D. Pramanik

Intra-DNA k-mer Conservation Patterns Encode Evolutionary Selection of Variants

The paper introduces kGain, a metric quantifying k-mer frequency shifts due to mutations, and shows it predicts adaptive potential across species and experimental systems.

Probing the Molecular Interactions of A22 with Prokaryotic Actin MreB and Eukaryotic Actin: A Computational and Experimental Study

This study investigates A22's interactions with prokaryotic MreB and eukaryotic actin using computational and experimental methods, revealing strong binding and toxicity to eukaryotic cells.

Interactive dynamics of matrix adhesion and reaction-diffusion predict diverse multiscale strategies of cancer cell invasion

This study models cancer cell invasion modes using a computational framework, revealing how matrix adhesion and reaction-diffusion drive distinct invasive strategies.

IRI-CCE: A Platform for Evaluating CRISPR-based Base Editing Tools and Its Components

The paper introduces IRI-CCE, a platform for evaluating CRISPR-based base editing tools in E. coli, showing different BE variants have distinct editing patterns based on promoter types.

ST6GAL1-mediated heterogeneity in sialic acid levels potentiates invasion of breast cancer epithelia

This study identifies 2,6-linked sialic acid heterogeneity in breast cancer cells and shows that medium-expressing cells exhibit greater ECM adhesion and invasion compared to high-expressing cells, with ST6GAL1 playing a key role.

An interplay between reaction-diffusion and cell-matrix adhesion regulates multiscale invasion in early breast carcinomatosis

This paper introduces a multiscale computational model to study how reaction-diffusion and cell-matrix adhesion regulate breast cancer invasion.

Can one trust kinetic and thermodynamic observables from biased metadynamics simulations: detailed quantitative benchmarks on millimolar drug fragment dissociation

This study benchmarks infrequent metadynamics against unbiased MD simulations to assess the reliability of kinetic and thermodynamic observables for ligand dissociation from FKBP.

Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization

This paper extends the SGOOP method to construct multi-dimensional reaction coordinates by using conditional probability factorization, demonstrating its effectiveness in simulating complex molecular systems.