A. Erbas

A polymer physics view of peripheral chromatin: de Gennes' self-similar carpet

The paper models peripheral chromatin as a flexible polymer chain using de Gennes' self-similar carpet theory to explain two experimental observations about chromatin density and molecular exclusion near the nuclear envelope.

Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus

This study uses a polymer model to show that chromatin phase separation and nuclear shape fluctuations are correlated, with heterochromatin levels and interactions affecting nuclear stability.

Protein-DNA Clusters Explain the Non-ExponentialDNA Residence Time Distributions of TranscriptionFactors

The paper shows that DNA-protein clusters cause multi-exponential residence time distributions of transcription factors, challenging the binary affinity model.

Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization

The paper uses simulations to model interphase chromosomes as colloids with cyclic polymers, showing how polymer structure affects chromosome segregation and 3D organization.

Facilitated Dissociation of Nucleoid Associated Proteins from DNA in the Bacterial Confinement

The paper uses simulations to show that bacterial NAPs exhibit different dissociation behaviors based on their DNA-binding specificity and chromosomal compaction.

Heterochromatin flexibility contributes to chromosome segregation in the cell nucleus

This study uses molecular dynamics simulations to show that heterochromatin flexibility influences its distribution in the nucleus, with less flexible heterochromatin segregating toward the interior in the absence of shell interactions.

Receptor-ligand rebinding kinetics in confinement

This study examines ligand-receptor rebinding kinetics in confined environments, revealing scaling laws and time-dependent behavior under different diffusion and reaction-limited conditions.

Facilitated Dissociation Of Transcription Factors From Single DNA Binding Sites

This study investigates facilitated dissociation (FD) of transcription factors from DNA binding sites using single-molecule imaging and molecular dynamics simulations, showing FD occurs at the single-binding-site level and is independent of salt concentration.