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Sumon Sahu

Publications and source records attributed to Sumon Sahu.

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MolCryst-MLIPs: A Machine-Learned Interatomic Potentials Database for Molecular Crystals

We present an open Molecular Crystal (MC) database of Machine-Learned Interatomic Potentials (MLIP) called MolCryst-MLIPs. The first release comprises fine-tuned MACE models for nine molecular crystal systems---Benzamide, Benzoic acid, Coumarin, Durene, Isonicotinamide, Nicotinic acid , Niacinamide, Pyrazinamide, and Resorcinol---developed using the Automated Machine Learning Pipeline (AMLP), which streamlines the entire MLIP development workflow, from reference data generation to model training and validation, into a reproducible and user-friendly pipeline. Models are fine-tuned from the MACE-MH-1 foundation model omol head), yielding a mean energy MAE of 0.141 kJ/mol/atom and a mean force MAE of 0.648 kJ/mol/Angstrom across all systems. Benchmarked against three state-of-the-art foundation models on the DFT-labelled polymorph set, only the fine-tuned models resolve the polymorphic energy landscape. Dynamical stability and structural integrity, as assessed through energy conservation, P2 orientational order parameters, and radial distribution functions, are evaluated using molecular dynamics simulations. The released models and datasets constitute a growing open database of validated MLIPs, ready for production MD simulations of molecular crystal polymorphism across the polymorphic landscape of each target compound under different thermodynamic conditions.

cs.LG

Crowder and Surface Effects on Self-organization of Microtubules

Microtubules are an essential physical building block of cellular systems. They are organized using specific crosslinkers, motors, and influencers of nucleation and growth. With the addition of anti-parallel crosslinkers, microtubule pattern goes through transition from fan-like structures to homogeneous tactoid condensates in vitro. Tactoids are reminiscent of biological mitotic spindles, the cell division machinery. To accomplish these organizations, we use polymer crowding agents. Here we study how altering the properties of the crowders, such as size, concentration, and molecular weight, affect microtubule organization. Using simulations with experiments, we observe a scaling law associated with the fan-like patterns in the absence of crosslinkers. Tactoids formed in the presence of crosslinkers show variable length, depending on the crowders. The subtle differences correlate to individual filament contour length changes, likely due to effects on nucleation and growth of the microtubules. Using quantitative image analysis, we deduce that the tactoids differ from traditional liquid crystal organization, as they are limited in width irrespective of crowders and surfaces, and behave as solid-like condensates.

physics.bio-ph