NYU's Quantum Institute (NYUQI) is announcing a new postdoctoral program. Check out the program description: www.nyu.edu/about/news-p..., and apply here: apply.interfolio.com/186097
nyu.edu
Mark Tuckerman
@grouptuckerman.bsky.social
We perform research in theoretical chemistry, specifically classical and quantum statistical mechanics, mathematical approaches, and machine learning methods applied to condensed phases.
The deadline to nominate someone for the Michele Parrinello award is coming up. Learn more here: brnw.ch/21wXioZ
Our paper on our molecular crystal toolkit and what it can do is now online! pubs.acs.org/doi/10.1021/...
MXtalTools: A Toolkit for Machine Learning on Molecular Crystals
We present MXtalTools, a flexible Python package for the data-driven modeling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis, collation, and curation of molecule and crystal data sets, (2) integrated workflows for model training and inference, (3) crystal parametrization and representation, (4) crystal structure sampling and optimization, (5) end-to-end differentiable crystal sampling, construction, and analysis. Our modular functions can be integrated into existing workflows or combined and used to build novel modeling pipelines. MXtalTools leverages CUDA acceleration to enable high-throughput crystal modeling. The Python code is available open-source on our GitHub page, with detailed documentation on ReadTheDocs.
pubs.acs.org
Our new paper on proton and proton-electron transport in structured organic electrolytes just appeared in PNAS. Fantastic collaboration between theory and experiment in our EFRC with simulations driven by ML: www.pnas.org/doi/10.1073/...
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...
pnas.org
At the ribbon cutting ceremony for the new Torch HPC platform at NYU: 38k CPUs, 504 GPUs, and efficient.
The "authors club" at the Varenna@40 meeting in Rome last week.
We were pleased to contribute to the special issue celebrating the 70th birthday of my colleague Zlatko Bacic. Our contribution focuses on generalizing ring-polymer contraction to open chains and staging transformations: www.tandfonline.com/doi/full/10....
Efficient evaluation of path integrals for equilibrium and dynamical properties via contraction of closed and open chains
An approach is introduced to reduce the computational cost associated with performing path integral simulations. This work is an extension of the ring-polymer contraction (RPC) approach of Markland...
tandfonline.com
Our new paper in Comms Chem paper explores how small modifications in drug molecules affect properties that influence their efficacy and the role molecular simulation can play in elucidating these effects: rdcu.be/eznSi
3D conformation and crystal interaction insights into drug development challenges for HCV drug analogues via molecular simulations
Communications Chemistry - ABT-333 and ABT-072 are non-nucleoside NS5B polymerase inhibitors for hepatitis C, differing by a minor substituent change that impacts their drug development profiles....
rdcu.be
Sun ejecting Plasma, as captured by the Parker Solar Probe. -Credits: NASA
In 2023, we published this article on our ufedmm branch of openMM implementing enhanced sampling techniques: onlinelibrary.wiley.com/doi/full/10.... . We are now organizing a tutorial for late August on how to use these tools. If you're interested, please apply here: forms.gle/NyUUJYJVbWu6...
It's always a pleasure to be back at NYU Shanghai and to see great colleagues and friends again. This summer was a school we taught on AI for molecular science, which was attended by undergraduates and graduate students alike. Thanks to all for organizing and participating!
Nadya Mason, dean of the Pritzker School of Engineering at U. Chicago gave a terrific interview with Physics World Weekly on research at the PME. The podcast also has an interview with Jeffrey Spangenberger at ANL on battery recycling. Great listening: podcasts.apple.com/us/podcast/m...
Molecular engineering and battery recycling: developing new technologies in quantum, medicine and energy
Podcast Episode · Physics World Weekly Podcast · 05/08/2025 · 36m
podcasts.apple.com
Our paper combining d-AFED/TAMD with REST2 is now out. This gives us a way to handle both energetic and entropic barriers on the energy landscapes of complex systems. pubs.acs.org/doi/10.1021/...
Solute Tempered Adiabatic Free Energy Dynamics for Enhancing Conformational Space Sampling
Collective variable (CV) and generalized ensemble-based enhanced sampling methods are widely used for accelerating barrier-crossing events and enhancing conformational sampling in molecular dynamics s...
pubs.acs.org
Congratulations to Giulia Galli on winning the 2025 Berni Alder Prize from CECAM!
Our paper on the use of enhanced sampling to compare different RNA force fields, including HB-CUFIX, is now available. Kudos to Akshaya on the great work. pubs.aip.org/aip/jcp/arti...
HB-CUFIX: Force field for accurate RNA simulations
Accurate modeling of the dynamic structures of ribonucleic acid (RNA) molecules is essential for understanding their biological roles. However, such modeling re
pubs.aip.org
For any who are interested in working on machine-learning driven simulations of battery electrolyes using path-integral techniques, I am opening a new postdoctoral position in my group. The Interfolio application site is here: apply.interfolio.com/167480
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Very glad to see this symposium being held in honor of John Perdew at Temple University in Phila.
Our paper in Applied Physics Reviews on ML versus MM force fields is now out. Kudos to Yuanqing for spearheading the effort to produce this. The link is here: pubs.aip.org/aip/apr/arti...
On the design space between molecular mechanics and machine learning force fields
A force field as accurate as quantum mechanics (QMs) and as fast as molecular mechanics (MMs), with which one can simulate a biomolecular system efficiently eno
pubs.aip.org
For anyone interested in an AI hackathon related to the prediction of the spatial distribution of biological cell types in a tissue slice using routine H&E slides. www.elucidata.io/elhackathon-...
El-Hackathon AI Challenge ‘25
Prediction of Cellular Organization From Histology Images. The challenge aims to advance the fields of AI-driven digital pathology and spatial biology.
elucidata.io
Preparing to attend and speak at the RARE meeting in Khajuraho next week. sites.google.com/view/rare202...
RARE 2025
RARE meetings are a series of International symposiums organized to discuss recent advances in the field of rare event sampling of molecular systems. RARE2025 is the fourth in the series, with very su...
sites.google.com
As a first post, I just began reading David Limmer's new book on Statistical Mechanics and Stochastic Thermodynamics. I highly recommend it. His explanations are incredibly clear without being overly detailed.
