Postdoc in Computational Biophysics: UCPH
Copenhagen, Denmark
Joined September 2019
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The bulk of my thesis work was recently published!
We used 19F NMR and weighted ensemble simulations among other methods to explore hidden dimer states of the HIV-1 capsid protein.
If this sounds interesting to you, see the full paper here:
pnas.org/doi/10.1073/pnas.24…
And huge thanks to Ken Chiacchia and Jorge Salazar for highlighting our work! Check out their articles for a breakdown of the paper :)
psc.edu/hiv-1-capsid-protein…
tacc.utexas.edu/news/latest-…
Darian retweeted
Watch your protein parameters go brrr 🚀
Check out our preprint on applying reinforcement learning (RL) to optimize Protein Language Models: arxiv.org/abs/2412.12979
With @mariartigues, Andi, @talaldotpdb, @marcguellc and @ferruz_noelia
Darian retweeted
My Latest work from @Gronenborn_lab. Using 19F NMR, we developed a multiplexed assay for tracking small GTPase activity. This method enables real-time, simultaneous monitoring of multiple proteins under physiological conditions. Check it out in @J_A_C_S pubs.acs.org/doi/10.1021/jac…
Darian retweeted
We often think of an "equilibrium" as something standing still, like a scale in perfect balance.
But many equilibria are dynamic, like a flowing river which is never changing—yet never standing still.
These dynamic equilibria are nicely described by so-called "detailed balance"
Darian retweeted
#HighlightOfTheWeek Animated time-evolution of a 2D probability distribution obtained using WEDAP, a python package to plot molecular simulation data.
Work by @darianyang and @ltchong.
#compchem
pubs.acs.org/doi/10.1021/acs…
Darian retweeted
Having trouble visualizing your data from WESTPA?
Try WEDAP! A user-friendly plotting package from @darianyang and @ltchong (1/4)
pubs.acs.org/doi/10.1021/acs…
Darian retweeted
Another great BPS with both vintage and fresh WESTPA developers/users from the @ltchong @RommieAmaro @DMZuckermanLab @Terrasztain and Ahn Labs!
Darian retweeted
Register now for the free WESTPA Workshop @Pitt_Chemistry, June 20-21. Explore rare event simulations like protein folding, ligand binding, & chemical reactions with our open-source software. Perfect for those using AMBER, NAMD, GROMACS, etc. Reg info:
forms.gle/6gJF6jJ72iexbDTq8
Darian retweeted
On this (relatively) cold day we are daydreaming of PS38 @ the Westin Bayshore Vancouver, July 23-26.
The annual meeting will feature 100+ speakers & 12 sessions over 3.5 days.
Graduate Students member reg. fee is $100 & abstract submission fee is $15. proteinsociety.org
ALT View from Westin Bayshore Vancouver, PS38 host hotel
Darian retweeted
Are you looking to make your microscopy images pop? I've been working on an add-on to make loading tifs in @Blender more accessible!
With tif2blender, 3D animations of z-stacks are hopefully easier to make in open-source format.🌈
Try it at: github.com/oanegros/tif2blen…
Darian retweeted
We propose amendments to PDBx/mmCIF to better reflect the complexity of biomolecules. This shift will accelerate the development of new tools and provide representative datasets for structural ensemble prediction. chemrxiv.org/engage/chemrxiv…
Darian retweeted
Congratulations, Xiaowei Bogetti, Ph.D! Xiaowei defended her thesis this morning. Good luck at Stony Brook during your postdoc 😄
Darian retweeted
Next up, Darian Yang from Pittsburgh/CMU tells us about conformations of the HIV-1 capsid protein CTD dimer. #EBSA2023 – at Stockholm, Sweden
Darian retweeted
Put the date in your diaries, the registration for the 2024 IUPAB congress and 62nd annual meeting of the biophysical society of Japan in Kyoto opens November 2023! Head to iupab.org/event/iupabcongres… to find out more. Please RT!
Darian retweeted
We are absolutely thrilled to finally share our new structure from @clemonslab of escape mechanism of the smallest phages (φX174) by breaching the peptidoglycan layer, now out in Science! science.org/doi/10.1126/scie…
🧵 In this thread, I'll give you a sneak peek of the YES complex👇🏼
Darian retweeted
Ending the day with Angela’s @Gronenborn_lab talk on a super cool cyclosporinA story
Darian retweeted
Secondary Structure cartoons are now part of #MolecularNodes !
v2.6.0: github.com/BradyAJohnston/Mo…
Every aspect of these are customisable. Width, thickness, colour, arrows / no arrows, cylinders.
In love with the final result. Done entirely within #GeometryNodes and #Blender3d
Darian retweeted
I'm excited to contribute to this community effort to provide practical guidance for benchmarking protein force fields against data from #NMR and room temperature crystallography:
arxiv.org/abs/2303.11056
