{"id":13841,"date":"2026-09-24T13:07:03","date_gmt":"2026-09-24T11:07:03","guid":{"rendered":"https:\/\/ikv-aachen.de\/student-research-theses\/simulation-in-fast-forward-machine-learning-for-molecular-dynamics-cells\/"},"modified":"2026-09-24T13:20:03","modified_gmt":"2026-09-24T11:20:03","slug":"simulation-in-fast-forward-machine-learning-for-molecular-dynamics-cells","status":"publish","type":"cpt_ikv_srt","link":"https:\/\/ikv-aachen.de\/en\/student-research-theses\/simulation-in-fast-forward-machine-learning-for-molecular-dynamics-cells\/","title":{"rendered":"Simulation in Fast Forward: Machine Learning for Molecular Dynamics Cells"},"content":{"rendered":"<style type=\"text\/css\">\n    #single-header-block_fec86bd009bb78c6499e5ca8671ad8d2 .swiperThumbsNavi .swiper-slide {\n        opacity: 0.4;\n    }\n\n    #single-header-block_fec86bd009bb78c6499e5ca8671ad8d2 .swiperThumbsNavi .swiper-slide-thumb-active {\n        opacity: 1;\n    }\n<\/style>\n    <section id=\"single-header-block_fec86bd009bb78c6499e5ca8671ad8d2\" class=\"block-single-header theGridWrapper \">\n        <div class=\"theGrid12\">\n            <div class=\" col-start-2 col-span-10 md:col-start-3  md:col-span-8\">\n                <h2 class=\"font-serif font-semibold text-blue text-sm w-4\/5\">\n                    Bachelor&#8217;s Thesis or Master&#8217;s Thesis                <\/h2>\n                                                    <div class=\"skewToMiddle\">\n                        <div class=\"relative  text-blue text-sm font after:border-2  after:border-blue rounded-xl bg-green-lighter  p-base -rotate-6 my-xl  after:block after:absolute after:w-full after:h-full after: after:-z-10 after:rounded-xl after:rotate-1  after:box-content  after:-top-2xs after:-left-2xs after:bg-blend-multiply  leading-snug \">\n                            <div class=\"skewToMiddleInner\">\n                                Development, training, and evaluation of a data-driven model that accelerates the assembly and equilibration of molecular dynamics cells while accounting for physical boundary conditions.                            <\/div>\n                        <\/div>\n                    <\/div>\n                            <\/div>\n        <\/div>\n    <\/section>\n\n\n<figure class=\" relative flex flex-col gap-2xs mb-xs md:mb-l xl:mb-xl\"><img decoding=\"async\"  class=\" w-full  \"  src=\"https:\/\/ikv-aachen.de\/wp-content\/uploads\/2026\/09\/Stuwi-Simulationim-Schnelldurchlauf-Maschinelles-Lernen-fuer-molekulardynamische-Zellen.png\" srcset=\"https:\/\/ikv-aachen.de\/wp-content\/uploads\/2026\/09\/Stuwi-Simulationim-Schnelldurchlauf-Maschinelles-Lernen-fuer-molekulardynamische-Zellen-748x499.png 748w, https:\/\/ikv-aachen.de\/wp-content\/uploads\/2026\/09\/Stuwi-Simulationim-Schnelldurchlauf-Maschinelles-Lernen-fuer-molekulardynamische-Zellen-1536x1024.png 1536w, https:\/\/ikv-aachen.de\/wp-content\/uploads\/2026\/09\/Stuwi-Simulationim-Schnelldurchlauf-Maschinelles-Lernen-fuer-molekulardynamische-Zellen-768x512.png 768w\" sizes=\"auto, (max-width: 1536px) 100vw, 1536px\" width=\"1536\" height=\"1024\" alt=\"Stuwi-Simulationim Schnelldurchlauf Maschinelles Lernen f\u00fcr molekulardynamische Zellen\" loading=\"lazy\" \/><span class=\" text-copyright order-3 justify-end text-right w-full  w-full \">&copy; IKV<\/span><figcaption class=\" w-full  text-figcaption justify-end text-right \">Amorphous simulation cell made of polymer and medium after equilibration<\/figcaption><\/figure>\n\n\n<h3 class=\"wp-block-heading\">Topic of the Thesis<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Before a molecular dynamics simulation yields a single useful result, nothing happens at first. The amorphous cell is assembled, packed, compressed, heated, cooled, and brought to equilibrium over hundreds of picoseconds. The cluster runs the calculations; you wait. And because a single cell is not statistically meaningful, this process is repeated multiple times for every combination. This equilibration is a clearly defined, highly repetitive process with known physical boundary conditions\u2014in other words, a nearly ideal application for machine learning.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">The paper is being written by this research group<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">In the Media Influence Research Group, we follow the Quantitative Structure-Property Relationship (QSPR) approach. The goal is to use the molecular structure of the polymer and the medium to infer the risk of environmental stress cracking (ESC). Molecular dynamics simulations provide key parameters for this, such as diffusion and interaction behavior. The number of combinations we can consider currently depends primarily on the computation time required to set up and equilibrate the cells. If we can learn this step rather than compute it, the screening can be expanded by several orders of magnitude. We use BIOVIA Materials Studio and LAMMPS on the CLAIX high-performance computer at RWTH Aachen University. We will work together to determine which approach you will take and where you will focus your research.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Objective<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Develop, train, and evaluate a data-driven model that accelerates the setup and equilibration of molecular dynamics cells while accounting for physical boundary conditions.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Your Assignment<\/h3>\n\n\n<style type=\"text\/css\">#table-from-csv-block_1674a7fa8699b9924b0d906d4381ca12 table:not(thead) td:before { content: attr(data-col-name); }\n<\/style><section id=\"table-from-csv-block_1674a7fa8699b9924b0d906d4381ca12\" class=\"block-table-from-csv theGridWrapper  text-sm   \">\n\n<table class='w-full'>\n\n<thead class='font-semibold font-serif hidden  text-blue  lg:table-row-group'>\n\t<tr class=' flex flex-col mt-xs lg:border-t border-dashed first:border-none lg:border-white lg:table-row tableToNormal   '>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a bachelor's thesis, you will work on the following tasks' >For a bachelor&#039;s thesis, you will work on the following tasks<\/td>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a master's thesis, you will work on the following tasks' >For a master&#039;s thesis, you will work on the following tasks<\/td>\n\t<\/tr>\n\n<\/thead>\n\n<tbody class='lg:table-row-group'>\n\t<tr class=' flex flex-col mt-xs lg:border-t border-dashed first:border-none lg:border-white lg:table-row tableToNormal     odd:bg-green-lighter even:bg-green-lightest py-8 xl:py-2 '>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a bachelor's thesis, you will work on the following tasks' >Familiarization with the existing workflow consisting of cell preparation and equilibration<\/td>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a master's thesis, you will work on the following tasks' >Familiarization with the existing workflow consisting of cell preparation and equilibration<\/td>\n\t<\/tr>\n\t<tr class=' flex flex-col mt-xs lg:border-t border-dashed first:border-none lg:border-white lg:table-row tableToNormal     odd:bg-green-lighter even:bg-green-lightest py-8 xl:py-2 '>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a bachelor's thesis, you will work on the following tasks' >Systematic generation and processing of training data on the high-performance computer<\/td>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a master's thesis, you will work on the following tasks' >Evaluation of potential approaches to accelerate and build an automated data pipeline<\/td>\n\t<\/tr>\n\t<tr class=' flex flex-col mt-xs lg:border-t border-dashed first:border-none lg:border-white lg:table-row tableToNormal     odd:bg-green-lighter even:bg-green-lightest py-8 xl:py-2 '>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a bachelor's thesis, you will work on the following tasks' >Development of an initial model for predicting the properties of equilibrated cells<\/td>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a master's thesis, you will work on the following tasks' >Development and training of a model incorporating physical boundary conditions<\/td>\n\t<\/tr>\n\t<tr class=' flex flex-col mt-xs lg:border-t border-dashed first:border-none lg:border-white lg:table-row tableToNormal     odd:bg-green-lighter even:bg-green-lightest py-8 xl:py-2 '>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a bachelor's thesis, you will work on the following tasks' >Evaluation of prediction accuracy compared to classical simulation and estimation of the reduction in computation time<\/td>\n\t\t<td class='grid grid-cols-2 gap-xs lg:table-cell before:block lg:before:hidden first:pl-2xs last:pr-2xs   before:text-right before:font-semibold before:font-serif align-top  py-3xs ' data-col-name='For a master's thesis, you will work on the following tasks' >Validation on unknown polymer\/medium combinations and evaluation of the achieved reduction in computation time<\/td>\n\t<\/tr>\n\n<\/tbody>\n<\/table>\n\n<\/section>\n\n\n<h3 class=\"wp-block-heading\">Your Profile<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>A degree in engineering or the natural sciences (e.g., mechanical engineering, industrial engineering, materials science, computational engineering science, simulation sciences, applied chemistry, or applied polymer science)<\/li>\n\n\n\n<li>Enjoyment of programming, ideally in Python<\/li>\n\n\n\n<li>Interest in machine learning and simulation; prior knowledge is welcome but not required<\/li>\n\n\n\n<li>Willingness to learn how to work on a high-performance computer<\/li>\n\n\n\n<li>An independent, structured, and team-oriented approach to work<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Here are your benefits<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Work in a young, motivated team<\/li>\n\n\n\n<li>Independent work with close supervision<\/li>\n\n\n\n<li>Opportunity to help shape a research topic that will serve as the foundation for future work<\/li>\n\n\n\n<li>Individual coordination of tasks, scope, and timeframe<\/li>\n\n\n\n<li>Access to the CLAIX supercomputer at RWTH Aachen University<\/li>\n\n\n\n<li>A varied mix of research, simulation, and data analysis<\/li>\n\n\n\n<li>Can start immediately<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">If you&#8217;re interested in writing a thesis at the IKV and in this topic, please feel free to contact me. We&#8217;ll work together to determine the approach you&#8217;ll take, how deeply you&#8217;ll delve into the modeling, and what the timeline will look like, so that the thesis aligns with your interests and prior knowledge.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The goal of your work is to use an AI model to accelerate the construction and equilibration of molecular dynamics cells.<\/p>\n","protected":false},"featured_media":13839,"parent":0,"template":"","srtk":[807,808],"research_fields":[817,1174],"esl":[685],"class_list":["post-13841","cpt_ikv_srt","type-cpt_ikv_srt","status-publish","has-post-thumbnail","hentry","srtk-bachelor-thesis","srtk-master-thesis","research_fields-materials-technology","research_fields-simulation-en","esl-simulative"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Simulation in Fast Forward: Machine Learning for Molecular Dynamics Cells | 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