{"id":422875,"date":"2022-03-28T22:12:22","date_gmt":"2022-03-28T19:12:22","guid":{"rendered":"https:\/\/en.buradabiliyorum.com\/a-new-model-to-aid-interpretation-of-atomic-resolution-molecular-images\/"},"modified":"2022-03-28T22:12:22","modified_gmt":"2022-03-28T19:12:22","slug":"a-new-model-to-aid-interpretation-of-atomic-resolution-molecular-images","status":"publish","type":"post","link":"https:\/\/buradabiliyorum.com\/en\/a-new-model-to-aid-interpretation-of-atomic-resolution-molecular-images\/","title":{"rendered":"#A new model to aid interpretation of atomic resolution molecular images"},"content":{"rendered":"<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_85 counter-hierarchy ez-toc-counter ez-toc-custom ez-toc-container-direction\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">Table of Contents<\/p>\n<label for=\"ez-toc-cssicon-toggle-item-6a36e7b547de1\" class=\"ez-toc-cssicon-toggle-label\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #dd3333;color:#dd3333\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #dd3333;color:#dd3333\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/label><input type=\"checkbox\"  id=\"ez-toc-cssicon-toggle-item-6a36e7b547de1\" checked aria-label=\"Toggle\" \/><nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/buradabiliyorum.com\/en\/a-new-model-to-aid-interpretation-of-atomic-resolution-molecular-images\/#%E2%80%9CA_new_model_to_aid_interpretation_of_atomic_resolution_molecular_images%E2%80%9D\" >&#8220;A new model to aid interpretation of atomic resolution molecular images&#8221;<\/a><\/li><\/ul><\/nav><\/div>\n<h1><span class=\"ez-toc-section\" id=\"%E2%80%9CA_new_model_to_aid_interpretation_of_atomic_resolution_molecular_images%E2%80%9D\"><\/span>&#8220;A new model to aid interpretation of atomic resolution molecular images&#8221;<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<div>\n<div class=\"article-gallery lightGallery\">\n<div data-thumb=\"https:\/\/scx1.b-cdn.net\/csz\/news\/tmb\/2022\/visualizing-the-invisi-1.jpg\" data-src=\"https:\/\/scx2.b-cdn.net\/gfx\/news\/2022\/visualizing-the-invisi-1.jpg\" data-sub-html=\"The familiar periodic table of elements with each kind of atom shown as colored balls. The size of each atom in the CPK model (above) is larger than those in the Z-correlated model (below), as it is based on the distribution of electrons around an atom rather than on the size of the nucleus itself. This is important in electron microscopy where the electron cloud is not visible. Credit: \u00a9 2021 Nakamura, Harano et al.\">\n<figure class=\"article-img\">\n            <img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/scx1.b-cdn.net\/csz\/news\/800a\/2022\/visualizing-the-invisi-1.jpg\" alt=\"Visualizing the invisible\" title=\"The familiar periodic table of elements with each kind of atom shown as colored balls. The size of each atom in the CPK model (above) is larger than those in the Z-correlated model (below), as it is based on the distribution of electrons around an atom rather than on the size of the nucleus itself. This is important in electron microscopy where the electron cloud is not visible. Credit: \u00a9 2021 Nakamura, Harano et al.\" width=\"800\" height=\"530\"\/><figcaption class=\"text-darken text-low-up text-truncate-js text-truncate mt-3\">\n                The familiar periodic table of elements with each kind of atom shown as colored balls. The size of each atom in the CPK model (above) is larger than those in the Z-correlated model (below), as it is based on the distribution of electrons around an atom rather than on the size of the nucleus itself. This is important in electron microscopy where the electron cloud is not visible. Credit: \u00a9 2021 Nakamura, Harano et al.<br \/>\n            <\/figcaption><\/figure>\n<\/p><\/div>\n<\/div>\n<p>There are multiple ways to create two- and three-dimensional models of atoms and molecules. With the advent of cutting-edge <a href=\"https:\/\/buradabiliyorum.com\/en\/category\/download-scripts-themes-apps\/\" data-internallinksmanager029f6b8e52c=\"9\" title=\"Download Scripts &amp; Themes &amp; Apps\" target=\"_blank\" rel=\"noopener\">app<\/a>aratus that can image samples at the atomic scale, scientists found that traditional molecular models did not fit the images they saw. Researchers have devised a better way to visualize molecules building on these traditional methods. Their models fit the imaging data they acquire well, and they hope the models can therefore help chemists with their intuition for interpreting molecular images.<\/p>\n<section class=\"article-banner first-banner ads-336x280\">\n         <!-- \/4988204\/Phys_Story_InText_Box --><\/p>\n<\/section>\n<p>Anyone reading this is likely familiar with traditional ball-and-stick models of atoms and molecules, where balls of different size and color represent the various atomic nuclei, and the sticks represent properties of the bonds between atoms. Although these are useful educational tools, they are far simpler than the reality they reflect. Chemists tend to use models such as the Corey\u2013Pauling\u2013Koltun (CPK) model, which is similar to the ball-and-stick model but with the balls inflated so that they overlap. The CPK model tells chemists more about the way components of a molecule interact far better than the ball-and-stick model.<\/p>\n<p>In recent years, it has finally become possible not only to capture the structures of molecules but even to record their motion and interactions in videos thanks to technologies like atomic resolution transmission electron microscopy (AR-TEM). This is sometimes called &#8220;cinematic molecular <a href=\"https:\/\/buradabiliyorum.com\/en\/category\/sciencee\/\" data-internallinksmanager029f6b8e52c=\"5\" title=\"Science\" target=\"_blank\" rel=\"noopener\">science<\/a>.&#8221; However, it is with this leap in our capacity to visualize the invisible that the ball-and-stick or CPK models become a hindrance rather than a help. When researchers from the Department of Chemistry at the University of Tokyo tried to fit these models with the images they were seeing, they ran into some problems.<\/p>\n<figure class=\"mb-4\" itemscope=\"\" itemtype=\"http:\/\/schema.org\/VideoObject\">\n    <meta itemprop=\"name\" content=\"Visualizing the invisible\"\/><br \/>\n    <meta itemprop=\"url\" content=\"https:\/\/scx2.b-cdn.net\/gfx\/video\/2022\/visualizing-the-invisi-1.mp4\"\/><br \/>\n    <meta itemprop=\"description\" content=\"The researchers\u2019 Z-correlated molecular model is compared to the ball-and-stick and the CPK models. Credit: \u00a9 2021 Nakamura, Harano et al.\"\/><br \/>\n    <meta itemprop=\"uploadDate\" content=\"2022-03-28T04:49:46-04:00\"\/><br \/>\n        <meta itemprop=\"thumbnailUrl\" content=\"https:\/\/scx1.b-cdn.net\/gfx\/video_tmb\/2022\/visualizing-the-invisi-1.mp4.jpg\"\/><br \/>\n    <meta itemprop=\"contentUrl\" content=\"https:\/\/scx2.b-cdn.net\/gfx\/video\/2022\/visualizing-the-invisi-1.mp4\"\/><br \/>\n            <video class=\"embed-responsive embed-responsive-16by9\" id=\"jwVID68810\" controls=\"\" poster=\"https:\/\/scx1.b-cdn.net\/gfx\/video_tmb\/2022\/visualizing-the-invisi-1.mp4.jpg\"><source src=\"https:\/\/scx2.b-cdn.net\/gfx\/video\/2022\/visualizing-the-invisi-1.mp4\" type=\"video\/mp4\"><\/source><\/video><figcaption class=\"text-darken text-low-up mt-4\" itemprop=\"caption\">The researchers\u2019 Z-correlated molecular model is compared to the ball-and-stick and the CPK models. Credit: \u00a9 2021 Nakamura, Harano et al.<\/figcaption><\/figure>\n<p>&#8220;The ball-and-stick model is far too simple to accurately describe what is really going on in our images,&#8221; said Professor Koji Harano. &#8220;And the CPK model, which technically shows the spread of the electron cloud around an atomic nucleus, is too dense to discern some details. The reason is that neither of those models demonstrate the true sizes of atoms that images from AR-TEM show.&#8221;<\/p>\n<p>In AR-TEM images, the size of each atom directly correlates with that atom&#8217;s atomic weight, known simply as Z. So Professor Eiichi Nakamura and his team opted to modify a ball-and-stick model to fit their images, where each nucleus in the model was sized according to the Z number of the nucleus it represents, and named it Z-correlated (ZC) molecular model. They kept the same color system used in the CPK model, originally introduced by American chemists Robert Corey and Linus Pauling in 1952.<\/p>\n<p>&#8220;A picture is worth a thousand words, and you can compare AR-TEM images to the first-ever photograph of a black hole,&#8221; said Nakamura. &#8220;They both show reality as never seen before, and both are far less clear than how people probably imagine those things should look. This is why models are so important, to bridge the gap between imagination and reality. We hope the Z-correlated molecular model will help chemists analyze electron microscope images based on intuition without even the need for any theoretical calculations, and open up a new world of &#8216;cinematic molecular science.'&#8221;<\/p>\n<p>The study is published in the <i>Proceedings of the National Academy of Sciences<\/i>.<\/p>\n<hr\/>\n<div class=\"article-main__explore my-4 d-print-none\">\n<p>                                            Groundbreaking visualization of atomic movements\n                                        <\/p><\/div>\n<hr class=\"mb-4\"\/>\n<div class=\"article-main__more p-4\">\n                                                                                                <strong>More information:<\/strong><br \/>\n                                                Junfei Xing et al. Atomic-Number (Z)-Correlated Atomic Sizes for Deciphering Electron Microscopic Molecular Images, <i>Proceedings of the National Academy of Sciences<\/i> (2022). <a rel=\"nofollow noopener\" target=\"_blank\" data-doi=\"1\" href=\"https:\/\/dx.doi.org\/10.1073\/pnas.2114432119\">DOI: 10.1073\/pnas.2114432119<\/a><\/p><\/div>\n<div class=\"d-inline-block text-medium my-4\">\n                                                Provided by<br \/>\n                                                                                                    University of Tokyo<br \/>\n                                                                                                        <a rel=\"nofollow noopener\" target=\"_blank\" class=\"icon_open\" href=\"http:\/\/www.u-tokyo.ac.jp\/\"><br \/>\n                                                        <svg>\n                                                            <use href=\"https:\/\/phys.b-cdn.net\/tmpl\/v6\/img\/svg\/sprite.svg#icon_open\" x=\"0\" y=\"0\"\/>\n                                                        <\/svg><br \/>\n                                                    <\/a><\/p><\/div>\n<p>                                        <!-- print only --><\/p>\n<div class=\"d-none d-print-block\">\n<p>                                                 <strong>Citation<\/strong>:<br \/>\n                                                 Visualizing the invisible: A new model to aid interpretation of atomic resolution molecular images (2022, March 28)<br \/>\n                                                 retrieved 28 March 2022<br \/>\n                                                 from https:\/\/phys.org\/<a href=\"https:\/\/buradabiliyorum.com\/en\/category\/news\/\" data-internallinksmanager029f6b8e52c=\"2\" title=\"News\" target=\"_blank\" rel=\"noopener\">news<\/a>\/2022-03-visualizing-invisible-aid-atomic-resolution.html<\/p>\n<p>                                            This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no<br \/>\n                                            part may be reproduced without the written permission. The content is provided for information purposes only.<\/p><\/div>\n<\/p><\/div>\n<p><script id=\"facebook-jssdk\" async=\"\" src=\"https:\/\/connect.facebook.net\/en_US\/sdk.js\"><\/script><\/p>\n<blockquote><p><strong><span style=\"color: #ff6600;\">If you liked the article, do not forget to share it with your friends. Follow us on\u00a0<span style=\"color: #ff0000;\"><a style=\"color: #ff0000;\" href=\"https:\/\/news.google.com\/publications\/CAAqBwgKMLG0nwswvr63Aw\" target=\"_blank\" rel=\"nofollow noopener noreferrer\">Google News<\/a><\/span>\u00a0too, click on the star and choose us from your favorites.<\/span><\/strong><\/p><\/blockquote>\n<blockquote>\n<p style=\"text-align: center;\">For forums sites go to <span style=\"color: #ff9900;\"><a style=\"color: #ff9900;\" href=\"https:\/\/forum.buradabiliyorum.com\/\" target=\"_blank\" rel=\"noopener\">Forum.BuradaBiliyorum.Com<\/a><\/span><\/strong>\n<\/p><\/blockquote>\n<blockquote>\n<p style=\"text-align: center;\"><strong>If you want to read more Like this articles, you can visit our <span style=\"color: #ff9900;\"><a style=\"color: #ff9900;\" href=\"https:\/\/en.buradabiliyorum.com\/science\/\" target=\"_blank\" rel=\"noopener\">Science category.<\/a><\/span><\/strong><\/p>\n<\/blockquote>\n<p><span style=\"color: black;\"><a style=\"color: #ff9900;\" href=\"https:\/\/phys.org\/news\/2022-03-visualizing-invisible-aid-atomic-resolution.html\" target=\"_blank\" rel=\"noopener\">Source<\/a><\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>&#8220;A new model to aid interpretation of atomic resolution molecular images&#8221; The familiar periodic table of elements with each kind of atom shown as colored balls. The size of each atom in the CPK model (above) is larger than those in the Z-correlated model (below), as it is based on the distribution of electrons around&#8230;<\/p>\n","protected":false},"author":1,"featured_media":422876,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"fifu_image_url":"https:\/\/scx2.b-cdn.net\/gfx\/news\/2022\/visualizing-the-invisi-1.jpg","fifu_image_alt":"","footnotes":""},"categories":[16],"tags":[],"class_list":["post-422875","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-sciencee"],"_links":{"self":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts\/422875","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/comments?post=422875"}],"version-history":[{"count":0,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts\/422875\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/media\/422876"}],"wp:attachment":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/media?parent=422875"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/categories?post=422875"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/tags?post=422875"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}