S. Brahmachari

Regulation of chromatin transcription dynamics by DNA supercoiling

This paper models chromatin torsion and RNAP translocation to show how DNA supercoiling and nucleosome dynamics regulate transcription velocity and gene expression.

Temporally correlated active forces drive segregation and enhanced dynamics in chromosome polymers

The paper models chromosome polymers with active forces, showing activity drives segregation and dynamic compaction, and alters compartmental organization.

Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes

This study uses a coarse-grained polymer model to simulate mitotic chromosome mechanics, finding they are ten times stiffer than interphase chromosomes and exhibit viscoelastic behavior.

Shaping the Genome via Lengthwise Compaction, Phase Separation, and Lamina Adhesion

The paper develops a polymer model of the genome to explore how physical interactions shape genome architecture across species.

DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases

The paper presents a theoretical model showing DNA supercoiling mediates long-range cooperation between co-transcribing RNA polymerases, affecting transcription elongation rates and orientation-dependent interactions.

Measurement of the torque in braided DNAs using a thermodynamic Maxwell relation

The paper measures torque in braided DNAs using magnetic tweezers and a thermodynamic Maxwell relation, finding torques up to 76 pN·nm and a twist modulus comparable to single DNA.

Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches

This study uses coarse-grained MD simulations to show that DNA plectoneme pinning at mismatches is deterministic under high force and salt, but probabilistic under physiological conditions, with pinning probability increasing with mismatch size.

Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures

The paper models chromosome disentanglement during cell division using loop-extruded brush structures, showing optimal loop organization minimizes entanglements and supports genome stability.

Defect-Facilitated Buckling in Supercoiled Double-Helix DNA

The paper develops a statistical-mechanical model to study DNA buckling and plectoneme domain behavior under stretching forces and ionic conditions, showing defect-facilitated kink formation and energy reduction.

Nucleation of multiple buckled structures in intertwined DNA double helices

The paper investigates the statistical-mechanical behavior of intertwined DNA double helices, finding that torsionally stressed braids undergo an abrupt buckling transition with nucleation of end loops and multiple domains.

Torque and buckling in stretched intertwined double-helix DNAs

This study develops a statistical-mechanical model to analyze torque and buckling in stretched intertwined DNAs, showing catenation-dependent behavior and predicting a buckling transition with a discontinuity in extension.