Sign in

Tim Duignan

@timothyduignan.bsky.social
529 followers 809 following 101 posts

Researcher at Orbital Materials. Working on molecular simulation with ML for chemical engineering applications.

PostsRepliesMedia
Tim Duignan @timothyduignan.bsky.social · 20/10/2025
When generating training data on specific systems the MLIP/NNP community needs to get organized and agree on one particular level of theory, settings and data storage standards as much as possible so we can pool all the data for training foundation/universal models right?
120
Tim Duignan @timothyduignan.bsky.social · 10/10/2025
When agentic AI started popping up I remember thinking, yeah that is the logical next step but we're not there yet. Its a several years away, well I think its here now and it came much faster then I expected. It's still early days but seems it will have a profound impact.
100
Tim Duignan @timothyduignan.bsky.social · 09/10/2025
Couple of very nice new papers on understanding the SEI formation in lithium ion batteries using neural network/machine learning interatomic potentials (NNPs/MLIPs).
120
Tim Duignan @timothyduignan.bsky.social · 18/09/2025
Universal machine learning forcefields beating tailor made classical potentials for zeolites quite convincingly. Great to see all these benchmarking papers! Again demonstrates accurate training data + speed should be key focus now. arxiv.org/abs/2509.07417
061
Tim Duignan @timothyduignan.bsky.social · 09/09/2025
I think neural network potentials are the eventual pathway to a virtual cell. The accuracy/memory are quite close to where you need them. Timescale is the last real hurdle. But we can port decades of great tools from classical FFs, so it’s becoming more of an engineering problem now.
100
Tim Duignan @timothyduignan.bsky.social · 08/09/2025
arxiv.org/pdf/2508.15614 This is right and it's a big deal. Been waiting my whole career for this point. So many things to simulate!
030
Tim Duignan @timothyduignan.bsky.social · 02/09/2025
Another very interesting benchmarking paper on NNPs. lnkd.in/gWbcTQw8 It seems the models are pretty much there. Very exciting times as these new large datasets continue to be built. Always need more though!
020
Tim Duignan @timothyduignan.bsky.social · 28/08/2025
Another remarkable jump in accuracy with these new OrbMol models for simulating chemistry. For example, they now quantitatively reproduce the structure of water. But they should be just as applicable for studying a vast range of different liquids.
281
Tim Duignan @timothyduignan.bsky.social · 24/07/2025
Another nice benchmarking paper highlighting the rapid exciting progress of universal MLIPS/NNPs: www.arxiv.org/abs/2507.11806
010
Tim Duignan @timothyduignan.bsky.social · 23/06/2025
Love this combination of LLMs and NNPs, a powerful pair of tools. www.sciencedirect.com/science/arti... Also wonderful to see people picking up Orb so quickly and getting good results!
020
Tim Duignan @timothyduignan.bsky.social · 19/06/2025
This is excellent! arxiv.org/abs/2506.14492
010
Reposted by Tim Duignan
Jan Hermann @hrmnn.net · 18/06/2025
🚀 After two+ years of intense research, we’re thrilled to introduce Skala — a scalable deep learning density functional that hits chemical accuracy on atomization energies and matches hybrid-level accuracy on main group chemistry — all at the cost of semi-local DFT ⚛️🔥🧪🧬
37225
Reposted by Tim Duignan
Rianne van den Berg @riannevdberg.bsky.social · 18/06/2025
So proud of this work with our amazing team 🤩
0143
Tim Duignan @timothyduignan.bsky.social · 18/06/2025
So many nice NNP papers coming out now it is impossible to stay on top of them. Four very cool recent ones:
131
Reposted by Tim Duignan
Joe Greener @jgreener64.bsky.social · 20/03/2025
Interesting work exploring an enzyme reaction with a machine learning potential. Looking forward to much more like this in the next few years.
031
Tim Duignan @timothyduignan.bsky.social · 19/03/2025
So Orb has blown me away again. I simulated the carbonic anhydrase enzyme with it: one of the most important and well studied enzymes in biology. (It converts CO2 to bicarbonate and is involved in many diseases and could also be useful for carbon capture.)
230
Tim Duignan @timothyduignan.bsky.social · 25/02/2025
Running out of memory used to be a common headache when running molecular simulations with neural network potentials. Not any more. Here Orb is simulating over half a million atoms on a single GPU (H200). This is a fully solvated COVID spike protein. Models here: github.com/orbital-mate...
1112
Tim Duignan @timothyduignan.bsky.social · 13/02/2025
Uranium is one of the hardest elements to simulate due to the large number of electrons, so I thought I would try it with Orb and remarkably it seems to behaves well even getting the melting point roughly correct. I think looking at this systematically for many metals would be a great project.
031
Tim Duignan @timothyduignan.bsky.social · 12/02/2025
Had a lot of fun outlining how I think AI accelerated simulation with tools like Orb are going to be profoundly useful for Chemical Engineering in this article for The Chemical Engineer: www.thechemicalengineer.com/features/vie...
031
Tim Duignan @timothyduignan.bsky.social · 10/02/2025
Here's a fun one you can't do in the lab: diamond melting at thousands of degrees simulated with Orb. Simulate anything you want with it here: colab.research.google.com/github/timdu...
030
Tim Duignan @timothyduignan.bsky.social · 09/02/2025
Very cool.
000
Tim Duignan @timothyduignan.bsky.social · 26/01/2025
Really enjoyed this discussion on all the ways AI tools like Orb can be used to accelerate the incredibly important task of accelerating materials science and biology. www.cognitiverevolution.ai/material-pro...
cognitiverevolution.ai
Material Progress: Developing AI's Scientific Intuition, with Orbital Materials' Jonathan & Tim
Jonathan Godwin, founder and CEO of Orbital Materials, alongside researcher Tim Duignan, discuss the transformative potential of AI in material science on the Cognitive Revolution podcast. Watch Epi...
020
Tim Duignan @timothyduignan.bsky.social · 21/01/2025
Wild times
020
Tim Duignan @timothyduignan.bsky.social · 19/01/2025
You can now run these yourself with this google colab: shorturl.at/cFMA7 The same script should work on the gpu on newer Macs too. All you need is a .xyz file of your atom types and positions and you can simulate your own systems.
shorturl.at
Google Colab
1141
Reposted by Tim Duignan
John Chodera @jchodera.bsky.social · 08/01/2025
Interested in building the future of open source ligand- and structure-based ML models for ADMET prediction? The ARPA-H funded OMSF (@omsf.bsky.social) OpenADMET project is hiring multiple positions to build ML models of ADMET properties and drive informative data collection! openadmet.org/jobs/
openadmet.org
OpenADMET Jobs
Seeking talented scientists for the OpenADMET Consortium
03713
Tim Duignan @timothyduignan.bsky.social · 08/01/2025
Simulating over 10,000 atoms for 10 ps a day on my Macbook with close to quantum chemical accuracy using Orb. I can do this for almost any element from the periodic table I want. Just a few years ago this would have been totally inconceivable with even the world's largest supercomputers.
261
Tim Duignan @timothyduignan.bsky.social · 07/01/2025
Lots of useful and interesting benchmarking of universal force fields in this paper. This fields really picking up now. Good to see all them doing well on silicon now. arxiv.org/abs/2412.10516
030
Reposted by Tim Duignan
Gianni De Fabritiis @gdefabritiis.bsky.social · 07/01/2025
Aceforce 1.0 is out and downloadable from Huggingface. It covers all interesting elements and charged molecules. Tested for relative binding affinity calculations. Just version 1.0, more to come. www.businesswire.com/news/home/20...
businesswire.com
Acellera Therapeutics Unveils AceForce 1.0: A Novel Family of Next-Generation Neural Network Potential Accelerating Drug Discovery
Acellera Therapeutics, a pioneer in computational chemistry and AI-driven drug discovery, today announced the launch of AceForce 1.0, its groundbreaki
0153
Tim Duignan @timothyduignan.bsky.social · 06/01/2025
Excellent perspective on using machine learning for coarse grained simulations. This is an incredibly promising field in my opinion. Lots of low hanging fruit to implement that will be really impactful, e.g, this is a great one: www.sciencedirect.com/science/arti...
030
Tim Duignan @timothyduignan.bsky.social · 17/12/2024
This is incredible, Orb can predict phase diagrams of metal alloys remarkably well. This is a very important class of materials that we now have a powerful new tool to study computationally starting from nothing but quantum mechanics. 1/2
230
Reposted by Tim Duignan
John Chodera @jchodera.bsky.social · 06/12/2024
Excited to speak at the ELLIS ML4Molecules Workshop 2024 in Berlin! moleculediscovery.github.io/workshop2024/
Photograph of Johannes Margraph and Günter Klambauer introducing the ELLIS ML4Molecules Workshop 2024 in Berlin at the Fritz-Haber Institute in Dahlem.
3464
Reposted by Tim Duignan
John Chodera @jchodera.bsky.social · 06/12/2024
Cecilia Clementi (@cecclementi.bsky.social) kicks off the afternoon session of the ELLIS ML4Molecules Workshop in Berlin!
Cecilia Clementi introduces her talk, "Navigating protein landscapes with machine learned coarse-grained models"
0395
Tim Duignan @timothyduignan.bsky.social · 02/12/2024
So I think I've found another pretty incredible example of the generalisability of neural network potentials: this is a problem I've been dreaming of tackling for a decade but never felt I had the the tools to get at until now: How do potassium ion channels work. 1/n
191
Tim Duignan @timothyduignan.bsky.social · 01/12/2024
These new Alphafold3 clones are awesome but we need to find a way to use AI to answer questions about protein function without relying on the information in the PBD, as that’s inherently limiting.
320
Tim Duignan @timothyduignan.bsky.social · 01/12/2024
This is awesome!
030
Reposted by Tim Duignan
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 29/11/2024
Meet the CALVADOS RNA model Ikki Yasuda, Sören von Bülow & Giulio Tesei have parameterized a simple model for disordered RNA. Despite it's simplicity (no sequence, no base pairing) we find that it captures several phenomena that depend on the charge, stickiness and polymer properties of RNA 🧬🧶🧪
48821
Reposted by Tim Duignan
calccon.bsky.social @calccon.bsky.social · 29/11/2024
What is a SemiEmpirical Theory ?
011
Tim Duignan @timothyduignan.bsky.social · 29/11/2024
Hmm seems to me the models must be missing some significant physical process? How well do we understand the chemistry of sulphates electrolyte droplets in the upper atmosphere?
111
Tim Duignan @timothyduignan.bsky.social · 28/11/2024
Amazing ai accelerated simulation is coming for all physical scales. arxiv.org/pdf/2405.13063
0121
Tim Duignan @timothyduignan.bsky.social · 28/11/2024
Love this night science/day science framework. ‘Popping in’ and ‘popping out’ the best thing about it is it that it has a physical analogy which I suspect has an underlying mathematical cause: pca.st/podcast/f80f...
pca.st
Night Science
Where do ideas come from? In each episode, scientists Itai Yanai and Martin Lercher explore science's creative side with a leading colleague. New episodes come out every second Monday.
100
Tim Duignan @timothyduignan.bsky.social · 28/11/2024
This seems to boil down to it’s too expensive, which is true, but 20 years ago you could have written identical articles about solar and batteries. We urgently need to get DAC on the same exponential price decline curve. The only way to do that is to get started now.
120
Reposted by Tim Duignan
amelie-iska @amelie-iska.bsky.social · 27/11/2024
youtu.be/MO6ZvA7U3F0
youtu.be
AI Could Make Quantum Computing Obsolete, Nobel Prize Winner Says
YouTube video by Sabine Hossenfelder
094
Reposted by Tim Duignan
Mathieu Alain @miniapeur.bsky.social · 26/11/2024
Scientific machine learning starter pack go.bsky.app/9a1GVeq
184413
Reposted by Tim Duignan
Andrew S. Rosen @andrewrosen.bsky.social · 26/11/2024
Should it benefit anyone here, I'm happy to share the notes from my reaction engineering course: github.com/Andrew-S-Ros.... Thank you @typst.app for making me not want to explode when putting this together, and we'll try it again next year! Lots of ideas for round two!
github.com
3213
Tim Duignan @timothyduignan.bsky.social · 26/11/2024
One day soon we will have universal NNPs that can simulate thousands of atoms for nanoseconds per day with close to CCSD(T) accuracy. That will be transformative for much of biology and chemistry won’t it? Like it almost seems inevitable to me.
000
Reposted by Tim Duignan
Matthew Clark @matthew-batisio.bsky.social · 25/11/2024
I am excited to share this animation of the budding yeast inner kinetochore. Created for David Barford's lab @mrclmb.bsky.social This DNA-binding protein complex acts as an anchor for the spindles that pull chromosomes apart during mitosis. www.science.org/doi/10.1126/... #blender #animation #b3d
713531
Tim Duignan @timothyduignan.bsky.social · 25/11/2024
We normally think of AI as only being useful if the training data contains many examples that are similar to what you’re interested. But with these new universal neural network potentials like Orb this really doesn’t seem to be the case.
130
Tim Duignan @timothyduignan.bsky.social · 21/11/2024
Ok let’s go: I think we’re using AI for science wrong. We’re trying to use it to shortcut us to the solution. To one shot it. To have an oracle that just tells us what to do. That’s not it. It’s not there yet. 1/n
140