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Aniruddha Seal

@aniruddha.bsky.social
450 followers 248 following 9 posts

UChicago Theoretical Chemistry PhD Student sites.google.com/view/aniseal

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livecomsjournal.bsky.social @livecomsjournal.bsky.social · 11/08/2025
Our latest Best Practices article "Developing Monte Carlo Methodologies in Molecular Simulations" is out now and describes how to derive acceptance probabilities for a variety of Monte Carlo moves: doi.org/10.33011/liv... #compchem
Table of contents figure
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Dr Bee Hockin @beehockin.bsky.social · 30/06/2025
Hey #chemsky and #compchemsky - we're welcoming submissions to this @pccp.rsc.org Festschrift on topics including:   • Molecular reaction dynamics   • Computational chemical dynamics   • Potential energy surfaces & free energy landscapes   • Electronic structure theory & computation
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Jan Hermann @hrmnn.net · 26/06/2025
🚀 Strong correlation is the Everest of quantum chemistry. Next to the coupled cluster highway, the multireference molecular terrain is underserved—gravel roads and promenades. With Orbformer, we're building a new infrastructure by marrying neural network wavefunctions with cost amortization at scale
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Aniruddha Seal @aniruddha.bsky.social · 18/06/2025
If you’re at CTEST and interested in training MLPs with multi-reference electronic structure, check out Laura’s talk on our Weighted Active Space protocol #compchem
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Krupa Ramasesha @kramasesha.bsky.social · 04/06/2025
Review alert! Our review in Chemical Physics Reviews describes ~25 years of work on ultrafast dynamics in transition metal carbonyls, revealing insights into excited state pathways and ligand loss mechanisms in these exemplary organometallic molecules. doi.org/10.1063/5.02...
doi.org
Ultrafast photochemistry of gas-phase transition metal carbonyls
Organometallic photochemistry lies at the heart of photochemical energy conversions in applications such as photocatalysis, photovoltaic cells, and luminescent
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Ganna (Anya) Gryn’ova 🇺🇦 @grynova.bsky.social · 29/05/2025
In today’s #Journal_Club Stiv Llenga reviews #quantum-inspired #representations #ML #chemistry feat. papers by Miller, von Lilienfeld, @insilphotochem.bsky.social, Penfold, Ribas-Arino, @corminboeuf-lab.bsky.social et al. www.grynova-ccc.org/journal-club...
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Aniruddha Seal @aniruddha.bsky.social · 20/05/2025
Huge thanks to the amazing collaborators Simone, Matthew, Luigi, Umberto, Andy —for pushing the boundaries of ML and electronic structure in catalysis. Feedback and comments welcome!
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Aniruddha Seal @aniruddha.bsky.social · 20/05/2025
3/ We applied this framework to C–H activation catalyzed by a transition metal carbide. Training MLPs on MC-PDFT data lets us simulate long-timescale catalytic dynamics with multireference accuracy—something not achievable with standard methods.
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Aniruddha Seal @aniruddha.bsky.social · 20/05/2025
2/ Sampling is just as critical as accuracy. We combine WASP with enhanced sampling (OPES) and active learning (DEAL) to efficiently generate a minimal, diverse training set—capturing key regions like transition states while keeping data cost low.
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Aniruddha Seal @aniruddha.bsky.social · 20/05/2025
1/ Multireference methods like MC-PDFT are key for strongly correlated systems, but training MLPs requires a consistent active space across diverse, uncorrelated geometries. WASP solves this using a weighted sum of MO coefficients to generate consistent initial guesses.
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Aniruddha Seal @aniruddha.bsky.social · 20/05/2025
Excited to share my first preprint from grad school! Working with @gagliardilaura.bsky.social and Parrinello Group, we introduce WASP-the Weighted Active Space Protocol, a method to enable multireference-quality ML potentials for transition metal-based catalysis. #compchem arxiv.org/abs/2505.10505
arxiv.org
Weighted Active Space Protocol for Multireference Machine-Learned Potentials
Multireference methods such as multiconfiguration pair-density functional theory (MC-PDFT) offer an effective means of capturing electronic correlation in systems with significant multiconfigurational...
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PLUMED @plumed.org · 04/03/2025
The paper describing our community effort to collect and organize #plumed tutorials has been published in the Journal of Chemical Physics, as part of the Michele Parrinello Festschrift! doi.org/10.1063/5.02...
doi.org
PLUMED Tutorials: A collaborative, community-driven learning ecosystem
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes
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Mario Barbatti @mbarbatti.bsky.social · 01/03/2025
It started as X discussion in Aug 2024. Now it's a preprint: When Theory Came First: A Review of Theoretical Chemical Predictions Ahead of Experiments 🧪#compchem doi.org/10.26434/che...
doi.org
When Theory Came First: A Review of Theoretical Chemical Predictions Ahead of Experiments
For decades, computational theoretical chemistry has provided critical insights into molecular behavior, often anticipating experimental discoveries. This review surveys twenty notable examples from t...
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Chris Reilly @christopherreilly.bsky.social · 28/02/2025
We've made a short animation summarizing the research! t.co/zXyiQqseBh
t.co
https://youtu.be/7jt2uUdl0yM
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Laura Gagliardi @gagliardilaura.bsky.social · 28/01/2025
Very excited today to give the inaugural lecture of the Solvay Chair in Chemistry for 2025. www.solvayinstitutes.be/html/chair.h...
solvayinstitutes.be
Solvay Institutes
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Laura Gagliardi @gagliardilaura.bsky.social · 14/01/2025
Our latest multiconfiguration pair-density functional MC23 www.pnas.org/doi/abs/10.1... has been featured also for non experts pme.uchicago.edu/news/new-met...
pme.uchicago.edu
New method improves quantum chemistry simulations
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Erik Thiede @erikhthiede.bsky.social · 11/01/2025
How I've been generating nice equations in google slides:
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Jerelle Joseph @jerelleaj.bsky.social · 26/12/2024
“Biomolecular condensates control and are defined by RNA–RNA interactions that arise in viral replication”. New results from a wonderful collaboration with @gladfelterlab.bsky.social and Christine Roden (who just started her lab at University of Montreal!!) www.biorxiv.org/content/10.1...
biorxiv.org
Biomolecular condensates control and are defined by RNA-RNA interactions that arise in viral replication
Cells must limit RNA-RNA interactions to avoid irreversible RNA entanglement. Cells may prevent deleterious RNA-RNA interactions by genome organization to avoid complementarity however, RNA viruses ge...
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Torsten Schwede @torstenschwede.bsky.social · 08/12/2024
A great day for computational structural biology! 2024 Nobel Prize lectures in chemistry by David Baker, Demis Hassabis and John Jumper: www.youtube.com/watch?v=HnT1... 🧪🧬
youtube.com
2024 Nobel Prize lectures in chemistry | David Baker, Demis Hassabis and John Jumper
YouTube video by Nobel Prize
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Vojtech Spiwok @spiwokv.bsky.social · 06/12/2024
go.bsky.app/4HD8BE7
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Aniruddha Seal @aniruddha.bsky.social · 07/12/2024
Thrilled to contribute to this work! Check out our tutorial on discovering Permutationally Invariant collective variables with PINES, alongside many other fantastic resources in this collection from the Plumed community! #compchem
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Umberto Raucci @uraucci.bsky.social · 03/12/2024
Excited to share our latest work on enzyme catalysis using ML-based collective variables (ML-CVs)! 🚀🎉 Using α-amylase as a model, we applied ML-CVs to link reactive conformations to catalytic activity across different sugars. #SudipDas #RNeves #MRamos #MParrinello www.pnas.org/doi/abs/10.1...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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ChemRxiv Bot @chemrxivbot.bsky.social · 03/12/2024
On the connection between the Exact Factorization and the Born-Huang representation of the molecular wavefunction Authors: Peter Schürger, Yorick Lassmann, Federica Agostini, Basile Curchod DOI: 10.26434/chemrxiv-2024-1819d
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Maris Ozols @marisozols.bsky.social · 30/11/2024
If you're curious about quantum computing and want to learn the basics, check out the "Quantum Quest" created by me and Michael Walter! www.quantum-quest.org/material
quantum-quest.org
The Quantum Quest - Material
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César Sánchez @twistedbacteria.bsky.social · 29/11/2024
All cells are encapsulated by a membrane of complex lipidic composition, right? Not anymore! @JamesSaenz.bsky.social et al. show that a ‘minimal’ bacterial cell only needs 2 lipid species #microNatComms #Microbiology #CellBiology #lipids Read the paper: www.nature.com/artic...
nature.com
A tuneable minimal cell membrane reveals that two lipid species suffice for life
Nature Communications - All cells are encapsulated by a membrane of complex lipidic composition, and understanding the roles of different lipids in membrane function is experimentally challenging...
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Mario Krenn @mariokrenn.bsky.social · 27/11/2024
What is a paper that has changed your view or direction research? I am searching for inspiring gems. For me, it was the 2013 IBM paper on Computational Creativity. It showed that computers can be used in entirely different ways in Science, which was a complete eye-opener: arxiv.org/abs/1311.1213
arxiv.org
A Big Data Approach to Computational Creativity
Computational creativity is an emerging branch of artificial intelligence that places computers in the center of the creative process. Broadly, creativity involves a generative step to produce many id...
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Patrick A. Robertson @ghettsmart.bsky.social · 20/11/2024
A fully funded PhD position in my research group is available. Details on our research can be found here: www.nurd.org.uk The project would suit anyone with an MSci in chemistry or physics with an interest/experience in reaction dynamics, ultrafast laser spectroscopy, and instrument development
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Jan Hermann @hrmnn.net · 26/11/2024
rowansci.substack.com/p/quantum-ch...
rowansci.substack.com
Quantum Chemistry in Drug Discovery
How it's used at present, and opportunities for the future.
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Stefano Martiniani @stemartiniani.bsky.social · 25/11/2024
First came the crystals, then the quasicrystals, and then the *gyromorphs*, the ideal isotropic bandgap material Learn about correlated disorder with delta peaks in our new preprint "Gyromorphs: a new class of functional disordered materials". arxiv.org/abs/2410.09023 #Skyprint below
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Jean-Philip Piquemal @jppiquem.bsky.social · 21/11/2024
#compchem Good read: The Dynamic Diversity and Invariance of Ab Initio Water #compchemsky pubs.acs.org/doi/10.1021/...
pubs.acs.org
The Dynamic Diversity and Invariance of Ab Initio Water
Comprehending water dynamics is crucial in various fields, such as water desalination, ion separation, electrocatalysis, and biochemical processes. While ab initio molecular dynamics (AIMD) accurately...
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Mark Levin @levinchem.bsky.social · 18/11/2024
You still have a chance to sign up for the UChicago Chemistry PhD info session, held on Nov 21st: apply-psd.uchicago.edu/register/?id... Prospective students, especially those interested in the application process and/or fee waivers are encouraged to attend!
apply-psd.uchicago.edu
UChicago Chemistry PhD Program Info Session
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Ashley Ringer McDonald @aringermcdonald.bsky.social · 16/11/2024
If you want to help your students move from just writing code and scripts to actually developing scientific software that is useable and maintainable in the long-term, check out our latest paper in JCE. pubs.acs.org/doi/10.1021/...
pubs.acs.org
Cookiecutter for Computational Molecular Sciences: A Best Practices Ready Python Project Generator
Scientific software development takes far more than good programming abilities and scientific reasoning. Concepts such as version control, continuous integration, packaging, deployment, automatic documentation compiling, licensing, and even file structure are not traditionally taught to scientific programmers. The skill gap leads to inconsistent code quality and difficulty deploying products to the broader audience. Most of the implementation of these skills however can be constructed at project inception. The Cookiecutter for Computational Molecular Sciences generates ready-to-go Python projects that incorporate all of the concepts above from a single command. The final product is then a software project which lets developers focus on the science and minimizes worries about nonscientific and nonprogramming concepts because the best practices, as established by the Molecular Sciences Software Institute, have already been incorporated for them. This is a community driven project with widespread adoption across the computational molecular sciences. The Molecular Sciences Software Institute and Computational Molecular Sciences community also continually contribute and update the Cookiecutter for Computational Molecular Science, ensuring that the project is responsive to community needs and tool updates. All are welcome to suggest changes and contribute to making this the best starting point for Python-based scientific code.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/11/2024
An AF3-like model available with an MIT license “Our model and code are released under MIT License, and can be freely used for both academic and commercial purposes.”
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Mario Barbatti @mbarbatti.bsky.social · 16/11/2024
A starter pack on the molecular theoretical quantum world. #compchem #molphys #theochem 🧪 go.bsky.app/UGFPoE2
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Aniruddha Seal @aniruddha.bsky.social · 17/11/2024
Could you add me too?
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Laura Gagliardi @gagliardilaura.bsky.social · 17/11/2024
So excited that two new graduate students, Hellen Clifford and Youghwan Kim, joined our group last week. There is hope for the future. I am looking forward to embarking on the journey of their Ph.D. with them and the rest of our amazing group. gagliardigroup.uchicago.edu/members/ #ChemSky
A picture of the Gagliardi research group in front of an ivied wall and doors at U Chicago
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Aniruddha Seal @aniruddha.bsky.social · 14/11/2024
👋
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jefflotthammer.bsky.social @jefflotthammer.bsky.social · 12/11/2024
I’m excited to share my most recent manuscript describing an approach to assess local conformational sampling in simulations of intrinsically disordered proteins. This one’s for my computational biophysics aficionados www.biorxiv.org/content/10.1... a 🧵
biorxiv.org
Disentangling folding from energetic traps in simulations of disordered proteins
Protein conformational heterogeneity plays an essential role in a myriad of different biological processes. Extensive conformational heterogeneity is especially characteristic of intrinsically disorde...
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Christoph Dellago @chhdellago.bsky.social · 12/11/2024
We are looking for a new PhD student at @univie.ac.at ⬇️
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