P. Bera

Predicting Future Kinetic States of Physicochemical Systems Using Generative Pre-trained Transformer

This paper shows that a transformer model can predict future states of physicochemical systems faster than traditional simulations by learning from time-discretized molecular dynamics data.

Protein Translation Can Fluidize Bacterial Cytoplasm

This study shows that protein synthesis, particularly ribosome dynamics, enhances fluidity in bacterial cytoplasm by counteracting its glassy nature through metabolic activity.

Machine Learning Unravels Inherent Structural Patterns in Escherichia Coli Hi-C Matrices and Predicts DNA Dynamics

This paper uses machine learning to analyze Hi-C data from E. Coli, revealing structural patterns and predicting DNA dynamics, showing that a subset of contact pairs suffices for accurate predictions.

Spatiotemporal dynamics and emergent ordering in a mixture of morphologically distinct bacteria having different cell motility

This study uses agent-based modeling to show how morphology and motility differences between bacterial species affect their spatial organization and collective behavior in mixed populations.

On the Spatial Positioning of Ribosomes around chromosome in E. coli Cytoplasm

This study shows ribosomes in E. coli are not entirely excluded from the nucleoid, with some located in a central void, suggesting dynamic localization for efficient translation.

Development of a Data-driven Integrative Model of Bacterial Chromosome

The paper develops a data-driven integrative model of E. coli chromosome that simulates its conformation and predicts higher-resolution contact maps and segregation behavior.

A mechanistic understanding of biofilm morphogenesis: Coexistence of mobile and sessile aggregates and phase-separated patterns

This study develops a biophysical model to understand how bacterial microcolony morphology is shaped by EPS production and mechanical interactions, showing phase-separated patterns and coexistence of motile and sessile aggregates.

Hi-C Contacts Encode Heterogeneity in Sub-diffusive Motion of E. coli Chromosomal Loci

The paper uses Hi-C data to show that E. coli chromosome loci exhibit coordinate-dependent sub-diffusive motion, driven by Hi-C-guided long-range interactions.

Mechanistic underpinning of nonuniform collective motions in swarming bacteria

This study uses simulations to show that bacterial swarming speed and vorticity depend non-monotonically on cell aspect ratio due to size-dependent motility forces and mechanical interactions.