Nature did a short piece on our preprint about how LLMs will affect the practice of science; my more detailed thread is below.

Scientists using LLMs will ‘do more, less well’, modelling study predicts

Research suggests that the combination of incentives to publish and the use of large language models will lead to more papers, but they will be less refined.

nature.com

Carl T. Bergstrom@carlbergstrom.com · 2w ago

1. We—@eduede.bsky.social, @mjcrockett.bsky.social, Kevin Gross, and I—have a new preprint on the arXiv today, based on ideas that emerged during an @sfiscience.bsky.social workshop in November 2024: The unintended consequences of large language models as a labor-augmenting technology in science.

Fully-funded #PhD opportunity for Sept 2026! (UK students only) Apply *by July 24th*, see: lnkd.in/e5MjVKqj Simulation-guided redesign of polyketide synthase enzymes to obtain novel antibiotics Use advanced simulation & AI to propose complex enzyme variants & test them in the lab! #compchem

NEW: A lot of bad has happened to American science over the last year but nothing comes even close to what’s about to happen if we don’t speak out in opposition to the OMB rule changes and I hope @aaas-socsci.bsky.social @apsphysics.bsky.social and others will launch public campaigns about this. 🧪🔭⚛️

It's the End of American Science As We Know It

We have 45 days to express our opposition to catastrophic changes.

news.chanda.science

Registration is open for the #CCPBioSim Annual Conference, 6-8 July, Bristol, UK! See: www.ccpbiosim.ac.uk/bristol2026 Delighted to be hosting the conference @bristoluni.bsky.social, with the theme "Biomolecular simulation across scales, for understanding and design" #compchem #compbio #biodesign

New paper out @chemicalscience.rsc.org! 🚀 Simulating enzyme catalysis with electrostatically embedded machine learning potentials Paper: pubs.rsc.org/en/content/a... Code & data: github.com/chemle/emle-... #CompChem #Enzymes 1/7

GitHub - chemle/emle-enzymes-paper: Supporting data for "Simulating enzyme catalysis with electrostatically embedded machine learning potentials"

Supporting data for "Simulating enzyme catalysis with electrostatically embedded machine learning potentials" - chemle/emle-enzymes-paper

github.com

Not been active here (or other social media) for a while, but the group has not been standing still! I will try to post some updates over the coming days/weeks. Starting with a just accepted paper that I'm really excited about....

I happened to listen for a bit to the main Dutch news&sports radio station, on a Champions League night. Between updates, a ~5 min interview with a professional female footballer about (her) #Endometriosis! Great to hear this getting attention! #EndometriosisAwarenessMonth

As always, accuracy is critical. What I said was: "In some respects this government under Keir Starmer looks more Tory than the Tories". I had just spelt out exactly which respects I meant: its anti-protest laws and the Planning and Infrastructure Bill.

Alex Andreou@sturdyalex.bsky.social · 9mo ago

George Monbiot: "This government is more Tory than the Tories." Bernard Jenkin: "This is the most left-wing government we have ever seen." Labour MP: 🤷🏽‍♂️ #PoliticsLive

Would you like to fight against antimicrobial resistance (AMR) developing antibiotics? Apply to the PhD opportunity below and come to York. Collaboration with colegroupncl.bsky.social, @dghilarov.bsky.social and Inspiralis Ltd. Fully funded via DiMeN DTP 💡 www.findaphd.com/phds/project...

MRC DiMeN Doctoral Training Partnership: Computational Drug Discovery Targeting DNA Gyrase to Tackle Antimicrobial Resistance at University of York on FindAPhD.com

PhD Project - MRC DiMeN Doctoral Training Partnership: Computational Drug Discovery Targeting DNA Gyrase to Tackle Antimicrobial Resistance at University of York, listed on FindAPhD.com

findaphd.com

On my way to a first academic visit to beautiful St Andrews! 🚝💺 Plenty of time on the train (I hope) to finish my slides for tomorrow’s seminar… “Multi-scale simulation of enzymes: Insights into biocatalysts and antibiotic resistance” 🖥️🧪

On 15th Sept, billionaire & Royal Society fellow Elon Musk called for political & interethnic violence, to pre-empt (ie, begin) a civil war. ("Whether you choose violence or not, violence is coming to you. You either fight back or you die."). A fortnight later, the Society expresses its disapproval

The Royal Society@royalsociety.org · 10mo ago

"I am increasingly concerned over threats to the values that allow science to flourish." Read the full statement from the President of the Royal Society Sir Adrian Smith: royalsociety.org/news/2025/10...

Due to popular demand, I am sharing my slide deck on #environmental costs of #ML in #compchem & #materials_science www.grynova-ccc.org/other.html - incl. work by @skepteis.bsky.social @pschwllr.bsky.social and others. Please send any other relevant resources my way, I’ll be maintaining this deck.

Other

3.  G. Gryn’ova , T. Bereau, C. Müller, P. Friederich, R. C. Wade, A. Nunes-Alves, T. A. Soares, K. Merz Jr.,  EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput...

grynova-ccc.org

I’d like to give the BBC the benefit of the doubt, but I can’t remember push notifications on “How much trouble is the Conservative Party in and is Sunak* the right man for the job”… 🤔 (* or Truss, Johnson etc)

Discover the pilot call for assignment of HPC resources to African-based researchers opened by CECAM in collaboration with ICTP and the support of CSCS and CINECA. Deadline for submission Oct. 31 2025. www.cecam.org/compaf

PhD project with @gw4biomeddtp.bsky.social available (Sept '26)! Use #compchem multiscale reaction simulations & experiment to understand and combat antimicrobial resistance by Class C beta-lactamase #enzymes. More info: gw4biomed.ac.uk/overcoming-%... Deadline Oct 20th, but contact me by Oct 5th.

A concrete thing every UK person who cares about trans rights can do right now: 1. Email a link of this report to your MP, with highlights from the executive summary in your email. Ask them what it means for your constituency and their party - highlight trans people's legally mandated human rights

Trans Legal Project@translegalproject.bsky.social · 12mo ago

TW. Needs to be widely shared with cisgender people, especially politicians. Utterly horrifying that Britain has come to this- that most of Britain is just looking the other way while a whole community is being eliminated from society because of lies and hatred. transactual.org.uk/wp-content/u...

www.researchprofessional.com/0/rr/news/uk...

A reminder that the mRNA vaccine technology saved millions of lives during the Covid pandemic and received the 2023 Nobel Prize for Medicine

It’s mind boggling how many additional people this administration is killing. “I have been in this business for over 50 years on the front lines of public health…And I can say unequivocally that this was the most dangerous public health decision I have ever seen made by a government body.”

Federal mRNA funding cut is 'most dangerous public health decision' ever, expert says

Many public health experts and scientists say they are stunned by Health Secretary Robert F. Kennedy Jr’s decision to cancel nearly half a billion dollars in federal funding for future vaccine develop...

pbs.org

Happy Birthday, Rosalind Franklin. She captured an X-ray diffraction image of DNA and stated that a helical structure was probable. Watson and Crick then created a detailed model based on her results. They initially received credit for the discovery and were awarded the Nobel Prize after her death.🧪

HITS Journalist in Residence 2️⃣0️⃣2️⃣6️⃣ Call for experienced science journalists: Explore new research areas and learn about #ML and data-driven science in Germany. The program offers a stay of 3-6 months (€ 6,000/mo.). Apply until 5 October 2025: ow.ly/8lew50Wt6yS #HITSJIR2025 Photo © Christin Hume

#compchem #enzymes #catalysis

Marc van der Kamp@marcvanderkamp.bsky.social · last yr.

🚨 Preprint! 🚨 We show that enzyme catalysis can be accurately simulated with ML/MM, >1000x faster than with DFT/MM! Combining gasphase MLPs with our EMLE approach, we show ML(EMLE)/MM fully captures catalysis in two enzyme reactions. See also: github.com/chemle/ doi.org/10.26434/che...

🚨 Preprint! 🚨 We show that enzyme catalysis can be accurately simulated with ML/MM, >1000x faster than with DFT/MM! Combining gasphase MLPs with our EMLE approach, we show ML(EMLE)/MM fully captures catalysis in two enzyme reactions. See also: github.com/chemle/ doi.org/10.26434/che...

Simulating enzyme catalysis with electrostatically embedded machine learning potentials

To simulate enzyme reactions, multiscale quantum mechanics/molecular mechanics (QM/MM) approaches are well established and popular. However, accurately and efficiently estimating enzyme activity is a ...

doi.org

🚨 Check out the updated version of our latest preprint with @adrianmulholla1.bsky.social, @marcvanderkamp.bsky.social, and many others! 📄 Read it here 👉https://chemrxiv.org/engage/chemrxiv/article-details/685d6114c1cb1ecda080add6

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.

Dan Garisto@dangaristo.bsky.social · last yr.

NEW: NSF will be kicked out of their building. Announcement will be made tomorrow by HUD Sec. and Governor of VA. HUD will take over the NSF building over the next two years. NSF staffer: "There is no planning for NSF, no identified future location, appropriation for a new building or a move."

Our first foray into Class C beta-lactamases - explaining how #antibiotic ceftazidime is broken down more easily by AmpC variants. #AMR #enzymes #compchem Great work by @andersonlimaaa.bsky.social, as @royalsociety.org fellow ACS Catalysis (Open Access): pubs.acs.org/doi/10.1021/...

Insights into the Enhanced Ceftazidime Hydrolysis by Ent385 AmpC β-Lactamase from Multiscale Simulations

The emergence of multidrug-resistant bacteria poses a significant threat to public health. Particularly, they are becoming increasingly resistant to β-lactam antibiotics, which are one of the most important drug classes for the treatment of bacterial infections. Ceftazidime-avibactam has shown promising activity against highly drug-resistant bacteria, including carbapenem-resistant Enterobacterales. However, an Ala294-Pro295 deletion in the Class CE. cloacaeAmpC β-lactamase can confer reduced susceptibility to these agents. In this study, we investigated the molecular mechanisms underlying the enhanced hydrolysis of ceftazidime by E. cloacae Ent385 AmpC β-lactamase with the deletion using quantum mechanics/molecular mechanics (QM/MM) simulations. We used constant pH molecular dynamics simulations of the β-lactamase-ceftazidime acyl-enzyme complex to verify the likely protonation states, confirming Tyr150 primarily exists as a tyrosinate. We then used QM/MM (DFTB2/ff14SB) umbrella sampling to calculate the reaction-free energy barriers (Δ‡G) for the deacylation step of cephalosporin hydrolysis. This reveals that Tyr150 (rather than the substrate) acts as the base. Importantly, the difference in Δ‡G between the canonical E. cloacae AmpC (P99) and the Ent385 variant with Ala294-Pro295 reinserted, on the one hand, and the Ent385 variant, on the other, was in very good agreement with the difference deduced from experimental kinetic data. Detailed analysis of the transition state ensembles, alongside additional simulations, shows that the Ala294-Pro295 deletion allows the entrance of an additional water molecule that helps stabilize the tetrahedral intermediate. Overall, our QM/MM simulations provide valuable insights into the reaction mechanism and reasons for enhanced ceftazidime breakdown. The protocol used in this study successfully captures the kinetic differences observed among the studied variants. This approach can be employed to investigate other Class C β-lactamase variants with similar features, providing insights into their mechanisms and potential contributions to reduced susceptibility to antibiotic treatments.

pubs.acs.org

Springer-Nature launched a series of "Discover" journals that closely mimic MDPI titles -- sharing *identical* journal names, and likely similar business model. What is going on, and why researcher will - as always - fall for it? A 🧵 the-strain-on-scientific-publishing.github.io/website/post...

Springer Nature Discovers MDPI – The Strain on Scientific Publishing

Home page for the paper ‘The Strain on Scientific Publishing’ by Mark A Hanson, Dan Brockington, Paolo Crosetto and Pablo Gomez Barreiro

the-strain-on-scientific-publishing.github.io

QBIC VII in Berlin. Registration is open: slots for oral presentations are available. @humboldtuni.bsky.social #chemsky #compchem

Matthias Stein@matthiasstein.bsky.social · last yr.

Registration for the Quantum Bio-Inorganic Chemistry Conference QBIC VII in Berlin (26-29 August 2025) has opened: buff.ly/PdqOoIE.