New synchronization criteria for an array of neural networks with hybrid coupling and time-varying delays

This paper is concerned with the global exponential synchronization for an array of hybrid coupled neural networks with time-varying leakage delay, discrete and distributed delays. Applying a novel Lyapunov functional and the property of outer coupling matrices of the neural networks, sufficient conditions are obtained for the global exponential synchronization of the system. The derived synchronization criteria are closely related with the time-varying delays and the coupling structure of the networks. The maximal allowable upper bounds of the time-varying delays can be obtained guaranteeing the global synchronization for the neural networks. The method we adopt in this paper is different from the commonly used linear matrix inequality (LMI) technique, and our synchronization conditions are new, which are easy to check in comparison with the previously reported LMI-based ones. Some examples are given to show the effectiveness of the obtained theoretical results

Dynamical Systems on Networks: A Tutorial

We give a tutorial for the study of dynamical systems on networks. We focus especially on "simple" situations that are tractable analytically, because they can be very insightful and provide useful springboards for the study of more complicated scenarios. We briefly motivate why examining dynamical systems on networks is interesting and important, and we then give several fascinating examples and discuss some theoretical results. We also briefly discuss dynamical systems on dynamical (i.e., time-dependent) networks, overview software implementations, and give an outlook on the field.Comment: 39 pages, 1 figure, submitted, more examples and discussion than original version, some reorganization and also more pointers to interesting direction

The Stability and Control of Stochastically Switching Dynamical Systems

Inherent randomness and unpredictability is an underlying property in most realistic phenomena. In this work, we present a new framework for introducing stochasticity into dynamical systems via intermittently switching between deterministic regimes. Extending the work by Belykh, Belykh, and Hasler, we provide analytical insight into how randomly switching network topologies behave with respect to their averaged, static counterparts (obtained by replacing the stochastic variables with their expectation) when switching is fast. Beyond fast switching, we uncover a highly nontrivial phenomenon by which a network can switch between two asynchronous regimes and synchronize against all odds. Then, we establish rigorous theory for this framework in discrete-time systems for arbitrary switching periods (not limited to switching at each time step). Using stability and ergodic theories, we are able to provide analytical criteria for the stability of synchronization for two coupled maps and the ability of a single map to control an arbitrary network of maps. This work not only presents new phenomena in stochastically switching dynamical systems, but also provides the first rigorous analysis of switching dynamical systems with an arbitrary switching period

Markov field models of molecular kinetics

Computer simulations such as molecular dynamics (MD) provide a possible means to understand protein dynamics and mechanisms on an atomistic scale. The resulting simulation data can be analyzed with Markov state models (MSMs), yielding a quantitative kinetic model that, e.g., encodes state populations and transition rates. However, the larger an investigated system, the more data is required to estimate a valid kinetic model. In this work, we show that this scaling problem can be escaped when decomposing a system into smaller ones, leveraging weak couplings between local domains. Our approach, termed independent Markov decomposition (IMD), is a first-order approximation neglecting couplings, i.e., it represents a decomposition of the underlying global dynamics into a set of independent local ones. We demonstrate that for truly independent systems, IMD can reduce the sampling by three orders of magnitude. IMD is applied to two biomolecular systems. First, synaptotagmin-1 is analyzed, a rapid calcium switch from the neurotransmitter release machinery. Within its C2A domain, local conformational switches are identified and modeled with independent MSMs, shedding light on the mechanism of its calcium-mediated activation. Second, the catalytic site of the serine protease TMPRSS2 is analyzed with a local drug-binding model. Equilibrium populations of different drug-binding modes are derived for three inhibitors, mirroring experimentally determined drug efficiencies. IMD is subsequently extended to an end-to-end deep learning framework called iVAMPnets, which learns a domain decomposition from simulation data and simultaneously models the kinetics in the local domains. We finally classify IMD and iVAMPnets as Markov field models (MFM), which we define as a class of models that describe dynamics by decomposing systems into local domains. Overall, this thesis introduces a local approach to Markov modeling that enables to quantitatively assess the kinetics of large macromolecular complexes, opening up possibilities to tackle current and future computational molecular biology questions