arXiv subjects

Farisan Dary

Publications and source records attributed to Farisan Dary.

3 recordsLinked to original sources

arXiv2026

Helical stability of double-stranded semiflexible chains with interstrand interactions

The mechanical and structural properties of dsDNA have been successfully described by models with varying levels of complexity and coarse-graining schemes. Prior work has characterized local stacking/twist effects and force-torque phase diagrams under external constraints. However, the role of base-pairing and torsional elasticity in global morphological transitions remain poorly characterized in the absence of external constraints. Here we investigate the delicate balance required for the strength of base-pairing interactions and the twisting energy to preserve the double-helix structure in a model made up of two semiflexible chains. We found that the model exhibits several distinct morphological phases: flat, random coil, double-helix, and the unwound double-helix. We calculate the Gauss linking number to characterize transitions between these phases.

cond-mat.soft↗

arXiv2026

Emergence of Hexanematic Order in a Growing Confluent Cell Monolayer

Collective migration of epithelial layers underlies processes ranging from wound healing to cancer invasion. A defining yet challenging feature is the emergence of distinct cell morphologies within a single migrating confluent sheet, with larger, elongated cells at the active boundary and smaller, hexatically ordered cells in the bulk. Here, we develop a stochastic particle-Voronoi framework that captures this hexanematic organization without prescribing target geometries and distinct cell types. We show that boundary-driven collective motion generates an outward velocity gradient. This gradient, coupled to a density and velocity-dependent division rule, produces peripheral cells that are larger, more elongated, and more defect-prone, while bulk cells remain smaller, isotropic, and hexagonally packed. These results show how minimal, non-equilibrium mechanical interactions give rise to emergent, self-organized tissue-scale patterning during collective migration.

cond-mat.soft↗

arXiv2021

Statistics and Topology of Fluctuating Ribbons

Ribbons are a class of slender structures whose length, width, and thickness are widely separated from each other. This scale separation gives a ribbon unusual mechanical properties in athermal macroscopic settings, e.g. it can bend without twisting, but cannot twist without bending. Given the ubiquity of ribbon-like biopolymers in biology and chemistry, here we study the statistical mechanics of microscopic inextensible, fluctuating ribbons loaded by forces and torques. We show that these ribbons exhibit a range of topologically and geometrically complex morphologies exemplified by three phases - a twist-dominated helical phase (HT), a writhe-dominated helical phase (HW), and an entangled phase - that arise as the applied torque and force is varied. Furthermore, the transition from HW to HT phases is characterized by the spontaneous breaking of parity symmetry and the disappearance of perversions that characterize chirality reversals. This leads to a universal response curve of a topological quantity, the link, as a function of the applied torque that is similar to magnetization curves in second-order phase transitions.

cond-mat.stat-mech↗