{"id":857,"date":"2013-03-05T09:55:51","date_gmt":"2013-03-05T07:55:51","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae"},"modified":"2022-09-26T20:28:23","modified_gmt":"2022-09-26T18:28:23","slug":"namd-modelling-of-streptococcus-pneumoniae","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae\/","title":{"rendered":"NAMD modelling of Streptococcus pneumoniae"},"content":{"rendered":"Neann Mathai is completing a PhD in computer science, below is a pr\u00e9cis\u00a0of her work:\r\n\r\n<span style=\"font-family: 'times new roman', times; color: #333333;\">\" My project focuses on modelling Streptococcus Pnuemoniea Serogroup 6 outer polysaccharides, some of which are used in vaccines. About 91 strains of the S.Pnuemonae \u00a0bacteria are disease causing bacteria, causing Invasive Pneumococcal Disease a leading cause of death in children under 5. The objective of this project is to relate structure to function in order to explain the various efficacies of Serogroup 6 serotypes used in conjugate vaccines, thereby improving vaccines. I am currently using the ICTS HPC facilities to run molecular dynamics simulations on these polysaccharides. \u00a0The results of these simulations will elucidate structural details of these serotypes, not normally visible through traditional experimental methods. \u00a0These simulations are very computationally expensive, and as a result the Dell C6145 64 core nodes on the ICTS cluster has been especially useful in hastening calculations and the rate at which data is produced. \"<\/span>\r\n\r\n<a href=\"http:\/\/en.wikipedia.org\/wiki\/Streptococcus_pneumoniae\"><img src=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/Pneumococcus_CDC_PHIL_ID1003.jpg\" alt=\"Pneumococcus\" border=\"0\" \/><\/a>","protected":false},"excerpt":{"rendered":"<p>Neann Mathai is completing a PhD in computer science, below is a pr&eacute;cis&nbsp;of her work:<\/p>\n<p><span>&#8221; My project focuses on modelling Streptococcus Pnuemoniea Serogroup 6 outer polysaccharides, some of which are used in vaccines. About 91 strains of the S.Pnuemonae &nbsp;bacteria are disease causing bacteria, causing Invasive Pneumococcal Disease a leading cause of death in children under 5. The objective of this project is to relate structure to function in order to explain the various efficacies of Serogroup 6 serotypes used in conjugate vaccines, thereby improving vaccines. I am currently using the ICTS HPC facilities to run molecular dynamics simulations on these polysaccharides. &nbsp;The results of these simulations will elucidate structural details of these serotypes, not normally visible through traditional experimental methods. &nbsp;These simulations are very computationally expensive, and as a result the Dell C6145 64 core nodes on the ICTS cluster has been especially useful in hastening calculations and the rate at which data is produced. &#8220;<\/span><\/p>\n<p><a href=\"http:\/\/en.wikipedia.org\/wiki\/Streptococcus_pneumoniae\"><img decoding=\"async\" src=\"http:\/\/blogs.uct.ac.za\/gallery\/1253\/Pneumococcus_CDC_PHIL_ID1003.jpg\" border=\"0\" alt=\"Pneumococcus\"><\/a>&nbsp;<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[9,4],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>NAMD modelling of Streptococcus pneumoniae - UCT HPC<\/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:\/\/ucthpc.uct.ac.za\/index.php\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"NAMD modelling of Streptococcus pneumoniae - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"Neann Mathai is completing a PhD in computer science, below is a pr&eacute;cis&nbsp;of her work:&quot; My project focuses on modelling Streptococcus Pnuemoniea Serogroup 6 outer polysaccharides, some of which are used in vaccines. About 91 strains of the S.Pnuemonae &nbsp;bacteria are disease causing bacteria, causing Invasive Pneumococcal Disease a leading cause of death in children under 5. The objective of this project is to relate structure to function in order to explain the various efficacies of Serogroup 6 serotypes used in conjugate vaccines, thereby improving vaccines. I am currently using the ICTS HPC facilities to run molecular dynamics simulations on these polysaccharides. &nbsp;The results of these simulations will elucidate structural details of these serotypes, not normally visible through traditional experimental methods. &nbsp;These simulations are very computationally expensive, and as a result the Dell C6145 64 core nodes on the ICTS cluster has been especially useful in hastening calculations and the rate at which data is produced. &quot;&nbsp;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2013-03-05T07:55:51+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-09-26T18:28:23+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/Pneumococcus_CDC_PHIL_ID1003.jpg\" \/>\n<meta name=\"author\" content=\"Andrew Lewis\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Andrew Lewis\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae\/\"},\"author\":{\"name\":\"Andrew Lewis\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/c183ad1c0a1063124a72d63963ae9c7e\"},\"headline\":\"NAMD modelling of Streptococcus pneumoniae\",\"datePublished\":\"2013-03-05T07:55:51+00:00\",\"dateModified\":\"2022-09-26T18:28:23+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae\/\"},\"wordCount\":159,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"application\",\"hpc\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/03\/05\/namd-modelling-of-streptococcus-pneumoniae\/\",\"name\":\"NAMD modelling of Streptococcus pneumoniae - 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