In the Zernike Institute Advent Calendar, we are presenting 24 short spotlights in December. In these specials, we highlight PhD students, postdocs, support staff and technicians of our research groups and team - providing a glimpse in their typical day at work. In Episode 2 meet Vasista Adupa, PhD student in the Micromechanics group of Prof. Patrick Onck.
As a member of the micromechanics group led by Patrick R. Onck, my research dives into the intricate world of biological molecules. I’m part of an interdisciplinary consortium that studies how chaperones can guard the phase state of intrinsically-disordered proteins in our cells. My special focus is on the molecular chaperone DNAJB6b (endowed with extraordinary anti-aggregation powers) and I study the structure and dynamics of this protein at an atomistic level using computational modelling and simulations. Molecular chaperones are like the guardians of the cell, ensuring that proteins fold correctly and maintain their proper conformation. We perform all-atom molecular dynamics (MD) simulations to reveal the dynamics of the molecular chaperones and relate this to the functioning of the protein in a broader biological context. We perform these simulations on high-performance computing clusters, such as Nieuwpoort (local cluster at the Berendsen Center), Hábrók (from the university) and the Dutch national super computer, Snellius (operated by NWO).
What does a typical workday look like for you?
Title – “Writing a lot of scripts to analyse and automate tebibytes of data”
A typical workday for me starts with downloading the data to my local workstation from the clusters and do my favourite part of the day, look at the trajectories of these proteins which is very satisfying. Next, find anything interesting in those trajectories and write analysis scripts to quantify what I am seeing. Most of the time, this is not sufficient to describe complex processes, so thinking out of the box and writing more sophisticated analysis scripts to get the data out from the trajectory is the challenging step of the day. In that perspective, every day contains new challenges to tackle.
What are you currently working on?
I am currently working on understanding the action of the molecular chaperone DNAJB6b on neurodegenerative disease-causing proteins, such as polyQ responsible for Huntington’s disease.
What if you’re not at work?
I like watching and understanding how new technology works. In that sense, I would call myself a tech-geek. I also love going for long hikes in the mountains.
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