{"id":2026,"date":"2013-10-15T11:13:45","date_gmt":"2013-10-15T15:13:45","guid":{"rendered":"http:\/\/blogs.wabash.edu\/fyi\/?p=2026"},"modified":"2025-12-10T10:42:46","modified_gmt":"2025-12-10T15:42:46","slug":"big-step-in-understanding-chemisty","status":"publish","type":"post","link":"https:\/\/blog.wabash.edu\/fyi\/2013\/10\/15\/big-step-in-understanding-chemisty\/","title":{"rendered":"Big Step in Understanding Chemistry"},"content":{"rendered":"

Richard Paige<\/em> – Maybe it was the Nobel Prize, or my wanting to become a bit more familiar with things here on campus in what is week three for me at Wabash.\u00a0 Perhaps it was the lure of free pizza.<\/p>\n

No matter the reason, I swallowed hard, and climbed the stairs to Hays 319 for what was to be my first science lecture in a quarter century.<\/p>\n

I was curious, and isn\u2019t that half the battle?<\/p>\n

West Virginia University\u2019s Dr. Blake Mertz was giving a noontime talk on computational chemistry entitled, \u201cNovel PIP2 Lipid Binding to Focal Adhesion Kinase Probed Through Coarse-Grained Molecular Dynamics Simulations.\u201d<\/p>\n

Computational chemistry is a branch of the science that uses the computer to help predict how molecules interact, which can be essential to understanding the nature of diseases and the production of medicine.<\/p>\n

Last week, three scientists \u2013 Martin Karplus, Michael Levitt and Arieh Warshel \u2013 shared the Nobel Prize for chemistry with pioneering work in this area, much of it dating back to the early 1970s.<\/p>\n

\"several<\/a>\u201cThat (the Nobel Prize) is pretty amazing based on what others with their ideas,\u201d said Dr. Scott Feller, the Howell Professor of Chemistry.\u00a0 They developed a new approach to chemistry.\u201d<\/p>\n

Feller continued by saying that the average person just wants science to come up with a cure for cancer so to speak, but that Karplus, Levitt and Warshel, \u201cenabled others to find that cure with a new way to think about and study a problem.\u201d<\/p>\n

Mertz\u2019s talk opened with some basics, that amino acids are the building blocks of proteins.\u00a0 Check. I remember that from way back when. And much of what was discussed today, i.e. molecular dynamics, would be based on Newton\u2019s second law of motion (F=ma).\u00a0 Check.\u00a0 I remember that, too.<\/p>\n

From that point, much of what was discussed went clear over my head.\u00a0 The simple thought is that one still needs to understand the theory behind the problem, how the forces change in an experiment, before all is plugged into the computer and the results are produced.<\/p>\n

Before all of this can happen, four questions need to be answered:<\/p>\n

1.)\u00a0\u00a0\u00a0 Can I answer my question using simulation?\u00a0 The simpler the question, the more likely that this is the case.<\/p>\n

2.)\u00a0\u00a0\u00a0 What is the timescale of what I want to observe?<\/p>\n

3.)\u00a0\u00a0\u00a0 How accurate does my model need to be?<\/p>\n

4.)\u00a0\u00a0\u00a0 Do I have a computer that can handle the calculations?<\/p>\n

What I found as interesting was the fact that as these computer simulations become more powerful, there remains the potential that such simulations could render traditional experiments obsolete.<\/p>\n

\u201cI think eventually we\u2019ll find a happy medium,\u201d said Mertz.\u00a0 \u201cThere is still huge bias toward experimental results in the scientific community, like \u2018If I can\u2019t see it, then I\u2019m not going to believe it.\u2019<\/p>\n

\u201cCertainly, these are questions that need to be answered,\u201d he continued.\u00a0 \u201cThe benefit of doing simulations is that you can really look at things on an atomic level.\u00a0 Experimentalists are trying to get to that level where they can see atoms, but that level is so small that you can\u2019t answer those questions with an experiment.\u00a0 Ultimately, I think that computational chemistry is another tool for us to use.\u00a0 What separates the men from the boys in the lab is how judiciously you use them.\u201d<\/p>\n

Now that\u2019s language that I can understand.<\/p>\n","protected":false},"excerpt":{"rendered":"

Richard Paige – Maybe it was the Nobel Prize, or my wanting to become a bit more familiar with things here on campus in what is week three for me at Wabash.\u00a0 […]<\/p>\n","protected":false},"author":5,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-2026","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"w_featured_image_url":"https:\/\/blog.wabash.edu\/fyi\/wp-content\/uploads\/sites\/4\/2013\/10\/RichardBlogPic.jpg","_links":{"self":[{"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/posts\/2026","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/comments?post=2026"}],"version-history":[{"count":1,"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/posts\/2026\/revisions"}],"predecessor-version":[{"id":3794,"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/posts\/2026\/revisions\/3794"}],"wp:attachment":[{"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/media?parent=2026"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/categories?post=2026"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blog.wabash.edu\/fyi\/wp-json\/wp\/v2\/tags?post=2026"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}