Biology subjects

Mohanta, D.

Publications and source records attributed to Mohanta, D..

4 recordsLinked to original sources

bioRxiv2026

Molecular origins of heterogeneous aging and spatial organization in RNA condensates

The molecular origins of aging of biomolecular condensates, which play a central role in cellular organization, is poorly understood. Here, we use coarse-grained molecular simulations to investigate how RNA sequence and chain connectivity govern condensate aging over extended timescales. Condensates formed by CAG-repeat RNA undergo pronounced aging characterized by progressive dynamical slowing, loss of ergodicity, and the emergence of two distinct relaxation timescales. Aging proceeds heterogeneously in space, giving rise to a dynamically arrested, solid-like core surrounded by a more fluid shell. We demonstrate that aging is driven by sequence-encoded base pairing that favors RNA expansion, alignment and the formation of a dense interchain interaction network. These structural changes lead to increased topological entanglement, stabilizing long-lived conformations and reinforcing dynamic arrest in the condensate interior. Strikingly, a scrambled sequence with identical composition remains largely liquid-like. Our results establish RNA sequence patterning as a key determinant not only of phase separation but also of condensate aging and spatial organization. These findings provide a molecular framework for understanding the persistence and solidification of repeat RNA assemblies observed in diseases and suggest general physical principles by which entangled polymer networks drive aging in biomolecular condensates.

biophysics↗

bioRxiv2025

Sequence Complexity Dictates Polymer Mixing

Polymer association in confined spaces governs diverse phenomena from protein aggregation to DNA condensation. We investigate the sequence-level mechanisms underlying this behavior through exact enumeration of two confined AB-type block copolymers on a two-dimensional lattice, revealing how sequence complexity controls mixing against de-mixing. We reveal that sequence complexity (heterogeneity), quantified by Shannon entropy H2, acts as a determinant between self-folded low-mixed state and high-mixed state. High-complexity sequences (H2 = 1.86 bits) with short-length repeats achieve near-complete inter-chain overlap through cooperative chain collapse, while low-complexity blocky sequences (H2 = 1.26 bits) maintain extended conformations with less overlapping. Free energy analysis reveals a steep increase in mixing barriers for low-complexity compared to surmountable barrier for high-complexity sequences. We find that geometric confinement modulates but does not override these sequence-dependent behaviors, with asymmetric confinement enhancing heterogeneity in overlapping for both sequence type (pronounced in high-H2 sequences). Our theory could be applicable in assessing the phase behavior of repeat protein and nucleic acid sequences.

biophysics↗

bioRxiv2024

Heterogeneity induced Block Copolymer Segregation in Confinement

Motivated by the work on block copolymer models that provide insights into epigenetics driven chromosome organization, we investigate the segregation behavior of five distinct 2-block co-polymers (BCPs) system with varying block sizes, confined within both symmetric and lateral geometries. Using exact enumeration method and Langevin dynamics simulation, our simple self-avoiding polymer model reveals robust behaviors (across statics and dynamic studies) despite strong finite-size effects. We observe that as block length increases, polymer compaction intensifies relying on non-specific interaction, leading to longer segregation times. The dynamic study clearly demonstrates the formation of globular lamellar phases and condensed, stable complex structures in long-range block copolymer (BCP) systems, providing a simplified analogy to lamellar-mediated chromatin compaction, which involves structures that are difficult to segregate under physiological conditions. Dominance of specific interaction over non-specific interaction in long range BCP systems leads to phase separation driven self assemblies which provides a simplified analogy to heterochromatin--inactive or stable domains. In contrast, short-range block sequences remain in a coiled state, exhibiting minimal overlap or interaction due to strong short range attraction, which may corresponds to euchromatin regions where diverse epigenetic states coexist, resulting in active, non-condensed structures. We also observe that asymmetric or lateral confinement favors more segregation between the BCPs irrespective of their underlying sequence.

biophysics↗

bioRxiv2024

Random sampling of ligand arrangements on a one-dimensional lattice

We introduce a transfer-matrix-based sequential sampling scheme for generating random samples of ligand arrangements on one-dimensional templates. The number of ligand types is arbitrary, the binding constants can have positional dependence, and cooperativity parameters are included. From the random arrangements, any (linear or non-linear) observable can be calculated using sample averaging. We provide a publically available software with a computational time that scales linearly with the lattice size. As an example application, we study the competitive binding of three ligand types (the sequence-specific binder netropsin, YOYO-1 and ethidium bromide) to a DNA molecule.

biophysics↗