arXiv subjects

Sukanta Mukherjee

Publications and source records attributed to Sukanta Mukherjee.

2 recordsLinked to original sources

arXiv2024

A self-organised liquid reaction container for cellular memory

Epigenetic inheritance during cell division is essential for preserving cell identity by stabilizing the overall chromatin organisation. Heterochromatin,the condensed and transcriptionally silent fraction of chromatin,is marked by specific epigenetic modifications that are diluted during each cell division. Here we build a physical model,based on the formation of a biomolecular condensate,a liquid 'droplet',that promotes the restoration of epigenetic marks. Heterochromatin facilitates the droplet formation via polymer-assisted condensation(PAC). The resulting condensate serves as a reaction chamber to reconstruct the lost epigenetic marks. We incorporate the enzymatic reactions into a particle-based simulation and monitor the progress of the epigenetic markers through an in silico analogue of the cell cycle. We demonstrate that the proposed mechanism is robust and stabilizes the heterochromatin domains over many cell generations. This mechanism and variations thereof might be at work for other epigenetic marks as well.

physics.bio-ph↗

arXiv2024

Stretched exponential to power-law: crossover of relaxation in a kinetically constrained model

The autocorrelation function in many complex systems shows a crossover in the form of its decay: from stretched exponential relaxation (SER) at short times to power law at long times. Studies of the mechanisms leading to such multiple relaxation patterns are rare. Additionally, the inherent complexity of these systems makes it hard to understand the underlying mechanism leading to the crossover. Here we develop a simple one-dimensional spin model, which we call a Domain Wall (DW) to Doublon model, that shows such a crossover as the nature of the excitations governing the relaxation dynamics changes with temperature and time. The relevant excitations are DWs and bound pairs of DWs, which we term `doublons'. The diffusive motion of the DWs govern the relaxation at short times, whereas the diffusive motion of the doublons yields the long time decay. This change of excitations and their relaxation leads to a crossover from SER to power law in the decay pattern of the autocorrelation function. We augment our numerical results with simple physical arguments and analytic derivations.

cond-mat.stat-mech↗