Prof Ramin Golestanian

Abstract:

Using a stochastic susceptible-infected-removed meta-population model of disease transmission, we present analytical calculations and numerical simulations dissecting the interplay between stochasticity and the division of a population into mutually independent sub-populations. We show that subdivision activates two stochastic effects-extinction and desynchronization-diminishing the overall impact of the outbreak even when the total population has already left the stochastic regime and the basic reproduction number is not altered by the subdivision. Both effects are quantitatively captured by our theoretical estimates, allowing us to determine their individual contributions to the observed reduction of the peak of the epidemic.

Abstract:

The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA, which is an open software that calculates elastic parameters of double-stranded nucleic acids from dinucleotide length up to the whole molecule using ensembles from numerical simulations. The program reveals that global bendability emerge from local periodic bending angles in phase with the DNA helicoidal shape. We apply SerraNA to the whole set of 136 tetra-bp combinations and we observe a high degree of sequence-dependence with differences over 200% for all elastic parameters. Tetramers with TA and CA base-pair steps are especially flexible, while the ones containing AA and AT tend to be the most rigid. Thus, AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly. Our results also indicate base mismatches would make DNA more flexible, while protein binding would make it more rigid. SerraNA is a tool to be applied in the next generation of interdisciplinary investigations to further understand what determines the elasticity of DNA.

Abstract:

In nature, interactions between biopolymers and motor proteins give rise to biologically essential emergent behaviors. Besides cytoskeleton mechanics, active nematics arise from such interactions. Here we present a study on 3D active nematics made of microtubules, kinesin motors, and depleting agent. It shows a rich behavior evolving from a nematically ordered space-filling distribution of microtubule bundles toward a flattened and contracted 2D ribbon that undergoes a wrinkling instability and subsequently transitions into a 3D active turbulent state. The wrinkle wavelength is independent of the ATP concentration and our theoretical model describes its relation with the appearance time. We compare the experimental results with a numerical simulation that confirms the key role of kinesin motors in cross-linking and sliding the microtubules. Our results on the active contraction of the network and the independence of wrinkle wavelength on ATP concentration are important steps forward for the understanding of these 3D systems.

Abstract:

We investigate the collective motion of magnetic rotors suspended in a viscous fluid under a uniform rotating magnetic field. The rotors are positioned on a square lattice, and low Reynolds hydrodynamics is assumed. For a 3 × 3 array of magnets, we observe three characteristic dynamical patterns as the external field strength is varied: a synchronized pattern, an oscillating pattern, and a chessboard pattern. The relative stability of these depends on the competition between the energy due to the external magnetic field and the energy of the magnetic dipole-dipole interactions among the rotors. We argue that the chessboard pattern can be understood as an alternation in the stability of two degenerate states, characterized by striped and spin-ice configurations, as the applied magnetic field rotates. For larger arrays, we observe propagation of slip waves that are similar to metachronal waves. The rotor arrays have potential as microfluidic devices that can mix fluids and create vortices of different sizes.