R. Padinhateeri

Dynamical properties of chromatin provide insights into key folding principles

The paper shows that loop extrusion dominates dynamic properties of chromatin, even when intra-chromatin interactions dominate static structure.

Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop

The paper uses shear flow to differentiate between two types of molecular machine activities in chromatin loops through simulation analysis.

Role of diffusion and reaction of the constituents in spreading of histone modification marks

The paper studies histone modification spreading using a reaction-diffusion model, showing diffusion and enzyme degradation limit domain size and produce modification profiles comparable to S. pombe H3K9me3 data.

Protein search processes mediated by chromatin topology

The paper investigates how chromatin compaction affects protein search kinetics using models and experimental data, finding optimal compaction minimizes protein residence time.

Nonequilibrium switching of segmental states can influence compaction of chromatin

This paper presents a diblock copolymer model of chromatin that simulates nonequilibrium switching between segmental states, showing how this affects chromatin compaction and contact probabilities.

Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

The paper systematically coarse-grains chromatin using Micro-C data to predict polymer properties, showing beads are soft and overlapping with distinct behavior at TAD boundaries.

Spatiotemporal solidification of α-synuclein inside the liquid droplets

This study investigates the spatiotemporal solidification of α-synuclein within liquid droplets, showing how solid-like cores form and propagate during droplet aging and fusion.

Role of non-specific interactions in the phase-separation and maturation of macromolecules

This paper investigates how non-specific interactions influence phase separation and maturation of polymers, showing an optimal range of interaction strengths for forming functional biomolecular complexes.

High fidelity epigenetic inheritance: Information theoretic model predicts k-threshold filling of histone modifications post replication

The paper develops an information-theoretic model to predict how histone modifications are inherited post-replication, showing that enzymes may use a k-threshold filling algorithm to recover parental modifications.

Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains

The paper simulates chromatin domains using interaction strength parameters derived from contact maps to study their organization, dynamics, and response to epigenetic changes.

The accidental ally: Nucleosomal barriers can accelerate cohesin mediated loop formation in chromatin

The paper shows that nucleosomes can reduce loop formation times for cohesin by acting as barriers at high concentrations, contrary to their role at low densities.

Computing 3D chromatin configurations from contact probability maps by Inverse Brownian Dynamics

This paper introduces an Inverse Brownian Dynamics method to compute 3D chromatin configurations from contact probability maps, showing that average distances cannot be derived solely from contact probabilities.

Regulation of Microtubule Disassembly by Spatially Heterogeneous Patterns of Acetylation

This study investigates how spatially heterogeneous acetylation patterns on microtubules affect their disassembly kinetics, finding that clustered patterns increase disassembly times by up to 50% compared to uniform patterns.

Irregular chromatin: packing density, fiber width and occurrence of heterogeneous clusters

The paper investigates how chromatin is folded at the gene scale, showing that non-histone proteins contribute to irregular packing without altering fiber width or density.

Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer

The paper proposes a model explaining how nucleosome positioning is inherited during DNA replication by coupling replisome movement with nucleosome dynamics.