Marcelo D. Polêto

Worked on some plugin examples for the upcoming @avogadro.cc 2.0 release.

I think we're at 12 as of tonight... woudn't be surprised if we get to at least double that by the end of the month.

Any requests?
- electrostatics
- energies / potentials
- file formats
- commands / builders

#compchem

Mapping the yeast atructural interactome with AlphaFold3: an open call for collaboration We are excited to announce the early-stage release of our S. cerevisiae  structural interactome mapping project. Using AlphaFold3 (AF3), w...

We have started a project trying to predic the interactions/structures of all yeast protein pairs using an AlphaFold pooling approach. We are making the current dataset open and we welcome collaborations.
www.evocellnet.com/2026/03/mapp...

Christofascism is a far-right ideology merging fascist, authoritarian, and ultranationalist political doctrines with Christian theology, aimed at imposing a specific religious, cultural, and political order.

"They were girls who went to school to learn, with hopes and dreams for their future," Nobel Peace Prize winner Malala Yousafzai said. "Today, their lives were brutally cut short.”

Read more: https://wapo.st/4r7izC7

Image of the Lemkul lab members at BPS 2026. From left: Justin Lemkul, Esmat Mohammadi, Ashley Goodberlet, Patrick Gilles (back), and Rakshitha Hosahalli.

We had a great time at BPS 2026! Sad to conclude my time on the Theory & Comp subgroup committee but I enjoyed that service and made new friends along the way. Until Philly in 2027!

Selfie at BPS 2026

I’m at the BPS2026 meeting @biophysicalsoc.bsky.social in San Francisco. Find me to talk science or if you want some @mdanalysis.bsky.social stickers.

Avogadro Stories (for 2.0 Release) As we finish up the 2.0 (final!) release, I’d like to feature some stories (and citations) about how Avogadro has shaped research and teaching. So if Avogadro has helped your research, please let me ...

Has @avogadro.cc helped your research? Teaching?

As we prepare Avogadro 2.0 for release this spring, I'm hoping to feature some stories (and citations).

#compchem #opensource #openscience ⚗️

Let me know:
discuss.avogadro.cc/t/avogadro-s...

A theoretical framework for random acceleration molecular dynamics simulations The dissociation of a ligand bound to a receptor is a rare event occurring on a timescale that is far longer than can be afforded by standard simulation methodo

We developed a simple theory and showed that Random Acceleration Molecular Dynamics (RAMD) is consistent with a Smoluchowski equation with an effective temperature and diffusion coefficient that depend quadratically on the magnitude of the random force.
pubs.aip.org/aip/jcp/arti...

Okay, as promised, here's a summary of "keeping up with the literature" tools #chemsky

What I want is a "sort by best" tool that learns my preferences.

I'm not sure there's a perfect solution now, but there are some promising tools...

Happy Chinese New Year!💐💐💐🎁🎁🎁

Hey #chemchat #chemsky question - an app I used to track journal feeds will be dead soon.

Any good tools to keep track of new literature articles? Ideally I'd like something I can 👍👎 and filter out topics or authors (e.g., "exclude this paper mill")

Suggestions welcome - I'll post a summary

I like storkapp.me

Even though it doesn't have the features you mentioned, I feel pretty updated.

Racist comment number #6382628 from M*sk that will be ignored by the @royalsociety.org .

In times of "societies meeting at islands for unspeakable reasons" (🤬), one would think that Scientific societies would be more careful about who they accept as Fellow...

Pra ouvir ********* dizer que esse é o "agro" que dá certo......................

Noam Chomsky, Jeffrey Epstein and the Politics of Betrayal I don’t expect much from politicians, corporate tycoons, the presidents of prestigious universities, billionaire philanthropists, celebrities, royalty or oligarchs.

Something to highlight is that, very often, men who complain (or theorise a lot) against "cancel culture" seem way more worried about the "canceled" than the issues that lead to "cancelation". And sometimes we find them happy in the company of some very bad people that should be more than canceled.

Ni-SACs are great at reactive carbon capture, too! For more on details of the electrochemical interface that drive selectivity, check out our new theory+experiment paper in @jacs.acspublications.org
👉 doi.org/10.1021/jacs.5c11791

#compchem #chemsky #compchemsky

@uclacb.bsky.social

Robust and Automated Force Field Parameterization Using Validation Sets and Active Learning Molecular mechanics force fields enable atomistic simulations of complex systems that are too large for a quantum mechanical treatment. Simulation accuracy depends on the parameters employed in the fo...

"In contrast to previous attempts at iterative optimization, we employ a validation set to determine convergence. Using a validation set circumvents problems with parameter convergence and flags when overfitting occurs"

pubs.acs.org/doi/full/10....

Isso ou o arrasta de uma galera aí.

Já tá na geladeira só esperando pelo "pop!"

Rendering of highest occupied molecular orbital (HOMO) of a conjugated molecule showing conventional orbital isosurfaces in red and blue bubbles.

Rendering of highest occupied molecular orbital (HOMO) of a conjugated molecule showing volumetric electron density in shades of red and blue clouds

Obviously a lot is going on (gestures widely)

Amid chaos, I cope by doing *something* -- anything. Lately, it's been coding for @avogadro.cc because it feels like some small change I can do myself

For *years* I've wanted to show electron density volumes .. little clouds ☁️☁️

#compchem

Imagine what’s happening in the camps.

Abolish Ice. Make racism illegal like it is in Brazil. It helps

The CP2K Program Package Made Simple CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfac...

Have you always wanted to use CP2K but found the online manual too superficial and our JCP 2020 code review paper (doi.org/10.1063/5.00...) too theoretical? Then our new overview paper "The CP2K Program Package Made Simple" from the user's perspective is just right for you!
doi.org/10.1021/acs....

Jornalistas, o que falta para chamarem os EUA de ditadura? Agentes do governo executando e pretendendo opositores políticos? Já está acontecendo!!

It’s a dark night when you look at the news and are forced to admit that you no longer believe in the power of the FIFA peace prize

The bombing of Venezuela is an act of aggression: unprovoked, unjustified and unjustifiable.

Brazilian Supreme Court ruled last June that platforms are responsible for the content generated by "chatbots and/or bots".

Which means that any Brazilian that is harmed by whatever grotesque image Grok spits out can directly sue the platform, streamlining the due process 💪

Brazil is no joke 🥰🇧🇷

Com alt

O segredo é errar a mão feio quando te convocarem no ano que vem. Botar o dobro de sal, botar açúcar, etc.

Aí 2027 vc tá livre 😅

Assistir Jornal Hoje - Cientistas inauguram laboratório a céu aberto online | Globoplay Pesquisadores simulam aumento de CO2 para entender os impactos na Amazônia.

Estamos no Jornal Hoje se hoje globoplay.globo.com/v/14207137/

Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design https://www.biorxiv.org/content/10.64898/2025.12.20.695737v1