Computational mechanisms in genetic regulation by RNA

The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics similar to artificial neural networks. Here we present a simple mechanism allowing ncRNA to perform computations equivalent to neural network algorithms such as Boltzmann machines and the Hopfield model. The quantities analogous to the neural couplings are the equilibrium constants between different RNA species. The relatively rapid equilibration of RNA binding and unbinding is regulated by a slower process that degrades and creates new RNA. The model requires that the creation rate for each species be an increasing function of the ratio of total to unbound RNA. Similar mechanisms have already been found to exist experimentally for ncRNA regulation. With the overall concentration of RNA regulated, equilibrium constants can be chosen to store many different patterns, or many different input-output relations. The network is also quite insensitive to random mutations in equilibrium constants. Therefore one expects that this kind of mechanism will have a much higher mutation rate than ones typically regarded as being under evolutionary constraint.Comment: 18 pages, 10 figure

The path-coalescence transition and its applications

We analyse the motion of a system of particles subjected a random force fluctuating in both space and time, and experiencing viscous damping. When the damping exceeds a certain threshold, the system undergoes a phase transition: the particle trajectories coalesce. We analyse this transition by mapping it to a Kramers problem which we solve exactly. In the limit of weak random force we characterise the dynamics by computing the rate at which caustics are crossed, and the statistics of the particle density in the coalescing phase. Last but not least we describe possible realisations of the effect, ranging from trajectories of raindrops on glass surfaces to animal migration patterns.Comment: 4 pages, 3 figures; revised version, as publishe