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Riku Linna

Publications and source records attributed to Riku Linna.

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Dimensional criterion for forecasting nonlinear systems by reservoir computing

Reservoir computers (RC) have proven useful as surrogate models in forecasting and replicating systems of chaotic dynamics. The quality of surrogate models based on RCs is crucially dependent on their optimal implementation that involves selecting optimal reservoir topology and hyperparameters. By systematically applying Bayesian hyperparameter optimization and using ensembles of reservoirs of various topology we show that connectednes of reservoirs is of significance only in forecasting and replication of chaotic system of sufficient complexity. By applying RCs of different topology in forecasting and replicating the Lorenz system, a coupled Wilson-Cowan system, and the Kuramoto-Sivashinsky system, we show that simple reservoirs of unconnected nodes (RUN) outperform reservoirs of connected nodes for target systems whose estimated fractal dimension dimension is $d \lesssim 5.5$ and that linked reservoirs are better for systems with $d > 5.5$. This finding is highly important for evaluation of reservoir computing methods and on selecting a method for prediction of signals measured on nonlinear systems.

cs.LG

Sedimentation of Knotted Polymers

We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number n_c of the corresponding ideal knot. To the best of our knowledge, this provides the first direct computational confirmation of this relation, postulated on the basis of experiments in "The effect of ionic conditions on the conformations of supercoiled DNA. I. sedimentation analysis" by Rybenkov et al., for the case of sedimentation. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration R_g^-1, more specifically with the inverse of the R_g component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, R_g^-1 remains to a good precision linearly dependent on n_c. Therefore, R_g^-1 is a good measure of a knot's complexity.

physics.bio-ph