Merge pull request #2680 from clairbarrass/main

Publish Alice Pettitt blog and case study

_casestudies/2024-12-17-viral-protein.md

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+---
+status: live
+pdf_link: viral-protein/Archer2_Viral_Protein_AW_LOW.pdf
+image_src: ./viral-protein/viral-protein.jpg
+image_alt: reactors
+title: Simulating a flexible infectious viral protein
+text:  Disordered proteins play important roles in various diseases, including cancer and certain viral infections. These proteins can change shape depending on their biological context, making them challenging to study. Through an ARCHER2 Pioneer Project, researchers from University College London, King’s College London, and the Francis Crick Institute conducted extensive, computationally demanding simulations to characterise a specific region of a protein from SARS-CoV-2, the virus responsible for causing COVID-19. 
+---

_posts/2024-12-17-archer2-research-support-impact.md

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+---
+layout: post
+title: ARCHER2 Support Service Research Impact 
+date: 2024-12-17 11:00:00
+author: Alice Pettitt
+tags: [blog] 
+categories: [news]
+---
+
+Alice Pettitt, a researcher working on their PhD, has written about how the ARCHER2 service supported their work and development.
+
+<!--more-->
+
+## Why did you need to use ARCHER2 for your research (need for computational research and that size of machine)?
+
+For my PhD project, I characterised a protein called ORF6 from SARS-CoV-2, the virus that causes COVID-19. Given ORF6's high flexibility, I used computational methods such as molecular dynamics simulations to achieve a precise characterisation of the protein. Due to the large system size of ORF6 in solvent and the computational complexity of accurately modelling such a system, I needed the advanced architecture and large core availability of ARCHER2. Flexible proteins require enhanced sampling techniques and the integration of experimental restraints to capture their motions, and these techniques demand significant computational power. Moreover, these simulations need to be run over long timescales to provide meaningful insights. ARCHER2 allowed me to achieve a performance of 66 ns/day for a system size of 39,050 atoms, enabling me to characterise the biologically relevant region of ORF6 in a feasible timeframe and in unprecedented detail. 
+
+![image]({{ site.baseurl }}/img/blog/241217-support.jpg)
+{: .img-center style="width: 50%" 
+alt="ARCHER2" 
+title="ARCHER2"}
+
+## What support did you need to succeed with your research and PhD?
+
+When I started my PhD, my background was primarily in wet lab research, and I had limited experience with high-performance computing (HPC). To run my molecular dynamics simulations, I needed to install and integrate the same version of two software tools, GROMACS and PLUMED, on both my local system and various HPC platforms. This process was initially quite challenging. The ARCHER2 service desk provided invaluable support throughout this process. They gave clear, step-by-step guidance to help me install and integrate the software and quickly resolved any issues I encountered. They also assisted me in setting up and optimising submission scripts to ensure my simulations ran efficiently on the system. This support was instrumental in overcoming the steep learning curve of using HPC and played a significant role in the success of my PhD project.
+
+
+## Where is your career going next and will it involve computational science, or what next for the outcome or the research? 
+
+The next step in this research could involve using ARCHER2 with the GROMACS and PLUMED software to investigate ORF6 in its bound state to gain further mechanistic insights into how ORF6 interacts with host proteins and suppresses the immune response. Furthermore, this computational approach could be used to explore how small molecules interact with ORF6 as potential therapeutic strategies.
+
+After completing my PhD, I plan to move into the commercialisation of scientific research. While this work may not directly involve computational science, I am keen to apply the computational skills I gained during my PhD to identify and assess exciting new technologies. The experience I’ve developed with HPC and molecular dynamics simulations has provided me with valuable insights into the power of computational tools, and I look forward to leveraging this knowledge in my future career. 
+
+
+[Case study based on Alice's research]({{ site.baseurl }}/research/case-studies/viral-protein/Archer2_Viral_Protein_AW_LOW.pdf)
+
+![image]({{ site.baseurl }}/img/blog/241217-alice.jpg)
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+
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