Innovations in Metal-Organic Frameworks Research:

Combining Molecular Simulations and Machine Learning

Orlando Mendible, a fourth-year graduate student in Assistant Professor Yamil Colón's research group within the Department of Chemical and Biomolecular Engineering, is at the forefront of innovative materials design and discovery. His work uniquely blends molecular simulations and machine learning, with a particular focus on metal-organic frameworks (MOFs). These crystalline structures, made up of metal nodes and organic linkers, have wide-ranging applications in gas adsorption, gas separations, catalysis, and drug delivery. Orlando's primary research focus is to understand the mechanisms and variables that influence their self-assembly.

In molecular simulations, there are two main approaches: classical and ab-initio simulations. Classical simulations use predefined parameters and equations to describe atomic interactions, making them ideal for studying dynamical and mechanical properties. However, they fall short in modeling bond-breaking and bond-forming interactions, which are crucial for understanding MOF self-assembly. Conversely, ab-initio simulations utilize quantum-level theory to compute atomic interactions and accurately simulate chemical bond dynamics. Despite their precision, these simulations are computationally intensive and costly.

To bridge the gap between these two approaches, neural network forcefields (NNFFs) have emerged as a promising solution. NNFFs can achieve ab-initio accuracy in modeling atomic interactions while significantly reducing computational costs. This innovation enables the study of complex systems that were previously unattainable with direct ab-initio methods, allowing for more precise simulations of systems relevant to current research interests.

The successful implementation of this research workflow relies on integrating various open-source packages and programs. Orlando acknowledges the crucial support of the CRC team, particularly in compiling essential software components to operationalize this research. Their invaluable assistance has been instrumental in advancing Orlando's research endeavors, for which he is deeply grateful.

MATLAB Trainings

MATLAB is a commercial software developed by MathWorks. MATLAB is widely used in different fields, e.g., mathematics, physics, engineering, and economics. 

MathWorks provides online, self-paced trainings to users. University of Notre Dame owns an academic license for MATLAB, and users from our university have access to many useful online trainings. To get access to them, users need to create a Mathworks account using their Notre Dame email. After logging in, a selection of different trainings will be available.

There are two types of trainings available. There are onramp type and course type trainings available. The onramp trainings are short introductory courses, e.g., MATLAB Onramp, Simulink Onramp. These trainings can be completed within a few hours. The course type trainings usually cover a specific topic, and require more effort. For example, the Image Processing with MATLAB training takes about 11 hours to complete.

These trainings usually use videos and slides to explain concepts, and also contain hands-on tasks for each section. The courses use the online version of MATLAB, and the tasks are usually implemented in Live Editors.

If you have just started using MATLAB, or if you have been using MATLAB for years and are willing to learn more about it, you can find the available courses here.

This training is available to new users and current users interested in a refresher course on how to use CRC resources. Attendees learn the basics of accessing CRC resources and submitting jobs on the CRC clusters. This course is a co-requisite when receiving a CRC account.

You must have a CRC User Account to participate in this class. To acquire an account, please fill out and submit the CRC Account Request Form.

All Training will take place via Zoom (in-person training is available by request).  Please click HERE to register for User Training. After registering monitor email for message containing Zoom Meeting Link and Password.

For more information, please contact CRCsupport@nd.edu.

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This training is available to new users and current users interested in a refresher course on how to use CRC resources. Attendees learn the basics of accessing CRC resources and submitting jobs on the CRC clusters. Learn more.

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