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Yair A. G. Fosado

Publications and source records attributed to Yair A. G. Fosado.

2 recordsLinked to original sources

Entangled nematic disclinations using multi-particle collision dynamics

Colloids dispersed in nematic liquid crystals form topological composites in which colloid-associated defects mediate interactions while adhering to fundamental topological constraints. Better realising the promise of such materials requires numerical methods that model nematic inclusions in dynamic and complex scenarios. We employ a mesoscale approach for simulating colloids as mobile surfaces embedded in a fluctuating nematohydrodynamic medium to study the kinetics of colloidal entanglement. In addition to reproducing far-field interactions, topological properties of disclination loops are resolved to reveal their metastable states and topological transitions during relaxation towards ground state. The intrinsic hydrodynamic fluctuations distinguish formerly unexplored far-from-equilibrium disclination states, including configurations with localised positive winding profiles. The adaptability and precision of this numerical approach offers promising avenues for studying the dynamics of colloids and topological defects in designed and out-of-equilibrium situations.

cond-mat.soft↗

Fluidification of entanglements by a DNA bending protein

In spite of the nanoscale and single-molecule insights into how nucleoid associated proteins (NAPs) interact with DNA, their role in modulating the mesoscale viscoelasticity of the entangled genome in vivo has been overlooked so far. By combining microrheology and molecular dynamics simulation we find that the important NAP called Integration Host Factor (IHF) lowers the viscosity of entangled $λ$DNA 20-fold at physiological concentrations and stoichiometries. We argue that IHF may act as a "genomic fluidiser", reducing the effective viscosity of the nucleoid $\sim$200-fold. Our results suggest a previously unappreciated key role of IHF in regulating DNA dynamics and re-organisation in vivo

cond-mat.soft↗