iiinova — where your digital self keeps evolving

Reposted by Nicolas

The Matter Lab @thematterlab.bsky.social · 29/09/2026

Are you interested in learning about how agentic AI systems like El Agente operate? Curious on how to incorporate them into your research workflow? Join our live webinar as we show El Agente in action 🤖 🗓️ 24 Nov 2026, 10 AM - 11AM EST ✅ Registration & qns: register.gotowebinar.com/register/828...

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Nicolas @nicolasn.bsky.social · 27/09/2026

Some updates on my Molecular Dynamics with Julia project! #compchem #chemsky youtube.com/post/UgkxAiD...

youtube.com

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Nicolas @nicolasn.bsky.social · 25/09/2026

For #fluorescencefriday a new #corrole with a bromoalkyl chain for further derivatization! #realtimechem #chemsky

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Nicolas @nicolasn.bsky.social · 21/09/2026

We put some steel wires for climbing plants on the gallery side. We need shade in the spring summer and the trees in the back are not enough. It took the whole day to put the wires up.

View of the same backyard from another side of the gallery, where newly placed still wires can be seen between the floor and the wooden beams of the gallery roof. Two large wild quince plants are just outside the gallery, filled with red-pink flowers.

A backyard seen from a gallery with steel wires supporting a climbing plant

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Nicolas @nicolasn.bsky.social · 18/09/2026

Update: I have not yet found the damn bug, but at least I have narrowed it down (I think). ChatGPT was only useful in suggesting me to simplify the code to narrow down the problems. But it did not find any bug, and is extremely annoying, verbose and obsequious, and it gets worse the longer we chat.

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Nicolas @nicolasn.bsky.social · 16/09/2026

Like 10 years ago I made a Hartree Fock code in MATLAB. It allowed integrals with angular momentum through Obara-Saika RRs. I worked on it for years at a time, but there was a bug somewhere which I could never fix. Last night I picked it up and started asking ChatGPT to find if there was 1/n

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Nicolas @nicolasn.bsky.social · 15/09/2026

I made a small update, calculating the step where an amine attacks an activated acetylester, coupled to proton abstraction bay carbonate. This is just a clip of the MD at several constrained N-C distances. #compchem #chemsky 🧪 youtu.be/eiDxQvySQgo

youtu.be

Coupling relaxed surface scans with molecular dynamics: a teaser

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 06/09/2026

I've made a video explaining how to combine relaxed surface scans with molecular dynamics in #orca in order to sample conformations along a reaction profile, and get energies with error bars for your barriers! #compchem #chemsky #science #education #XTB youtu.be/4HjqXlz_mEo

youtu.be

Do you know if your Transition State calculation is correct?

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 04/09/2026

I've been playing around with #Orca, setting up a compound script to run a constrained MD run on each step of a relaxed surface scan. From the MD I got a mean energy and standard deviation for each step in the scan. This allows IMO a better description of the dynamics of the process. #compchem

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Reposted by Nicolas

Geoff Hutchison @geoffhutchison.net · 29/08/2026

A few weeks ago, I posted for the 2026 Avogadro Community Feedback Survey. Over 50 people responded, and several wrote multi-paragraph responses! I posted a summary to the forum and I want to include a few notes for #compchem discuss.avogadro.cc/t/avogadro-2...

discuss.avogadro.cc

Avogadro 2026 Survey Results

A few weeks ago, I posted the 2026 Community Feedback Survey - and I’d like to start doing this annually. Thank you to the 49 50 of you who filled out the development survey. Several people wrote…

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Nicolas @nicolasn.bsky.social · 23/08/2026

New video showing my attempts at fixing the polymer builder tool in Julia, to make a chain of polyNIPAM for molecular dynamics! #compchem #julia #orca #chemcraft #programming #chemsky youtu.be/29Wi-BhcUpY

youtu.be

Trying to Fix the Polymer Builder: What is the best approach?

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 22/08/2026

Tried to install ambertools yesterday on the cluster. I needed the admins help to resolve colds versions, and then when actually trying to install it took forever and failed because of some system incompatibility. Why does any kind of MD have such a high barrier to entry?? 1/2

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Reposted by Nicolas

Thiago Carvalho @cyrilpedia.bsky.social · 18/08/2026

'But in April, CONICET announced the results would not be released until August 2027 because of a backlog of applications and cuts in the number of positions available. When the postdocs’ fellowships ended on 31 July, they were left without salaries and scrambling to find work.'

science.org

Budget cuts and delays leave hundreds of Argentine postdocs in limbo

Many scientists are scrambling to make ends meet and reconsidering their future in research

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Nicolas @nicolasn.bsky.social · 04/08/2026

Short video showing #julia tools to parse Orca output files and get Löwdin charges and spins just from the optimized geometries in a relaxed surface scan. #compchem #chemsky youtu.be/E3MnlHahj84

youtu.be

Molecular Dynamics of Polymers with Julia: parse Orca output for charges

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 02/08/2026

I'm glad my "proposed method or framework" and "specific technical challenge addressed" were of interest to you!

Screen capture of spam email inviting me to submit a paper. The placeholder text where examples of my research should be have been left as in the template e-mail.

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Nicolas @nicolasn.bsky.social · 01/08/2026

My quest to make an MD package for polymers is taking me to unsuspected places. I am now doing DFT relaxed surface scans on alkenes and biphenyls with various substituents to try to find general ways of predicting torsion parameters. Next it will be alkanes and dienes with uncommon substituents

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Nicolas @nicolasn.bsky.social · 31/07/2026

In case this reaches new people, reposting my first video on MD of Polymers with Julia series, showing a project I'm working on to generate polymer structures and do MD with them in a more or less automatic way. #julia #compchem #compchemsky #science #chemsky #academicchatter youtu.be/OrYavnmyyOo

youtu.be

Molecular Dynamics of Polymers with Julia - Intro

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 28/07/2026

A few flowers from my garden. Spring is close! The peach tree looks really good for this year!

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Nicolas @nicolasn.bsky.social · 27/07/2026

This video shows the process I use to create a monomer geometry to for the polymer generation script, and highlights many of the things to take into consideration. #compchem #chemsky #science #julia

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Nicolas @nicolasn.bsky.social · 23/07/2026

I had two good news today! One is that a paper I'm a co-author in got accepted! The other is more on the personal side. Plus, I made a couple of figures and wrote a few paragraphs of a paper I've been trying to finish for months. Still missing one figure and some stuff in the SI.

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Reposted by Nicolas

Acceleration Consortium @accelerationc.bsky.social · 22/07/2026

💰 Funding alert for Associate and Assistant Professors with caregiving responsibilities! Apply now to access resources that help maintain research group productivity during parental leave. Program details: acceleration.utoronto.ca/programs/car...

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Nicolas @nicolasn.bsky.social · 22/07/2026

My MD program is getting quite complicated, I think I'm duplicating a lot of existent functionality.

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Nicolas @nicolasn.bsky.social · 19/07/2026

Short teaser for the next video on MD of polymers with Julia. I've been improving the linear polymer generator module, and now I can generate starting XYZ files for subsequent MD. #compchem #julia #compchemsky #science youtu.be/VbRFpzY-js4

youtu.be

Teaser: Molecular Dynamics of Polymers with Julia

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 16/07/2026

Small video update on atom typing and future implementing of GAFF, as well as using Orca compound scripts to obtain forces from relaxed surface scans. #julia #compchem #compchemsky #science #chemsky #polymer youtu.be/Hkrxcvv3r5I

youtu.be

Molecular Dynamics of Polymers with Julia - An update on atom types and where the project is going

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 14/07/2026

This is already the second video on the series, where I go a little bit deeper on the code and what it does. #julia #compchem #compchemsky #science youtu.be/CgHZgsZynr4

youtu.be

Molecular Dynamics of Polymers with Julia - What the code does so far

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 14/07/2026

New video! An intro to a molecular dynamics project for polymers using #Julia #JuliaMolSim #Molly.jl This is an overview of the idea and in future videos I will delve into the code, and the progress of the project! #compchem #chemsky #science #compchemsky youtu.be/OrYavnmyyOo

youtu.be

Molecular Dynamics of Polymers with Julia - Intro

YouTube video by Prof Nicolas

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Nicolas @nicolasn.bsky.social · 12/07/2026

This is a slightly more visually polished simulation of tetralactic acid. I still don't know how to change the orientation of the axis, which obscures the molecule. The FF parameters are only ballpark, but at least the molecule doesn't explode! #compchem #Julia #molly.jl #orca

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Nicolas @nicolasn.bsky.social · 10/07/2026

I've been building an MD interface using Molly.jl and #Julia. So far the FF parameters are incomplete and there are several missing things, but the (long term) idea is to be able to take arbitrary xyz files and generate a forcefield on the spot and run MD. This is dilactic acid. #compchem

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Nicolas @nicolasn.bsky.social · 09/07/2026

Celebrating Argentina's independence day with a barbecue with the family.

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Nicolas @nicolasn.bsky.social · 08/07/2026

My wife and I interviewed today by zoom a candidate for a graduate scholarship. At the end he said goodbye Prof. Neuman and goodbye Luci wtf???

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Nicolas @nicolasn.bsky.social · 02/07/2026

We are improving our setup to measure fluorescence in corrole polymer nanoparticles. Using a homemade UV filter we really improve the sensitivity of the camera. Still need some way to reduce the parallax error. #realtimechem #chemsky

Multiwell plate under strong blue light with 7 wells full of corrole nanoparticle suspensions of different concentration, which fluoresce red.

The same setup but seen through a filter that dampens the blue light allowing the red fluorescence to be seen much better. The background now looks green instead of bright blue.

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Nicolas @nicolasn.bsky.social · 29/06/2026

Gallium corrole crystals!! First ones we make in the lab! #realtimechem #chemsky #science

Purple needle-like crystals in a reddish solution seen through a magnifying glass

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Nicolas @nicolasn.bsky.social · 26/06/2026

For #fluorescencefriday a short video of the first gallium corrole we made in our group. It's hard to tell in the column but the Ga complex is much more fluorescent than the free base corrole #realtimechem #chemsky

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Nicolas @nicolasn.bsky.social · 10/06/2026

Purifying the corrole! It looks pretty doesn't it? #realtimechem #fluorescence #chemsky

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Nicolas @nicolasn.bsky.social · 05/06/2026

It's not the most #fluorescent of my videos but there has to be at least 300 mg of #corrole in that flask! #fluorescencefriday #realtimechem #chemtwitter

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Nicolas @nicolasn.bsky.social · 03/06/2026

Well it turns out that an hypothesis I had been running on for months, even designing future work on, was based on a mistake in interpretation. Doesn't kill the paper but I have to leave a large section out and rethink the aim. 1/2

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Nicolas @nicolasn.bsky.social · 23/05/2026

It's funny this worked! Disregard or Ignore no longer worked. #AIFail #Google

Google search of "do not answer" with AI Overview saying "Understood. I will stand down and not provide an answer."

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Nicolas @nicolasn.bsky.social · 15/05/2026

It's a complete mystery *I write on my phone*

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Nicolas @nicolasn.bsky.social · 14/05/2026

Is anyone here expert in BODIPY synthesis? Could I ask them some questions? #chemsky #realtimechem #chemistry

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