iiinova — where your digital self keeps evolving

Michael Shirts @michaelshirts.bsky.social · 13/08/2026

My 9 year old, Skógafoss, May 2024:

Reposted by Michael Shirts

Aaron Rupar @atrupar.com · 30/07/2026

New in PN: The new "science golden age" looks suspiciously like a grift "It’s impossible not to wonder whether part of Trump’s loathing for universities is that there's no way for him to corrupt the process and make money off it in the same way he can by giving billions to Silicon Valley types."

publicnotice.co

The new "science golden age" looks suspiciously like a grift

Trump wants to run scientific research like his family business.

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Andy Extance @andyextance.bsky.social · 25/06/2026

Reading @dereklowe.bsky.social's piece, I don't get why US industry-oriented science isn't fighting Trump's cuts to and politicisation of research. Can't they see the damage, now and in the future? www.science.org/content/blog... They, and anyone who can, must comment on the new regulations.

science.org

Action! Action Now.

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Michael Shirts @michaelshirts.bsky.social · 22/06/2026

Funneling congressionally-mandated money away from universities to business. 20-30% cuts in NSF programs to fund X-labs.

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Michael Shirts @michaelshirts.bsky.social · 22/06/2026

'Alchemical' was not an allowed word in the NYT 'Spelling Bee' today.

Meme of Michael Jordan saying ". . . and I took that personally"

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Michael Shirts @michaelshirts.bsky.social · 18/06/2026

Also, disingenuous to say that most large calls only get a few hundred submissions when most large calls don't have 56 (by my count) thrust areas.

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Michael Shirts @michaelshirts.bsky.social · 18/06/2026

The call on page 60 says that "Only a small fraction of Phase I teams will be selected for Phase II awards", so one might expect more Phase I than 50.

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Michael Shirts @michaelshirts.bsky.social · 18/06/2026

I think it's probably because 1) there was a lot of money that was mentioned, so people though it would be higher (50 awards at $750K = 37.5M, so 12.5% of the $300M that was said to be committed) and 2) worry that there wasn't going to be any more money afterwards for anything else.

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Michael Shirts @michaelshirts.bsky.social · 29/05/2026

Pretty much the death knell of US research universities as we know it. Industry scientists, if you want to have any graduate students applying to your posted jobs 5 years from now, have your bosses complain to congress/the administration. . .

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Reposted by Michael Shirts

Open Force Field @openforcefield.org · 12/05/2026

Have you read about our GNN model for assigning partial charges? It's at the heart of both our Sage 2.3.0 force field and the protein force field we're developing. The paper was published last month in JCTC. pubs.acs.org/doi/10.1021/...

pubs.acs.org

Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model

Partial atomic charges are a fundamental component underlying classical molecular simulations, but assigning charges remains a computational bottleneck; many common methods rely on quantum mechanical ...

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Reposted by Michael Shirts

livecomsjournal.bsky.social @livecomsjournal.bsky.social · 27/04/2026

We wrote a response to a recent @science.org news article "NIH’s proposed caps on open-access publishing fees roil scientific community", in which we highlight the importance of community-run journals. Sadly our letter was rejected, but you can read it here: livecomsjournal.org/index.php/li...

livecomsjournal.org

What the publishers of Science don't want you see! | Living Journal of Computational Molecular Science

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livecomsjournal.bsky.social @livecomsjournal.bsky.social · 29/01/2026

The first article of volume 7 is out now! Learn how to simulate molecular dynamics in electronic excited states, beyond the Born-Oppenheimer approximation, with this best practices article by Prlj et al on nonadiabatic dynamics! #compchem doi.org/10.33011/liv...

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Open Force Field @openforcefield.org · 06/01/2026

New preprint describing our GNN charge model, AshGC! Since QM methods of charge assignment scale poorly to larger molecules, and are also conformation dependent, AshGC leads to major performance improvements in this critical step in force field parameterization. chemrxiv.org/engage/chemr...

chemrxiv.org

Developing and benchmarking Sage 2.3.0 with the AshGC neural network charge model

We report a new charge model and a new general small molecule force field. Here, we address the development and benchmarking of both the Open Force Field (OpenFF) AshGC charge model, as well as the Sa...

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livecomsjournal.bsky.social @livecomsjournal.bsky.social · 21/11/2025

The latest article in our Lessons Learned category is out now! "The Journey of Data: Lessons Learned in Modeling Kinase Affinity, Selectivity, and Resistance" by López-Ríos de Castro et al helps guide the development of platforms for structure-enabled ML for drug discovery: doi.org/10.33011/liv...

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livecomsjournal.bsky.social @livecomsjournal.bsky.social · 28/10/2025

In the latest @livecomsjournal.bsky.social perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!: livecomsjournal.org/index.php/li... #compchem

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Oliver Beckstein [he/him] @orbeckst.bsky.social · 23/10/2025

If you're doing #alchemistry (alchemical free energy calculations) then here's release 2.5.0 of alchemlyb for you. github.com/alchemistry/... (There's also the alchemlyb @joss-openjournals.bsky.social paper doi.org/10.21105/jos... if you want to read & cite.)

github.com

2.5.0 · alchemistry alchemlyb · Discussion #445

New minor release of alchemlyb with fixes and enhancements. Supports Python 3.11 - 3.14. See CHANGES for details. What's Changed update action/checkout by @orbeckst in #417 Parallel read and prepro...

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Reposted by Michael Shirts

Open Force Field @openforcefield.org · 10/10/2025

We’re pleased to announce Sage 2.3.0 Release Candidate 2 (rc2)! Sage 2.3.0 will be the first OpenFF force field to use the AshGC neural network charge model, which was trained to AM1BCC ELF10 charges, and allows for rapid charge assignment for molecules with hundreds or thousands of heavy atoms.

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Reposted by Michael Shirts

livecomsjournal.bsky.social @livecomsjournal.bsky.social · 02/10/2025

📢 New software tutorial alert! Gravelle et al introduce a suite of tutorials for new users of the LAMMPS simulation package, including molecular simulation basics, reactive force fields, GCMC and enhanced sampling #compchem doi.org/10.33011/liv...

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livecomsjournal.bsky.social @livecomsjournal.bsky.social · 30/09/2025

Interested in biomolecular simulation? The latest article by Lier et al describes advanced tutorials for the GROMOS software, including free energy calculations, enhanced sampling and neural network potentials with SchNetPack! #compchem livecomsjournal.org/index.php/li...

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livecomsjournal.bsky.social @livecomsjournal.bsky.social · 11/08/2025

Our latest Best Practices article "Developing Monte Carlo Methodologies in Molecular Simulations" is out now and describes how to derive acceptance probabilities for a variety of Monte Carlo moves: doi.org/10.33011/liv... #compchem

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Michael Shirts @michaelshirts.bsky.social · 13/07/2025

Interesting history here that i was not really aware of. The same issues we’ve been dealing with in computational drug design for a while…

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Upol Ehsan | hiring PhDs for Fall'27 @upolehsan.bsky.social · 11/07/2025

“Flexible schedule” in academia means you are free to work whenever you feel guilty.

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Michael Shirts @michaelshirts.bsky.social · 03/07/2025

My contacts here on know these topics already, but this could very well be a good intro for undergrads starting research, etc. I've previewed all the material, nice easy pace with good detail by a calm, welcoming instructor 2/2

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Michael Shirts @michaelshirts.bsky.social · 03/07/2025

@ckohlmeier.bsky.social here at CU Boulder just released a Coursera intro to Python for scientific computing. Different from other intro courses by emphasizing doing engineering calculations, like optimization and numerical integration. 1/2

coursera.org

Introduction to Python for Scientific Computing

Offered by University of Colorado Boulder. Whether you’re a scientist, engineer, student, or industry professional working with data or ... Enroll for free.

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Derek Lowe @dereklowe.bsky.social · 24/06/2025

Journalists keep asking me, baffled, “What’s the Trump administration really trying to do to the science agencies?” So I say “They are trying to destroy them. Cut off their funding, ruin their facilities, harass their staff into leaving.” It’s not reform, and it never was. It’s destruction.

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Reposted by Michael Shirts

Jon Cooper @joncooper-us.bsky.social · 31/05/2025

“In nearly every industry, the United States’ most transformative innovations over the last eight decades depended on government funding, because the government was the most patient and reliable actor willing to take on risks for the public benefit.” And China will reap the benefits.

foreignaffairs.com

Trump Is Killing American Innovation

China will reap the benefits.

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Michael Shirts @michaelshirts.bsky.social · 31/05/2025

Key thread here. NSF's own projections are that the success rate for competitive awards would drop from 26% to 7%, and the number of students, postdocs, and senior researchers involved in NSF research will drop by ~70% each, ~80% for undergrads. Perfect "Make China Great Again" policy.

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Reposted by Michael Shirts

Joshua Weitz @joshuasweitz.bsky.social · 31/05/2025

How bad will it be? Catastrophic. Proposed cuts to #NSF, #NIH, and #NASA will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come. But, this is the WH's *proposed* budget. Speak up now before it is too late. (inflation adjusted $-s below)

NSF, NASA and NIH budgets per year, inflation adjusted from 2000-2025 along with the proposed cuts. NSF includes research component only. Massive cuts across all sectors, well below support spanning 25 years.

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Michael Shirts @michaelshirts.bsky.social · 31/05/2025

This is the president's budget request to congress for 2026 for the National Science Foundation. Down 56%. Say goodbye to science as we know it in the US if this is remotely reflected in the final congressional bill. Most of the NSF funding ends up paying for PhD students in science.

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Reposted by Michael Shirts

Dan Garisto @dangaristo.bsky.social · 08/04/2025

The NSF's flagship fellowship program typically gives offers to 2,000+ young scientists. This year, in the face of looming budget cuts, that number was halved: only 1,000 received an offer. Our story on what that means for the science talent pipeline: www.nature.com/articles/d41...

nature.com

NSF slashes prestigious PhD fellowship awards by half

US National Science Foundation announces lowest number of Graduate Research Fellowship Programme recipients in 15 years.

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Reposted by Michael Shirts

benjamin dickman @benjamindickman.bsky.social · 08/04/2025

unfortunate turn of events w total NSF #GRFP awards: www.research.gov/grfp/Awardee... year | awards offered: 2025 | 1000 2024 | 2036 2023 | 2555 2022 | 2193 ... 2011 | 2077 there have been >2k awarded since 2010 (i intended to leave grad school if not for getting it in 2011) damaging & dangerous!

research.gov

Research.gov :: GRFP

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Michael Shirts @michaelshirts.bsky.social · 04/04/2025

We are pleased to announce a 2025 i-CoMSE virtual workshop on machine learning for molecules, coming up soon, April 28th-May 2nd, 2025! See www.i-comse.org/workshops for more info, and disseminate widely. Direct registration link at: forms.gle/42Vzmw13F9Ht.... Register by Monday, April 21st!

i-comse.org

Workshops

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Reposted by Michael Shirts

John Chodera @jchodera.bsky.social · 28/03/2025

If you, like me, do not particularly want to die by bleeding out of your eye sockets from diseases like Ebola, and think it's dumb to cut funding for viral countermeasures for future pandemics "because the COVID pandemic is over", here's something you can do about it: resist.bot/petitions/PX...

resist.bot

Reinstate funding for pandemic prevention research and preparedness

Text SIGN PXNIDH to 50409 to send this to your officials.

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livecomsjournal.bsky.social @livecomsjournal.bsky.social · 25/03/2025

Do LiveCoMS articles make a mark? Check out our new blog post on our download & viewing statistics. We’re excited to see LiveCoMS is having an impact and large numbers of people find our work valuable! livecomsjournal.org/index.php/li...

LiveCoMS monthly PDF downloads from our current hosting site, where we moved in late 2021

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Open Free Energy @openfree.energy · 04/02/2025

We're changing the field of #compchem by creating free and open-source software for performing alchemical free energy calculations. Our flagship protocol calculates relative binding free energies of protein-ligand systems. Try it out in your browser: colab.research.google.com/github/OpenF...

Artistic rendering of a biochemical model: a small molecule ligand, shown as a ball-and-stick model colored by element, is bound in a pocket in a protein surface, shown as a space filling model colored off-white.

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