{"id":10454,"date":"2015-09-16T14:32:30","date_gmt":"2015-09-16T12:32:30","guid":{"rendered":"http:\/\/www.h-its.org\/?p=10454"},"modified":"2019-09-24T11:40:26","modified_gmt":"2019-09-24T09:40:26","slug":"lectures-and-hands-on-sessions-in-computational-biophysics","status":"publish","type":"post","link":"https:\/\/www.h-its.org\/de\/2015\/09\/16\/lectures-and-hands-on-sessions-in-computational-biophysics\/","title":{"rendered":"Lectures and Hands-on sessions in Computational Biophysics!"},"content":{"rendered":"\n<p>How can a bird sense magnetic fields, how does our ear detect sound waves, how does our bone feel gravitation? It is the physics of individual molecules that dictate these and many other processes in life.<\/p>\n\n\n\n<p>This course introduces computational methods to study the structure, dynamics and mechanics of biomolecules at different scales. It aims at endowing the students with an understanding of the principles, the capacity and limitations of different numerical simulation techniques with an emphasis on Molecular Dynamics simulations. The course comprises alternating lectures and hands-on computer tutorials of which the latter are meant to directly demonstrate the principles of running and analyzing computer simulations of biological matter. Lectures and hands-on computer tutorials will take place alternately in the seminar room SR043 and the CIP-Pool (both Bioquant). The lectures\/tutorials will take place once a week, on Wed from 4 to 5.30 pm (2 SWS), starting now on October 14, 2015. Lectures will be given by Prof. Frauke Gr\u00e4ter and &nbsp;Prof. Rebecca Wade.<\/p>\n\n\n\n<p>The lectures will be targeted to&nbsp;advanced Bachelor, Master and interested PhD students and will be complemented by hands-on computer sessions in which the students will have the opportunity to run molecular simulations supervised by Dr. Katra Kol\u0161ek, Dr. Csaba Daday and Ms. Ana Herrera-Rodriguez.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Lectures:<\/h2>\n\n\n\n<p>Introduction<\/p>\n\n\n\n<p>Examples for forces in biology: bone and gravity; birds and magnetic fields; muscle and motors; ears and sound waves<\/p>\n\n\n\n<p>Structure &amp; dynamics of biomolecules (proteins, RNA and DNA)<\/p>\n\n\n\n<p>Mechanics of biomolecules (polymer theories, rate theories, experiments)<\/p>\n\n\n\n<p>Atomistic scale:<\/p>\n\n\n\n<p>Molecular Dynamics I \u2013 approximations and force fields;<\/p>\n\n\n\n<p>Molecular Dynamics II \u2013 integration schemes;<\/p>\n\n\n\n<p>Molecular Dynamics III \u2013 boundaries, electrostatics, ensembles;<\/p>\n\n\n\n<p>Molecular Dynamics IV \u2013 probing mechanics;<\/p>\n\n\n\n<p>Monte Carlo<\/p>\n\n\n\n<p>Mesoscopic scale:<\/p>\n\n\n\n<p>Coarse-graining, Go models, Langevin and Brownian Dynamics<\/p>\n\n\n\n<p>continuum approximations<\/p>\n\n\n\n<p>Macroscopic scale:<\/p>\n\n\n\n<p>computational mechanics, finite element methods, fracture theories;<\/p>\n\n\n\n<p>Current challenges: bridging scales, whole virus\/cell simulations<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Tutorials<strong>:<\/strong><\/h2>\n\n\n\n<p>MD: phase transition of argon<\/p>\n\n\n\n<p>MD: structure and dynamics of the protein ubiquitin<\/p>\n\n\n\n<p>MD: mechanics of ubiquitin<\/p>\n\n\n\n<p>Brownian Dynamics<\/p>\n\n\n\n<p>finite-element analysis of DNA mechanics<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Resources:<\/h2>\n\n\n\n<ol class=\"wp-block-list\"><li>Schlick, \u201cMolecular Modelling and Simulation\u201d, Springer, 2010<\/li><\/ol>\n\n\n\n<p>M.P. Allen and Tildesley, &#8222;Computer Simulation of Liquids&#8220;, Oxford Science Publishers. (Great book with a focus on Molecular Dynamics simulations)<\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Frenkel und B. Smit. \u201cUnderstanding molecular simulation\u201d Academic, San Diego, 2002, (covers MD, MC and Stat Mech)<\/li><li>Dill and S. Bromberg, \u201cMolecular Driving Forces\u201d, Taylor &amp; Francis Inc, 2010<\/li><\/ol>\n\n\n\n<p><a href=\"http:\/\/www.gromacs.org\">www.gromacs.org<\/a>&nbsp;open source molecular simulation software used in the tutorial, for both atomistic MD and coarse-grained Brownian dynamics simulations. Comes with an extensive manual, which includes the principles of MD simulations and biomolecular force fields.<\/p>\n\n\n\n<p><a href=\"http:\/\/cando-dna-origami.org\/\">http:\/\/cando-dna-origami.org\/<\/a>&nbsp;web-based finite element software for mechanics\/dynamics of DNA sculptures<\/p>\n","protected":false},"excerpt":{"rendered":"<p>How can a bird sense magnetic fields, how does our ear detect sound waves, how does our bone feel gravitation? It &#8230;<\/p>\n","protected":false},"author":82,"featured_media":29743,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"categories":[1],"hits-research-group":[1296],"class_list":["post-10454","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-gruppen-news","hits-research-group-mbm-de"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Lectures and Hands-on sessions in Computational Biophysics! - HITS gGmbH<\/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:\/\/www.h-its.org\/de\/2015\/09\/16\/lectures-and-hands-on-sessions-in-computational-biophysics\/\" \/>\n<meta property=\"og:locale\" content=\"de_DE\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Lectures and Hands-on sessions in Computational Biophysics! - HITS gGmbH\" \/>\n<meta property=\"og:description\" content=\"How can a bird sense magnetic fields, how does our ear detect sound waves, how does our bone feel gravitation? 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