With the start of the second phase of the EuroCC 2 Project, we have initiated academic ‘Proof of Concept’ (PoC) studies to extend our collaborations with industry to our academic users. The primary objective of these studies is to pair academic researchers who have not previously utilized high-performance computing (HPC) technologies with experienced academics actively using HPC in their research. Through a six-month PoC study, we aim to help these researchers develop a certain level of HPC proficiency. Another goal is to provide undergraduate, master’s, and doctoral students who have not yet worked with these technologies the opportunity to experience how HPC is applied in academic research processes within a research group skilled in HPC. This way, research groups that have not previously used HPC technologies gain access to the benefits these technologies offer.

Below, we have shared the content and outcomes of the efforts conducted by NCC Türkiye so far.

1.Mechanistic Insights Into the [2+2] Cycloaddition-Retroelectrocyclization Reactions of Symmetric Alkynes Activated with Methoxy Groups

This project was conducted in collaboration with the Dengiz Research Group from the Department of Chemistry at Middle East Technical University (METU). Within the scope of the project, the mechanisms of [2+2] cycloaddition-retroelectrocyclization (CA-RE) reactions were investigated, and these mechanisms were modeled using theoretical calculations facilitated by the Turkish National High Performance Computing Center (TRUBA) infrastructure. While the Dengiz Research Group specializes in experimental studies, they received support from HPC experts at Turkey NCC (National Competence Center) for computational chemistry studies requiring HPC expertise as part of the project.

Click here for the detailed study report

2.Navigating Energy Surface of Functional Proteins

This study focuses on understanding protein dynamics and was conducted in collaboration with the Molecular Biology, Genetics and Bioengineering, Computer Engineering, and Materials Science and Nano Engineering departments at Sabancı University. The project aimed to investigate unresolved protein functions and how these functions are influenced by environmental changes, despite the successes of AlphaFold2 in protein structure prediction.

High-Performance Computing (HPC) infrastructure was utilized to map the conformational transitions and functions of proteins using molecular dynamics simulations and advanced sampling techniques. As part of the study, researchers and students at Sabancı University, guided by HPC experts, examined the structural changes of various proteins (calmodulin, TEM-1 β-lactamase, and Green Fluorescent Protein) and learned to effectively utilize HPC resources during this process.

Click here for the detailed study report. 

3.HPC and Shell Scripting For Chemists and Chemical Engineers

The PoC outlines a training initiative by Yeditepe University’s Chemical Engineering Department under EuroCC@Türkiye to enhance HPC literacy among students engaged in molecular modeling. Since students have little to no prior experience with HPC, the program focuses on teaching Linux shell commands, scripting, and job automation to improve their ability to run simulations efficiently. The training covers basic and advanced command-line operations, scripting languages like Bash, and hands-on practice. Expected benefits include optimized workflow efficiency, improved system navigation, and enhanced automation for HPC tasks. Challenges include the steep learning curve and limited prior knowledge of Linux and HPC concepts. Overall, the initiative aims to strengthen participants’ computational skills for high-performance research applications.

Click here for the detailed study report.