Biology subjects

Giri, D.

Publications and source records attributed to Giri, D..

3 recordsLinked to original sources

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↗

bioRxiv2019

Naturally occurring fluorescence protects the eutardigrade Paramacrobiotus sp. from ultraviolet radiation

Naturally occurring fluorescence has been observed in multiple species ranging from bacteria to birds. In macroscopic animals such as birds and fishes, fluorescence provides a visual communication signal. However, the functional significance of this phenomenon is not known in most cases. Though photoprotection is attributed to fluorescence under ultraviolet (UV) light in some organisms, it lacks direct experimental evidence. Here, we have identified a new species of eutardigrade belonging to the genus Paramacrobiotus, which exhibits fluorescence under UV light. Using a natural variant of the same species that lacks fluorescence, we show that the fluorescence confers tolerance to lethal UV radiation. Remarkably, we could transfer this property to UV-sensitive Hypsibius exemplaris, another eutardigrade, and also to C. elegans, a nematode. Using high performance liquid chromatography (HPLC) we isolated the fluorescent compound from Paramacrobiotus sp. This compound has excitation maxima ({lambda}ex) at 370 nm and emission maxima ({lambda}em) at 420-430 nm. We propose that Paramacrobiotus sp. uses a fluorescent shield that absorbs harmful UV radiation, and emits harmless blue light, thereby protecting itself from the lethal effects of UV radiation. Summary statementTardigrades are well known for their tolerance to extreme environmental conditions. In this study, we have identified a new tardigrade species that employs a fluorescent shield to protect itself from the germicidal ultra violet radiation.

ecology↗