Xin@QuantumChem
@xinquantum.bsky.social
📤 154
📥 357
📝 66
Computational Chemist @NJ/NYC Github:
https://github.com/XinChenQC
Centuries of human progress led us to uncover The Double Helix. In the end, we realized that all living things share the same codebook.
#science
#biology
about 8 hours ago
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Yesterday I posted an incorrect comparison. I accidentally copied the TS3 structure into TS1 for UMA and Orb-V3, so the MLIP results for TS1 were wrong. Really sorry about that misleading! In the next post I will share IRC of DFT calculation and wB97M-V/def2-TZVPD results.
#compchem
#compchemsky
add a skeleton here at some point
7 days ago
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A failure case for deep-learning potential: the TS1 geometry is so weird that UMA and Orb-v3 underestimate the barrier by ~15 kcal/mol, likely because it far from the training set. Handling chemical reactions is extremely hard for general deep learning models.
#compchem
#compchemsky
8 days ago
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UMA (small model) is very close to DFT M06-2X. Maybe I can deploy nanoreactors using UMA model for coarse reaction space sampling. This is a reactive trajectory of a compound with 24 Carbon atoms.
#CompChem
#ChemChemSky
18 days ago
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I'd like to name it as "QM/MM".
3 months ago
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playground.tracto.ai/playground/n...
The newly released open-source model from OpenAI can be tried on TractoAI playground for *FREE*.
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TractoAI | Cloud platform for AI and Data teams
Run AI and Data workloads in the cloud at scale
https://playground.tracto.ai/playground/navigation?path=//home/territorial_orange_opossum/notebooks/bulk-inference-gpt-oss-120b
3 months ago
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This old theory is revitalized by deep learning. Building accurate kinetic energy functionals (< 0.5 kcal/mol) may be harder than climbing to the top of exchange-correlation Jacob's ladder.🪜
add a skeleton here at some point
3 months ago
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Cunning ChatGPT bypassing 3D depth analysis, and calling the rdkit function to generate the coordinate of an Ibuprofen. Grok3 just failed this test and misrecognized it as glucose, as expected.
4 months ago
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Boltz2 can be run on a $430 RTX5060 Ti (16G) card, although it's much slower than ~$30,000 H100 (RTX 5060 Ti: 1min 47s, H100: 18s), but it doesn't matter, because the cold-start time is about 1 minute for both cards.
#CompChemSky
#CompChem
#GPU
4 months ago
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Kvass and Khinkali
4 months ago
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This is creepy, but lots of fun. Gemini Veo has a perception of spatial depth and can rotate the molecules. Inspired by
www.youtube.com/watch?v=mDyt...
#compchem
#compchemsky
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4 months ago
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I ran a benchmark on a protein with ~3450 atoms. AIMnet2 takes 4.6 seconds, and UMA(small) takes 7.9 seconds. CUDA 12.4 on a Tesla T4. Additionally, the AIMnet2 checkpoint file is only 11.1 MB. The testing notebook link is shared.
#compchemsky
#compchem
colab.research.google.com/drive/1g1PiW...
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Google Colab
https://colab.research.google.com/drive/1g1PiW-ap0JBqZCn9MQzLQyiEYA_bACLD?usp=sharing
4 months ago
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This is a very interesting package. I will try this on colab notebook.
add a skeleton here at some point
4 months ago
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UMA (uma-sm) combined with NEB successfully locates the transition state and path for a Ni-catalyzed reaction. UMA prediction lies between two DFT functional, and the transition state closely matches the result from a literature:
www.nature.com/articles/nat...
#compchemsky
#chemsky
#compchem
4 months ago
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The relationship between Ki and IC₅₀ is described by the Cheng–Prusoff equation. And William L. Jorgensen et al. did an effective calculation for predicting potency in his paper during pandemic.
pubs.acs.org/doi/10.1021/...
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5 months ago
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Guess the name?
#Cocktail
#Liquor
#Alcohol
#cursor
5 months ago
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reposted by
Xin@QuantumChem
Jan
5 months ago
2nd virtual lecture in the DFT&Application series starts today at 1500hrs CET (in 15 minutes!). Topics are Hartree Fock, SCF, and their connection to DFT. Join us in Zoom:
us06web.zoom.us/j/8607128794...
#compchem
#dft
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Join our Cloud HD Video Meeting
Zoom is the leader in modern enterprise cloud communications.
https://us06web.zoom.us/j/86071287942?pwd=KbXbDZyoaLPR6wgHyzC6AcI3UyXnMW.1
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reposted by
Xin@QuantumChem
Jo Ma
5 months ago
Hey Jan, I just completed UMA benchmark tests on large molecules (biomolecules, macrocycles, and more):
quantabricks.substack.com/p/uma-testin...
In short, when atoms number below 700, uma is more expensive. Otherwise, GFN2-xTB is more expensive
#compchem
#CompChemSky
add a skeleton here at some point
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An interesting opportunity to help the horseshoe crab (more closely related to spiders).
gothamist.com/news/new-yor...
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New York beaches are dating hot spots for horseshoe crabs
Beneath a full moon in Jamaica Bay, horseshoe crab love was in the air.
https://gothamist.com/news/new-york-beaches-are-dating-hot-spots-for-horseshoe-crabs?utm_source=sfmc&utm_medium=nypr-email&utm_campaign=Newsletter+-+Early+Addition+-+20250606&utm_term=First+headline&utm_id=455329&sfmc_id=85112797&utm_content=202566&nypr_member=Unknown
5 months ago
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Surprisingly, the UMA (by meta) model captures the bond-breaking process in the carbon nanotube stretching test, similar to GFN2-xTB. I hadn't expected deep learning models to extrapolate over bond lengths.
#compchemsky
#chemsky
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5 months ago
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It's a great time to participate in the horseshoe crab protection activity (helped with counting and tagging). I had only heard stories about the blue blood legend in evolution before, but this time I saw it with my own eyes.
#aquatic
#science
#NYC
#drug
6 months ago
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JupyterNotebook:
github.com/myzzzz6/AI4C...
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6 months ago
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Get Started with Meta’s Molecular AI Model UMA on Google Colab
open.substack.com/pub/quantabr...
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Get Started with Meta’s Molecular AI Model UMA on Google Colab
Meta and collaborators released the molecular foundation model UMA (Universal Model for Atoms) and its training dataset OMol25 (at ωB97M-V/def2-TZVPD level) this month.
https://open.substack.com/pub/quantabricks/p/get-started-with-metas-molecular?utm_campaign=post&utm_medium=web
6 months ago
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Interesting results for physical model, average RMSD<5A meaning that the ligands are plugged into the correct docking pocket. Unlike the AI methods, the charge models, protein ionization state or hydrated docking should be considered. This competition is also hosted by
@asapdiscovery.bsky.social
add a skeleton here at some point
8 months ago
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It's suitable for building AI agents.
add a skeleton here at some point
8 months ago
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go.bsky.app/52czHRA
#StarterPack
for
#CADD
(computational-aided drug design) enthusiasts, open to researchers, students from both industry and academia.
#compchemsky
#compchem
#chemistry
#drugdesign
add a skeleton here at some point
8 months ago
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LLM-based ESM3 has just been released. Protein structure predicting is just a starting point of workflows. More functions should be implemented.
add a skeleton here at some point
10 months ago
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Seeking Image-to-SMILES conversion for local tiny device deployment. Deep learning offers accuracy but is too heavy. Are there lightweight alternatives without deep learning? Mathpix (SaaS) appears best, but closed-source and need internet.
10 months ago
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Stretching of a carbon nanotube, a DFTB simulation. Do you know why I placed a nitrogen atom at the center?
#CompChem
#CompChemSky
#Science
#Chemistry
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11 months ago
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Lower speed collision of C60, like two elastic balls. (DFTB+)
#CompChemSky
#CompChem
#Chemistry
#Physics
@filtei.bsky.social
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11 months ago
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It looks like a Christmas Wreath
add a skeleton here at some point
11 months ago
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Collision Between Two C₆₀ Molecules: A Violent Encounter (An xTB-GFN2 Simulation)
#CompChemSky
#CompChem
#Chemistry
#Physics
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11 months ago
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Conchiglie with Kale and ham, The center part of the shell is raw and hard, but tastes good. Is it authentic?
#Italian
#Italianfood
12 months ago
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Simulation of a violent collision between two molecules. How many reactions can you find? Simulation using GFN2-xTB. On a preowned desktop computer. It takes about 20 minutes.
#compchem
#Chemistry
#computing
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12 months ago
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