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David L. Dotson

@dotsdl.bsky.social

physicist, entrepreneur, alchemist; opinions my own 🏳️‍🌈

24 Posts85 Follower87 Folgt
David L. Dotson@dotsdl.bsky.social · 8mo ago

As 2025 comes to a close, we'd like to solicit feedback from all alchemiscale users to help us determine where to prioritize effort in 2026! If you have a moment, share your thoughts in the discussion here: github.com/OpenFreeEner... Thanks in advance! #compchem #alchemistry #opensource

alchemiscale user survey 2025 · OpenFreeEnergy alchemiscale · Discussion #452

As 2025 comes to a close, we'd like to solicit feedback from our users to help us determine where to prioritize effort in 2026. If you have a moment, please answer the following questions as respon...

github.com

Jen Mercieca@jenmercieca.bsky.social · last yr.

If they suspend Habeas Corpus, it won't just be for "migrants" or "illegals" or "criminals." If they suspend Habeas Corpus it will be for you and me and whomever this regime decides is unfit, undesirable, and a threat or a problem. This is how it works. This is how it's always worked.

David L. Dotson@dotsdl.bsky.social · last yr.

Excited to announce that Achira (achira.ai) is supporting Datryllic in advancing alchemiscale in 2025! Details here: alchemiscale.org/advancements... Looking to scale free energy calculations for your applications? Don’t hesitate to reach out! #drugdiscovery #alchemistry #opensource #compchem

Achira support for Datryllic's efforts in 2025

In February, we published the alchemiscale project’s 2025 roadmap, detailing our objectives for the year, our available resources, and the path we intend to take to leverage these resources in service...

alchemiscale.org

John Chodera@jchodera.bsky.social · last yr.

Everything is chaos, but I wanted to share some awesome recent science from the lab that hints at where the future of biomolecular simulation is headed: Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.

Figure 1 from arXiv preprint https://doi.org/10.1101/2025.01.06.631610 Fig. 1 Espaloma is an end-to-end differentiable molecular mechanics parameter assignment scheme for arbitrary organic molecules. Espaloma (extensible surrogate potential optimized by message-passing) is a modular approach for directly computing molecular mechanics force field parameters FFF from a chemical graph G such as a small molecule or biopolymer via a process that is fully differentiable in the model parameters FNN. In Stage 1, a graph neural network is used to generate continuous latent atom embeddings describing local chemical environments from the chemical graph. In Stage 2, these atom embeddings are transformed into feature vectors that preserve appropriate symmetries for atom, bond, angle, and proper/improper torsion inference via Janossy pooling.54 In Stage 3, molecular mechanics parameters are directly predicted from these feature vectors using feed-forward neural networks. This parameter assignment process is performed once per molecular species, allowing the potential energy to be rapidly computed using standard molecular mechanics or molecular dynamics frameworks thereafter. The collection of parameters FNN describing the espaloma model can be considered as the equivalent complete specification of a traditional molecular mechanics force field such as GAFF38,39/AM1-BCC55,56 in that it encodes the equivalent of traditional typing rules, parameter assignment tables, and even partial charge models. Reproduced from ref. 49 with permission from the Royal Society of Chemistry.
David L. Dotson@dotsdl.bsky.social · last yr.

This month the alchemiscale project celebrates its 3rd anniversary since kicking off in 2022! We've come a long way, and there is much we look forward to improving this year. Read about where we're going in 2025: alchemiscale.org/roadmaps/alc... #compchem #opensource #alchemistry #drugdiscovery

alchemiscale roadmap 2025

It’s 2025, and this month the project now known as alchemiscale celebrates its 3rd anniversary since kicking off in 2022.

alchemiscale.org

David L. Dotson@dotsdl.bsky.social · 2y ago

Very pleased to announce that ASAP Discovery (asapdiscovery.org) is supporting Datryllic in advancing alchemiscale in 2025! More details here: alchemiscale.org/advancements... Looking to advance alchemiscale further? Don’t hesitate to reach out! #drugdiscovery #alchemistry #opensource #compchem

Datryllic efforts for ASAP Discovery in 2025

In October, we offered a detailed perspective on what we considered to be the alchemiscale project’s most attractive advancement opportunities in 2025.

alchemiscale.org

David L. Dotson@dotsdl.bsky.social · 2y ago

Tis the season for making space to realign the spirit with the mind and body. To rekindle the enthusiasm that set you down the path you're on, and to consider the possibilities beyond it. To take stock of what you have learned, and what you likely need to. To be ready to make a positive impact.

OMSF@omsf.io · 3y ago

We are now on Bluesky! OMSF supports the ever-growing ecosystem of open source molecular software. We love all things #opensource, #science, and #software - if you do too, follow us!