{"id":12077,"date":"2023-07-06T15:53:04","date_gmt":"2023-07-06T13:53:04","guid":{"rendered":"https:\/\/new.sano.science\/?post_type=people&p=12077"},"modified":"2024-06-23T12:00:18","modified_gmt":"2024-06-23T10:00:18","slug":"piotr-nowakowski","status":"publish","type":"people","link":"https:\/\/sano.science\/people\/piotr-nowakowski\/","title":{"rendered":"Piotr Nowakowski"},"excerpt":{"rendered":"

Scientific Programmers Manager<\/p>\n","protected":false},"featured_media":16992,"template":"","people_teams":[19,37],"class_list":["post-12077","people","type-people","status-publish","has-post-thumbnail","hentry","people_teams-research","people_teams-scientific-programmers"],"yoast_head":"\nPiotr Nowakowski - 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\/piotr-nowakowski\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Piotr Nowakowski\" \/>\n<meta property=\"og:description\" content=\"Scientific Programmers Manager\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sano.science\/people\/piotr-nowakowski\/\" \/>\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=\"2024-06-23T10:00:18+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/Piotr-Nowakowski.png\" \/>\n\t<meta property=\"og:image:width\" content=\"800\" \/>\n\t<meta property=\"og:image:height\" content=\"800\" \/>\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\\\/piotr-nowakowski\\\/\",\"url\":\"https:\\\/\\\/sano.science\\\/people\\\/piotr-nowakowski\\\/\",\"name\":\"Piotr Nowakowski - Centre for Computational Personalized Medicine\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/sano.science\\\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/piotr-nowakowski\\\/#primaryimage\"},\"image\":{\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/piotr-nowakowski\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/sano.science\\\/wp-content\\\/uploads\\\/2023\\\/07\\\/Piotr-Nowakowski.png\",\"datePublished\":\"2023-07-06T13:53:04+00:00\",\"dateModified\":\"2024-06-23T10:00:18+00:00\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/piotr-nowakowski\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/sano.science\\\/people\\\/piotr-nowakowski\\\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/piotr-nowakowski\\\/#primaryimage\",\"url\":\"https:\\\/\\\/sano.science\\\/wp-content\\\/uploads\\\/2023\\\/07\\\/Piotr-Nowakowski.png\",\"contentUrl\":\"https:\\\/\\\/sano.science\\\/wp-content\\\/uploads\\\/2023\\\/07\\\/Piotr-Nowakowski.png\",\"width\":800,\"height\":800},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/piotr-nowakowski\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/sano.science\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"People\",\"item\":\"https:\\\/\\\/sano.science\\\/people\\\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Research\",\"item\":\"https:\\\/\\\/sano.science\\\/people-teams\\\/research\\\/\"},{\"@type\":\"ListItem\",\"position\":4,\"name\":\"Piotr Nowakowski\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/sano.science\\\/#website\",\"url\":\"https:\\\/\\\/sano.science\\\/\",\"name\":\"Centre for Computational Personalized Medicine\",\"description\":\"Sano \u2013 Centre for Computational Medicine\",\"publisher\":{\"@id\":\"https:\\\/\\\/sano.science\\\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/sano.science\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\\\/\\\/sano.science\\\/#organization\",\"name\":\"Sano \u2013 Centre for Computational Medicine\",\"alternateName\":\"Sano\",\"url\":\"https:\\\/\\\/sano.science\\\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/sano.science\\\/#\\\/schema\\\/logo\\\/image\\\/\",\"url\":\"https:\\\/\\\/sano.science\\\/wp-content\\\/uploads\\\/2024\\\/05\\\/logo_sano_podstawowe.png\",\"contentUrl\":\"https:\\\/\\\/sano.science\\\/wp-content\\\/uploads\\\/2024\\\/05\\\/logo_sano_podstawowe.png\",\"width\":700,\"height\":265,\"caption\":\"Sano \u2013 Centre for Computational Medicine\"},\"image\":{\"@id\":\"https:\\\/\\\/sano.science\\\/#\\\/schema\\\/logo\\\/image\\\/\"},\"sameAs\":[\"https:\\\/\\\/www.facebook.com\\\/sano.science\\\/\",\"https:\\\/\\\/x.com\\\/sanoscience\",\"https:\\\/\\\/www.linkedin.com\\\/company\\\/sanoscience\\\/\",\"https:\\\/\\\/www.youtube.com\\\/channel\\\/UCDZ_8TcjMWUG2ZcgKKgfpwQ\",\"https:\\\/\\\/bsky.app\\\/profile\\\/sanoscience.bsky.social\"]}]}<\/script>\n<!-- \/ Yoast SEO Premium plugin. -->","yoast_head_json":{"title":"Piotr Nowakowski - Centre for Computational Personalized Medicine","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/sano.science\/people\/piotr-nowakowski\/","og_locale":"en_US","og_type":"article","og_title":"Piotr Nowakowski","og_description":"Scientific Programmers Manager","og_url":"https:\/\/sano.science\/people\/piotr-nowakowski\/","og_site_name":"Centre for Computational Personalized Medicine","article_publisher":"https:\/\/www.facebook.com\/sano.science\/","article_modified_time":"2024-06-23T10:00:18+00:00","og_image":[{"width":800,"height":800,"url":"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/Piotr-Nowakowski.png","type":"image\/png"}],"twitter_card":"summary_large_image","twitter_site":"@sanoscience","twitter_misc":{"Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/sano.science\/people\/piotr-nowakowski\/","url":"https:\/\/sano.science\/people\/piotr-nowakowski\/","name":"Piotr Nowakowski - Centre for Computational Personalized Medicine","isPartOf":{"@id":"https:\/\/sano.science\/#website"},"primaryImageOfPage":{"@id":"https:\/\/sano.science\/people\/piotr-nowakowski\/#primaryimage"},"image":{"@id":"https:\/\/sano.science\/people\/piotr-nowakowski\/#primaryimage"},"thumbnailUrl":"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/Piotr-Nowakowski.png","datePublished":"2023-07-06T13:53:04+00:00","dateModified":"2024-06-23T10:00:18+00:00","breadcrumb":{"@id":"https:\/\/sano.science\/people\/piotr-nowakowski\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/sano.science\/people\/piotr-nowakowski\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/sano.science\/people\/piotr-nowakowski\/#primaryimage","url":"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/Piotr-Nowakowski.png","contentUrl":"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/Piotr-Nowakowski.png","width":800,"height":800},{"@type":"BreadcrumbList","@id":"https:\/\/sano.science\/people\/piotr-nowakowski\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/sano.science\/"},{"@type":"ListItem","position":2,"name":"People","item":"https:\/\/sano.science\/people\/"},{"@type":"ListItem","position":3,"name":"Research","item":"https:\/\/sano.science\/people-teams\/research\/"},{"@type":"ListItem","position":4,"name":"Piotr Nowakowski"}]},{"@type":"WebSite","@id":"https:\/\/sano.science\/#website","url":"https:\/\/sano.science\/","name":"Centre for Computational Personalized Medicine","description":"Sano \u2013 Centre for Computational Medicine","publisher":{"@id":"https:\/\/sano.science\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/sano.science\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/sano.science\/#organization","name":"Sano \u2013 Centre for Computational Medicine","alternateName":"Sano","url":"https:\/\/sano.science\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/sano.science\/#\/schema\/logo\/image\/","url":"https:\/\/sano.science\/wp-content\/uploads\/2024\/05\/logo_sano_podstawowe.png","contentUrl":"https:\/\/sano.science\/wp-content\/uploads\/2024\/05\/logo_sano_podstawowe.png","width":700,"height":265,"caption":"Sano \u2013 Centre for Computational Medicine"},"image":{"@id":"https:\/\/sano.science\/#\/schema\/logo\/image\/"},"sameAs":["https:\/\/www.facebook.com\/sano.science\/","https:\/\/x.com\/sanoscience","https:\/\/www.linkedin.com\/company\/sanoscience\/","https:\/\/www.youtube.com\/channel\/UCDZ_8TcjMWUG2ZcgKKgfpwQ","https:\/\/bsky.app\/profile\/sanoscience.bsky.social"]}]}},"acf":[],"meta_data":{"description":"<p>Involved in the preparation of the Sano project since its inception, and currently assisting in the preparation of Sano\u2019s internal documents and regulations (including English translations of the relevant documentation). Has participated in numerous collaborative research projects, both national and European, performing development work on collaborative research environments and distributed data storage systems. Also works as a translator, with several dozen published book translations under his belt.<\/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":14937,"post_author":"5","post_date":"2024-01-16 13:33:06","post_date_gmt":"2024-01-16 12:33:06","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-G1GWMI\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Piotr Kica, Magdalena Otta, Krzysztof Czechowicz, Karol Zaj\u0105c, Piotr Nowakowski, Andrew Narracott, Ian Halliday, Maciej Malawski<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-vSoDxU\",\"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-sGaBCh\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Digital twins are virtual representations of physical objects or systems used for the purpose of analysis, most often via computer simulations, in many engineering and scientific disciplines. Recently, this approach has been introduced to computational medicine, within the concept of Digital Twin in Healthcare (DTH). Such research requires verification and validation of its models, as well as the corresponding sensitivity analysis and uncertainty quantification (VVUQ). From the computing perspective, VVUQ is a computationally intensive process, as it requires numerous runs with variations of input parameters. Researchers often use high-performance computing (HPC) solutions to run VVUQ studies where the number of parameter combinations can easily reach tens of thousands. However, there is a viable alternative to HPC for a substantial subset of computational models - serverless computing. In this paper we hypothesize that using the serverless computing model can be a practical and efficient approach to selected cases of running VVUQ calculations. We show this on the example of the EasyVVUQ library, which we extend by providing support for many serverless services. The resulting library - CloudVVUQ - is evaluated using two real-world applications from the computational medicine domain adapted for serverless execution. Our experiments demonstrate the scalability of the proposed approach.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-vSoDxU\",\"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_65a6776af10b8\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.computer.org\/csdl\/proceedings-article\/ccgrid\/2023\/011900a627\/1OFrjleAbTy\",\"_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":"Serverless Approach to Sensitivity Analysis of Computational Models","post_excerpt":"In: CCGrid2023, 2023.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"serverless-approach-to-sensitivity-analysis-of-computational-models","to_ping":"","pinged":"","post_modified":"2024-01-16 13:33:06","post_modified_gmt":"2024-01-16 12:33:06","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=14937","menu_order":27,"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"},{"ID":12582,"post_author":"5","post_date":"2023-07-12 15:39:45","post_date_gmt":"2023-07-12 13:39:45","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-J5dqk1\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Nowakowski, Piotr; Bubak, Marian; Barty\u0144ski, Tomasz; Guba\u0142a, Tomasz; Harce\u017clak, Daniel; Kasztelnik, Marek; Malawski, Maciej; Meizner, Jan<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-s1TArR\",\"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-a3R9xa\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">As virtualization technologies mature and become ever more widespread, cloud computing has emerged as a promising paradigm for e-science. In order to facilitate successful application of cloud computing in scientific research \u2013 particularly in a domain as security-minded as medical research \u2013 several technical challenges need to be addressed. This paper reports on the successful deployment and utilization of a cloud computing platform for the Virtual Physiological Human (VPH) research community, originating in the VPH-Share project and continuing beyond the end of this project. The platform tackles technical issues involved in porting existing desktop applications to the cloud environment and constitutes a uniform research space where application services can be developed, stored, accessed and shared using a variety of computational infrastructures. The paper also presents examples of application workflows which make use of the presented infrastructure \u2013 both internal and external to the VPH community.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-12Pdvl\",\"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_64aeacf54484e\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/dx.doi.org\/10.1016\/j.jocs.2017.06.012\",\"_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":"Cloud computing infrastructure for the VPH community\u00a0","post_excerpt":"In: Journal of Computational Science, vol. 24, pp. 169\u2013179, 2018, ISSN: 18777503.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"cloud-computing-infrastructure-for-the-vph-community","to_ping":"","pinged":"","post_modified":"2024-01-05 13:58:08","post_modified_gmt":"2024-01-05 12:58:08","post_content_filtered":"","post_parent":0,"guid":"https:\/\/new.sano.science\/?post_type=research&p=12582","menu_order":96,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":12568,"post_author":"5","post_date":"2023-07-12 14:05:16","post_date_gmt":"2023-07-12 12:05:16","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-KUhwAl\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Bubak, M; Czechowicz, K; Guba\u0142a, T; Hose, D R; Kasztelnik, M; Malawski, M; Meizner, J; Nowakowski, P; Wood, S<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-EBnA15\",\"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-N4wtZJ\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">The goal of this paper is to present a dedicated high-performance computing (HPC) infrastructure which is used in the development of a so-called reduced-order model (ROM) for simulating the outcomes of interventional procedures which are contemplated in the treatment of valvular heart conditions. Following a brief introduction to the problem, the paper presents the design of a model execution environment, in which representative cases can be simulated and the parameters of the ROM fine-tuned to enable subsequent deployment of a decision support system without further need for HPC. The presentation of the system is followed by information concerning its use in processing specific patient cases in the context of the EurValve international collaboration.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-I1PAzT\",\"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_64ae96e2d28c3\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/royalsocietypublishing.org\/doi\/10.1098\/rsfs.2020.0006\",\"_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":"The EurValve model execution environment\u00a0","post_excerpt":"In: Interface Focus, vol. 11, no. 1, pp. 20200006, 2021, ISSN: 2042-8898.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"the-eurvalve-model-execution-environment","to_ping":"","pinged":"","post_modified":"2024-01-05 14:00:04","post_modified_gmt":"2024-01-05 13:00:04","post_content_filtered":"","post_parent":0,"guid":"https:\/\/new.sano.science\/?post_type=research&p=12568","menu_order":79,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"}]},"_links":{"self":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12077","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\/12077\/revisions"}],"predecessor-version":[{"id":15315,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12077\/revisions\/15315"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media\/16992"}],"wp:attachment":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media?parent=12077"}],"wp:term":[{"taxonomy":"people_teams","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people_teams?post=12077"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}