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Hashem Fatemi

Publications and source records attributed to Hashem Fatemi.

4 recordsLinked to original sources

Confinement-Induced Optimization of Fluctuation-Induced Forces in Active Fluids

Active matter generates nonequilibrium fluctuations that mediate effective interactions between immersed objects. While fluctuation-induced (FI) forces in active fluids depend on activity, density, and geometry, their dependence on confinement remains poorly understood. We study FI forces between fixed intruders in two-dimensional active fluids composed of self-propelled circular or rodlike particles using Langevin dynamics simulations. We find that the FI force exhibits a pronounced nonmonotonic dependence on intruder separation, reaching a maximum at an optimal gap size well beyond the depletion regime, in contrast to the commonly assumed monotonic decay. This optimal confinement is robust across parameters and is more pronounced for elongated particles. The effect arises from a confinement-controlled balance between particle transport and crowding: narrow gaps hinder exchange between inner and outer regions, whereas large separations effectively decouple the intruders. At intermediate distances, enhanced crowding around the intruders generates maximal collision-rate asymmetries, leading to the strongest effective interactions. These results identify confinement geometry as a key control parameter for FI forces in active matter.

cond-mat.soft

Optimal chirality enhances long-range fluctuation-induced interactions in active fluids

Understanding interactions between chiral active particles -- self-propelling and self-rotating entities -- is crucial for uncovering how chiral active matter self-organizes into dynamic structures. Although fluctuation-induced forces in nonequilibrium active systems can drive structure formation, the role of chirality remains largely unexplored. We investigate effective fluctuation-induced forces between intruders immersed in chiral active fluids and reveal that the impact of chirality depends sensitively on particle shape. For circular particles, increasing the self-rotation to self-propulsion ratio suppresses the interaction, reflecting a transition from rotating flocks to localized spinners. Contrarily, a striking collective behavior emerges for rodlike particles: vortices spontaneously form around the intruders, most pronounced at an optimal chiral angle where the mean curvature of particle trajectories matches the intruder boundary curvature, maximizing the effective force. We map the attractive and repulsive force regimes across chirality, propulsion, and intruder separation, offering new insights and principles for designing and controlling self-assembled active systems.

cond-mat.soft

Insight into the Unwrapping of the Dinucleosome

Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin remodelling complexes cause their active displacements. Here we propose a theoretical analysis of dinucleosome wrapping and unwrapping dynamics in the presence of an external force. We explore the energy landscape and configurations of dinucleosome in different unwrapped states. Moreover, using a dynamical Monte-Carlo simulation algorithm, we demonstrate the dynamical features of the system such as the unwrapping force for partial and full wrapping processes. Furthermore, we show that in the short length of linker DNA ($\sim 10 - 90$ bp), the asymmetric unwrapping occurs. These findings could shed some light on chromatin dynamics and gene accessibility.

q-bio.BM

Elastic Model for Dinucleosome Structure and Energy

The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem does not depend on the length of the linker DNA. In addition it is shown that the two histone octamers are almost perpendicular to each other and the linker DNA in short lengths is almost straight. These findings could shed some light on the role of DNA elasticity in the chromatin structure.

physics.bio-ph