Our multi-resolution data integration strategy for modelling bacterial chromosome is now published in JCTC JCTC Papers. Outstanding efforts by Wasim Wasim Abdul (him/his) and Palash Palash Bera . pubs.acs.org/doi/10.1021/ac…

Highlight on our recent work published in soft matter

Just Out Nature Communications we observe chemotaxis of short peptide-based amylobots where motility & directionality were controlled by orthogonal catalysis of 2 loaded enzymes #nonequilibrium #nanomotor #systemschem rdcu.be/dmJq1 to SERB SJF grant IISER Kolkata(1/3)

Happy to share our recent work on spatial patterning in a growing microbial colony. Published in Soft Matter (RSC) : "pubs.rsc.org/en/content/art…” IISER Thiruvananthapuram School of Chemistry IISER TVM. Congratulations to Palash Bera and Wasim Abdul (him/his). Thanks to SERB.

In this recent preprint we show how deep learning and Random forest can be efficiently employed to identify structural pattern of bacterial chromosome and identify crucial features for its diffusive dynamics . Major effort by Palash Palash Bera biorxiv.org/content/10.110…

In New paper in The Journal of Physical Chemistry B, Wasim Abdul (him/his) and Palash Bera come up with a data-informed integrative model on organization of ribosomes around chromosome of E. coli. pubs.acs.org/doi/10.1021/ac… One key take-away is ribosomes are NOT 'inert crowder' as previously perceived.

latest preprint from the group uses Transformer based ML approach to predict future kinetic states of a physicochemical systems . biorxiv.org/content/10.110… System worked ranges from model potential, folded mini-proteins to IDP and even an out-of-equilibrium system!

Three of my outstanding and accomplished students have just submitted or submitting their thesis, with diverse skill sets in bio-simulation/physics based model/ML and would be looking for postdoctoral position abroad. In case your group is recruiting, please DM me!

Published in Nucleic Acids Research Nucleic Acids Res , outstanding Machine learning + physics-based modelling efforts by Palash Bera (currently in job market) to decode structural pattern and dynamics in E.Coli. Chromsome! academic.oup.com/nar/advance-ar…

A new article on the collective dynamics of two morphologically distinct bacteria having diverse motility aspects.👇 doi.org/10.1063/5.0220… Thanks to Kaustav Mondal, Palash Bera for their effort and SERB, IISER Thiruvananthapuram School of Chemistry IISER TVM for the support.

It is my great pleasure to host Jagannath Mondal here in Berlin next week! 🤩 You can join the colloquium in person or online. #compchem

LLMs are powerful sequence modeling tools! They not only can generate language, but also actions for playing video games, or numerical values for forecasting time series. Can we help LLMs better model these continuous "tokens"? Our answer: Fourier series! Let me explain… 🧵(1/n)

Humbled to receive this, particularly as it involved experience of navigating the diverse, interdisciplinary classrooms in a research institution

🎉 Congratulations to Dr. Palash Bera from Jagannath Mondal's lab TIFR Hyderabad for successfully defending this thesis! Palash decoded the dynamics of bacterial cytoplasmic particles and unveiled how metabolism drives bacterial behavior-powered by numerical simulations & ML models.

Just Published in PNAS Nexus we use physics based model and experimental data to show how state-switching of ribosome can fluidise the bacterial cytoplasm Palash Bera Wasim Abdul (him/his) took lead, great collaboration and bio-insights from Somenath Bakshi ow.ly/ZTZM50Uj5OL

Assessing Generative Diffusion Models for Enhanced Sampling of Folded and Disordered Protein States Across Scales and in All-atom Resolution 1. This study explores the application of Denoising Diffusion Probabilistic Models (DDPMs) to molecular dynamics (MD) simulations,

A "project Research Scientist" (aka postdoc) position in the area of computational biophysics is available in the group. Interested candidates can email with a CV. Start date is immediate, open until filled.

Published in Chemical Science our transformer-based Machine learning approach to understand MD simulation trajectory within the context of a language model . Congratulations to Palash Bera for designing and executing the idea. pubs.rsc.org/en/content/art…