHOB project, now working with MEE development and occasionally other programming tasks. His other passions are science (physics, mathematics (especially differential equations), astronomy), history and sports, like gym, swimming or skiing. Great fan of the Balkans culture, visited most of countries in this region, except for Albania. Foreign languages lover, currently studying English and Russian, in future plans to learn German, Italian and Serbo-Croatian.<\/p>\n","email":"","social_media":false,"tabs":false,"quote":"","position_with_team":{"text_before_link":"","link_text":"","text_after_link":"","link":""},"publications":[{"ID":15019,"post_author":"5","post_date":"2024-01-18 10:05:36","post_date_gmt":"2024-01-18 09:05:36","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-AM6OG4\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Marek Kasztelnik, Piotr Nowakowski, Jan Meizner, Maciej Malawski, Adam Nowak, Krzysztof Gadek, Karol Zajac, Antonino Amedeo La Mattina & Marian Bubak<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-2j4SBu\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-nW3zsl\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">The Digital Twin paradigm in medical care has recently gained popularity among proponents of translational medicine, to enable clinicians to make informed choices regarding treatment on the basis of digital simulations. In this paper we present an overview of functional and non-functional requirements related to specific IT solutions which enable such simulations - including the need to ensure repeatability and traceability of results - and propose an architecture that satisfies these requirements. We then describe a computational platform that facilitates digital twin simulations, and validate our approach in the context of a real-life medical use case: the BoneStrength application.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-2j4SBu\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_65a8e9d073e43\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/link.springer.com\/chapter\/10.1007\/978-3-031-36021-3_2\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_blank\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Digital twin simulation development and execution on HPC infrastructures","post_excerpt":"In: ICCS 2023: Computational Science \u2013 ICCS 2023.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"digital-twin-simulation-development-and-execution-on-hpc-infrastructures","to_ping":"","pinged":"","post_modified":"2024-01-18 10:05:37","post_modified_gmt":"2024-01-18 09:05:37","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=15019","menu_order":23,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":14952,"post_author":"8","post_date":"2024-01-16 13:45:59","post_date_gmt":"2024-01-16 12:45:59","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-w6ZXkN\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p id=\"h-\" class=\" eplus-wrapper\">Piotr Nowakowski, Marian Bubak, Krzysztof G\u0105dek, \u200bMarek Kasztelnik, Maciej Malawski, Jan Meizner, \u200bAdam Nowak, Piotr Po\u0142e\u0107, Karol Zaj\u0105c, Taras Zhyhulin\u200b<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-zQZ8SH\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_65a67a733ad67\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.cyfronet.pl\/zalacznik\/9789\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_blank\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Leveraging ACC Resources for Medical Research","post_excerpt":"In: KUKDM 2023, 2023.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"leveraging-acc-resources-for-medical-research","to_ping":"","pinged":"","post_modified":"2026-01-31 19:31:07","post_modified_gmt":"2026-01-31 18:31:07","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=14952","menu_order":26,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":14789,"post_author":"5","post_date":"2024-01-09 18:18:22","post_date_gmt":"2024-01-09 17:18:22","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-zKXsIA\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Irena Roterman, Katarzyna Stapor, K<strong>rzysztof G\u0105dek, Tomasz Guba\u0142a , Piotr Nowakowski<\/strong>, Piotr Fabian and Leszek Konieczny<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-fKs3Fp\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-acUE6q\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">The natural environment of proteins is the polar aquatic environment and the hydrophobic (amphipathic) environment of the membrane. The fuzzy oil drop model (FOD) used to characterize water-soluble proteins, as well as its modified version FOD-M, enables a mathematical description of the presence and influence of diverse environments on protein structure. The present work characterized the structures of membrane proteins, including those that act as channels, and a water-soluble protein for contrast. The purpose of the analysis was to verify the possibility that an external force field can be used in the simulation of the protein-folding process, taking into account the diverse nature of the environment that guarantees a structure showing biological activity.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-BByC5N\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_659d7fc271e60\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.mdpi.com\/2077-0375\/12\/1\/50\/htm\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_blank\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins","post_excerpt":"In: Membrane Biological Function in Health and Disease, 2021.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"dependence-of-protein-structure-on-environment-fod-model-applied-to-membrane-proteins","to_ping":"","pinged":"","post_modified":"2024-01-09 18:19:28","post_modified_gmt":"2024-01-09 17:19:28","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=14789","menu_order":87,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":14764,"post_author":"5","post_date":"2024-01-05 14:30:12","post_date_gmt":"2024-01-05 13:30:12","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-Izxvyr\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Irena Roterman, Katarzyna Stapor, Krzysztof G\u0105dek, Tomasz Guba\u0142a, Piotr Nowakowski, Piotr Fabian and Leszek Konieczny<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-gKCf9h\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:heading {\"level\":4,\"epAnimationGeneratedClass\":\"edplus_anim-MHYgSH\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h4 class=\"wp-block-heading eplus-wrapper\" id=\"html-abstract-title\">Abstract<\/h4>\n<!-- \/wp:heading -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-7hsrde\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Currently available analyses of amyloid proteins reveal the necessity of the existence of radical structural changes in amyloid transformation processes. The analysis carried out in this paper based on the model called fuzzy oil drop (FOD) and its modified form (FOD-M) allows quantifying the role of the environment, particularly including the aquatic environment. The starting point and basis for the present presentation is the statement about the presence of two fundamentally different methods of organizing polypeptides into ordered conformations\u2014globular proteins and amyloids. The present study shows the source of the differences between these two paths resulting from the specificity of the external force field coming from the environment, including the aquatic and hydrophobic one. The water environment expressed in the fuzzy oil drop model using the 3D Gauss function directs the folding process towards the construction of a micelle-like system with a hydrophobic core in the central part and the exposure of polarity on the surface. The hydrophobicity distribution of membrane proteins has the opposite characteristic: Exposure of hydrophobicity at the surface of the membrane protein with an often polar center (as in the case of ion channels) is expected. The structure of most proteins is influenced by a more or less modified force field generated by water through the appropriate presence of a non-polar (membrane-like) environment. The determination of the proportion of a factor different from polar water enables the assessment of the protein status by indicating factors favoring the structure it represents.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-iQLq1P\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Keywords<\/strong>:\u00a0amyloids;\u00a0prions;\u00a0hydrophobicity;\u00a0fuzzy oil drop model<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-nfg1MC\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_6598043a42469\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.mdpi.com\/1422-0067\/22\/24\/13494\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_blank\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"On the Dependence of Prion and Amyloid Structure on the Folding Environment","post_excerpt":"In: International Journal of Molecule Sciences, 2021.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"on-the-dependence-of-prion-and-amyloid-structure-on-the-folding-environment","to_ping":"","pinged":"","post_modified":"2024-01-05 14:30:13","post_modified_gmt":"2024-01-05 13:30:13","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=14764","menu_order":89,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"}]},"_links":{"self":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12100","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people"}],"about":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/types\/people"}],"version-history":[{"count":2,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12100\/revisions"}],"predecessor-version":[{"id":15318,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12100\/revisions\/15318"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media\/12086"}],"wp:attachment":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media?parent=12100"}],"wp:term":[{"taxonomy":"people_teams","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people_teams?post=12100"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}