{"id":1008,"date":"2024-12-10T15:26:00","date_gmt":"2024-12-10T15:26:00","guid":{"rendered":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/?p=1008"},"modified":"2024-12-10T15:30:42","modified_gmt":"2024-12-10T15:30:42","slug":"quantum-computing-applied-to-protein-folding-problems","status":"publish","type":"post","link":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/12\/10\/quantum-computing-applied-to-protein-folding-problems\/","title":{"rendered":"Quantum computing to untangle (or rather, entangle?) protein folding"},"content":{"rendered":"<p><span data-contrast=\"none\">It might take time, but with your list of clues you would probably be able to piece together your Lego set eventually. But in the case of protein folding, no supercomputer is powerful enough to make any significant advancement on its own. That\u2019s where quantum computers come into play.<\/span><span data-ccp-props=\"{}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\"><strong>Manya Bhargava<\/strong> returns to the IMSE blog to continue exploring the <a href=\"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/\" target=\"_blank\" rel=\"noopener\">protein folding problem<\/a>. In her previous blog, she explained <\/span><span data-contrast=\"none\">how AlphaFold (AI system) <\/span><span data-contrast=\"none\">uses known structures to predict <\/span><span data-contrast=\"none\">the structures of unknown proteins. However, any AI system relies heavily on experimentally obtained data<\/span><span data-contrast=\"none\">. <\/span><span data-contrast=\"none\">On this new blog entry, Manya explains how quantum computers help to advance <\/span><span data-contrast=\"none\">the problem by providing new solutions.<\/span><\/p>\n<p><!--more--><\/p>\n<h2>Superposition, being ON and OFF<\/h2>\n<p><span class=\"TextRun SCXW215552875 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><a href=\"https:\/\/www.ibm.com\/topics\/quantum-computing\" target=\"_blank\" rel=\"noopener\"><span class=\"NormalTextRun SCXW215552875 BCX8\">Quantum computers <\/span><\/a><span class=\"NormalTextRun SCXW215552875 BCX8\">utilize<\/span><span class=\"NormalTextRun SCXW215552875 BCX8\"><a href=\"https:\/\/www.iop.org\/explore-physics\/big-ideas-physics\/quantum-mechanics\" target=\"_blank\" rel=\"noopener\"> quantum mechanics<\/a> to perform calculations in a different, and often more efficient, way <\/span><span class=\"NormalTextRun ContextualSpellingAndGrammarErrorV2Themed SCXW215552875 BCX8\">to<\/span><span class=\"NormalTextRun SCXW215552875 BCX8\"> classical computers. <\/span><span class=\"NormalTextRun ContextualSpellingAndGrammarErrorV2Themed SCXW215552875 BCX8\">Everyday<\/span><span class=\"NormalTextRun SCXW215552875 BCX8\"> computers use bits which exist in<\/span> <span class=\"NormalTextRun SCXW215552875 BCX8\">one of two states, taking the value of either 0 or 1 to store information.<\/span><\/span><span class=\"TrackChangeTextInsertion TrackedChange SCXW215552875 BCX8\"><span class=\"TextRun SCXW215552875 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW215552875 BCX8\"> Just like a switch turning on or off<\/span><span class=\"NormalTextRun SCXW215552875 BCX8\">.\u00a0<\/span><\/span><\/span><span class=\"TextRun SCXW215552875 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"> <span class=\"NormalTextRun SCXW215552875 BCX8\">Quantum computers encode data using \u2018<a href=\"https:\/\/www.ibm.com\/topics\/qubit\" target=\"_blank\" rel=\"noopener\">qubits<\/a>\u2019 (quantum bits) which also have two states. These qubits could be electrons having \u2018up\u2019 and \u2018down\u2019 spins, or superconducting circuits with two energy levels. But unlike bits, they can exist in a combination of these states called a \u2018<a href=\"https:\/\/scienceexchange.caltech.edu\/topics\/quantum-science-explained\/quantum-superposition\" target=\"_blank\" rel=\"noopener\">superposition<\/a>\u2019 \u2013 they can exist in both states at the same time<\/span><\/span><span class=\"TrackChangeTextInsertion TrackedChange SCXW215552875 BCX8\"><span class=\"TextRun SCXW215552875 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW215552875 BCX8\">! <\/span><\/span><\/span><span class=\"TextRun SCXW215552875 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW215552875 BCX8\">This allows quantum computers to store much more information and perform more calculations in parallel compared to regular computers.<\/span><\/span><span class=\"EOP TrackedChange SCXW215552875 BCX8\" data-ccp-props=\"{}\"> It&#8217;s like having switches that can be both on and off at the same time.<\/span><\/p>\n<figure id=\"attachment_1019\" aria-describedby=\"caption-attachment-1019\" style=\"width: 412px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" width=\"412\" height=\"170\" class=\"size-full wp-image-1019\" src=\"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/files\/2024\/11\/classical-vs-quantum-computing.png\" alt=\"Classic computing vs quantum computing. \" \/><figcaption id=\"caption-attachment-1019\" class=\"wp-caption-text\">Classic computing vs quantum computing. Image credit: Manya Bhargava<\/figcaption><\/figure>\n<p><span class=\"TextRun SCXW252003234 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW252003234 BCX8\"><a href=\"https:\/\/scienceexchange.caltech.edu\/topics\/quantum-science-explained\/entanglement\" target=\"_blank\" rel=\"noopener\">Entanglement<\/a> is another intrinsic property forming the basis of quantum computing. When two particles are entangled, changing the state of one will instantly affect the state of the other, no matter how far apart they are. It&#8217;s like flipping two coins and seeing that if one lands on heads, the other will always land on tails. <span class=\"TextRun SCXW235526490 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW235526490 BCX8\">Researchers can create groups of entangled qubits which can be used to encode information on <a href=\"https:\/\/www.bluequbit.io\/quantum-circuit\" target=\"_blank\" rel=\"noopener\">quantum circuits<\/a>, immensely increasing the processing power of quantum computers.<\/span><\/span><span class=\"EOP TrackedChange SCXW235526490 BCX8\" data-ccp-props=\"{}\">\u00a0<\/span><\/span><\/span><\/p>\n<h2>Applying quantum computing to the protein folding problem<\/h2>\n<p><span class=\"TrackChangeTextInsertion TrackedChange SCXW25481033 BCX8\"><span class=\"TextRun SCXW25481033 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW25481033 BCX8\">Let\u2019s<\/span><span class=\"NormalTextRun SCXW25481033 BCX8\"> return to the protein folding problem. <\/span><\/span><\/span><span class=\"TextRun SCXW25481033 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW25481033 BCX8\">Scientists have been able to model amino acid chains on quantum circuits, encoding the properties of the amino acids onto qubits. Entangled qubits can <\/span><span class=\"NormalTextRun SCXW25481033 BCX8\">represent<\/span><span class=\"NormalTextRun SCXW25481033 BCX8\"> amino acids which are next to (and hence interacting with) each other in the protein chain<\/span><\/span><span class=\"TrackChangeTextInsertion TrackedChange TrackChangeHoverSelectColorRed SCXW25481033 BCX8\"><span class=\"TextRun SCXW25481033 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun TrackChangeHoverSelectHighlightRed SCXW25481033 BCX8\"> and capture attributes like the orientation or hydrophobic character of amino acids. <span class=\"NormalTextRun SCXW25481033 BCX8\">The quantum computer then encodes a superposition of many different protein configurations at the same time. Scientists can iterate through these, optimizing parameters until the lowest energy configuration is found \u2013 which corresponds to the native structure of the protein.<\/span><\/span><\/span><\/span><\/p>\n<figure id=\"attachment_1021\" aria-describedby=\"caption-attachment-1021\" style=\"width: 258px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" width=\"258\" height=\"223\" class=\"size-full wp-image-1021\" src=\"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/files\/2024\/12\/protein_rossman-protein-fold.png\" alt=\"Folded protein structure.\" \/><figcaption id=\"caption-attachment-1021\" class=\"wp-caption-text\">Folded protein structure. Image credit: Wikipedia.<\/figcaption><\/figure>\n<p>But this brings its own <a href=\"https:\/\/thequantuminsider.com\/2023\/03\/24\/quantum-computing-challenges\/\" target=\"_blank\" rel=\"noopener\">difficulties<\/a>. Quantum <span class=\"NormalTextRun SCXW163742868 BCX8\">computers with large numbers of qubits are incredibly difficult to build and <\/span><span class=\"NormalTextRun SCXW163742868 BCX8\">maintain<\/span><span class=\"NormalTextRun SCXW163742868 BCX8\">. As technology rapidly develops, researchers will be able to model increasingly complicated proteins. Quantum computers could provide us with a different solution to the PFP. Physical interactions between amino acids are simulated to reach a protein shape without the need for prior structure data. Used alongside programs like AlphaFold, this could be <\/span><span class=\"NormalTextRun SCXW163742868 BCX8\">an important step<\/span><span class=\"NormalTextRun SCXW163742868 BCX8\"> forwards towards holistic, <\/span><span class=\"NormalTextRun SCXW163742868 BCX8\">accurate<\/span><span class=\"NormalTextRun SCXW163742868 BCX8\"> and complete protein folding <\/span><span class=\"NormalTextRun CommentStart CommentHighlightPipeRest CommentHighlightRest SCXW163742868 BCX8\">simulation. Building practical quantum computers is an immense task, but exciting new developments bring important applications ever closer.<\/span><\/p>\n<p><span class=\"NormalTextRun SCXW218152430 BCX8\">The ability to precisely predict protein structures from only the amino acid sequence has been a holy grail of biology research for decades.\u00a0 Multidisciplinary collaboration between physics, <\/span><span class=\"NormalTextRun SCXW218152430 BCX8\">biology<\/span><span class=\"NormalTextRun SCXW218152430 BCX8\"> and computer science makes it <\/span><span class=\"NormalTextRun SCXW218152430 BCX8\">almost within<\/span><span class=\"NormalTextRun SCXW218152430 BCX8\"> reach. With rapid innovation and development, this is an exciting space to <\/span><span class=\"NormalTextRun CommentStart ContextualSpellingAndGrammarErrorV2Themed CommentHighlightPipeRest CommentHighlightRest SCXW218152430 BCX8\">watch.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>It might take time, but with your list of clues you would probably be able to piece together your Lego set eventually. But in the case of protein folding, no supercomputer is powerful enough to make any significant advancement on its own. That\u2019s where quantum computers come into play.\u00a0 Manya Bhargava returns to the IMSE [&hellip;]<\/p>\n","protected":false},"author":1794,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[81490,81460],"tags":[81493,81494,81473],"class_list":["post-1008","post","type-post","status-publish","format-standard","hentry","category-quantum","category-transdisciplinary-research","tag-entanglement","tag-protein-folding","tag-quantum-mechanics"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>quantum computing protein folding problems<\/title>\n<meta name=\"description\" content=\"Describing how quantum computing can help solve the protein folding problems by increasing the options to build structures\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, 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