Justin Lemkul

Excited to share a new update to the Drude polarizable force field - phosphorylated amino acids! A long-term project that took quite a bit of effort. Great work with PhD student Laura Gil Pineda, former undergrad Candace Miller, and @alexmackerell.bsky.social

authors.elsevier.com/a/1m2md1SPTB...

2. Focus on people. When recruiting, it’s sometimes less about credentials and more about attitude. I’ll gladly take a student with no prior experience but a great attitude and desire to learn over one that has lots of technical skills but poor work ethic or attitude.

1. Start small. It is tempting to dive in and shoot for some huge research goal like you’ve had in well established labs. Not going to work starting out. Do small things that will help you build toward realizing that larger vision. Funding and publications won’t come right away but will eventually.

Always! I think that little twinge of anxiety is a good thing - it means we still care about doing a good job.

Happy to announce our latest article, a tutorial on running Gaussian-accelerated MD simulations in NAMD. Tour de force work by @hmmichel.bsky.social with @mdpoleto.bsky.social that unifies theory and practice in one place!

livecomsjournal.org/index.php/li...

A powerful statement from courageous staff at the NIH. #standupforscience #academicsky

A bold graphic with the headline ‘75 Years of Incredible Discovery. Now Under Attack.’ displays four visuals representing threats to the National Science Foundation (NSF). A pie chart shows a proposed 56% budget cut, a ‘CANCELLED’ stamp is over a document to represent over 1,000 grants terminated, chained lab equipment symbolizes freezes on new and existing funding, and a person packing a box reflects the abolishment of 37 internal divisions.

(10/11)

75 years of scientific discovery—now on the chopping block.

Trump’s 2025 budget proposes a 56% cut to the NSF. Over 1,000 grants terminated. 37 divisions abolished. Funding frozen.

This isn’t just reckless—it’s a war on knowledge, a war on progress.

Really happy to have this one out in final form! Fun working with @biochem-anne.bsky.social and we had a great editorial experience with Cell Rep Phys Sci (thanks @andrewbissette.bsky.social et al. and the reviewers for their very constructive comments). #compchemsky

dx.doi.org/10.1016/j.xc...

La Crêperie, near the Panthéon - as the name might strongly suggest, they have really good crêpes.

I’m so sorry and angry on your behalf. I know the incredible work you and your team do and this is just awful.

Nobel laureate: I owe America my success. Today, its scientific future is in danger | CNN Dr. Ardem Patapoutian says he watches “with deep sadness as the United States’ remarkable scientific enterprise, which took generations of hard work and national investment to build, faces a concerted...

Published an op-ed for @cnn.com: “Nobel laureate: I owe America my success. Today, its scientific future is in danger.”
A personal reflection on what’s at stake as science funding gets slashed. I’d be grateful if you could amplify both in and beyond the science world.
www.cnn.com/2025/04/09/h...

I didn’t know that otherwise I would have tagged her 😂

Lemkul and Miranda Quintana group members at lunch. From left, Haley Michel, Lexin Chen, Laura Gil Pineda, Esmat Mohammadi, Ramon Miranda Quintana, and Justin Lemkul.

Great to meet up with Lexin and Ramon from @groupquintana.bsky.social today at #ACSSpring2025. Great work coming from their group and we are excited to work with them!

Haley has an #ACSCOMP poster on Drude SILCS nucleic acid simulations (Tues, 7 PM).

I present on the Drude FF for phosphoproteins (Hall F Room 5, Wed 5:40 PM).

We are heading to #ACSSpring2025!

Laura is at SciMix (Mon 8 PM) and #ACSCOMP posters (Tues 7 PM) presenting on IDPs.

Esmat has a poster (Tues 12 PM) on CADD for T2D drug discovery.

Wow, 50(!) of mine…

Ninja Bigfoot is a concern that no one is talking about!

spike protein domains and mutations in VOCs

Fiona's tang fish named Dorry matches the spike colors

A behemoth effort from @fionachembot.bsky.social in which she does amazing science (showing how VOCs reshape allosteric pathways) while also making the SARS2 spike color palette match her fish Dorry 😍🫠
www.biorxiv.org/content/10.1...

Tomorrow is @standupforscience.bsky.social
find your local protest and attend! It is our right to protest and we need to keep up the fight against this awful administration.

Science is what makes America great. Education is what makes American great.

JUST IN: A federal judge in Massachusetts has extended her nationwide block on Trump administration effort to slash funds for NIH research.

This is so important. Visual consistency takes the fatigue out of reviewing. I always use bold section headings and only underline short, key phrases. No italics except organism names (I find italics taxing to read in long blocks). Text boxes to summarize key concepts/questions for visual impact.

Lemkul lab members at BPS 2025. Standing, from left: Justin Lemkul, Ashley Goodberlet, Laura Gil Pineda, and Patrick Gilles. Seated, from left: Haley Michel and Kait Malewicz.

Thank you @biophysicalsoc.bsky.social for another excellent meeting. Had a blast in LA, now back to snowy VA. Until next year…

@biophysicalsoc.bsky.social you need to be sharing at the conference this week like our lives depend on it. Because they do.

Speak up. Stand up. Get out there and protect out democracy

Correction: my poster is on Tuesday 2/18 😅

Image of Lemkul Lab members attending the Biophysical Society and their presentation information - oral presentations, poster numbers, times, and locations.

The Lemkul Lab is heading to #BPS2025! We will have several posters and presentations, so please come chat with us about the latest in MD simulations of biomolecules, CADD, and the Drude polarizable force field! See you in LA! #compchemsky

Indeed. No harm done. More of a miscommunication about scope than anything else. It happens.

We were encouraged to submit there. The reviewers shot it down and we were told it wasn’t appropriate for the topic. The Biophysicist said the same since it’s not geared directly toward education (in the sense of teaching).

My only concern is the likelihood of updating it. The expectation of a living article works well for things like tutorials but this is somewhat different. I’m not sure it fits or would be updated much, if at all.

Inevitably, I will get a deluge of spam messages from predatory publishers but I am hoping some legitimate journal editors might see this :) And we welcome any suggestions from colleagues in the #compchem community!

Robustness in Biomolecular Simulations: Addressing Challenges in Data Generation, Analysis, and Curation Computational simulations of biomolecules provide a wealth of information about the thermodynamic landscape of biologically important systems, kinetics of important cellular processes, and the biophys...

@biochem-anne.bsky.social and I are looking for a home for a perspective we wrote on current technical challenges in biomolecular simulations. Preprint linked here; we aren't sure of the best venue. Shopped around a bit, so far rejected each time for "poor fit." #compchem

doi.org/10.26434/che...