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Register a new userStabilizing and Destabilizing Effects of Embedding 3-node Subgraphs on State Space of Boolean Networks
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We demonstrate the effects of embedding subgraphs using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical properties of network embedded seven different subgraphs including feedback and feedforward subgraphs, we found that complexity of the state space that increases with longer length of attractors and greater number of attractors is reduced for networks with more feedforward subgraphs. In addition, feedforward subgraphs can also provide higher mutual information with lower entropy in a temporal program of gene expression. Networks with other six subgraphs show opposite effects on dynamics of the networks, is roughly consistent with Thomass conjecture. These results suggest that feedforward subgraphs are one of the favorable local structures in biological complex networks.
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We demonstrate the advantages of feedforward loops using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical behaviors of network embedded feedback and feedforward loops, we found that feedforward loops can provide higher temporal order (coherence) with lower entropy (randomness) in a temporal program of gene expression. In addition, complexity of the state space that increases with longer length of attractors and greater number of attractors is also reduced for networks with more feedforward loops. Feedback loops show opposite effects on dynamics of the networks. These results suggest that feedforward loops are one of the favorable local structures in biomolecular and neuronal networks.
In this work we consider random Boolean networks that provide a general model for genetic regulatory networks. We extend the analysis of James Lynch who was able to proof Kauffmans conjecture that in the ordered phase of random networks, the number of ineffective and freezing gates is large, where as in the disordered phase their number is small. Lynch proved the conjecture only for networks with connectivity two and non-uniform probabilities for the Boolean functions. We show how to apply the proof to networks with arbitrary connectivity $K$ and to random networks with biased Boolean functions. It turns out that in these cases Lynchs parameter $lambda$ is equivalent to the expectation of average sensitivity of the Boolean functions used to construct the network. Hence we can apply a known theorem for the expectation of the average sensitivity. In order to prove the results for networks with biased functions, we deduct the expectation of the average sensitivity when only functions with specific connectivity and specific bias are chosen at random.
We demonstrate reservoir computing with a physical system using a single autonomous Boolean logic element with time-delay feedback. The system generates a chaotic transient with a window of consistency lasting between 30 and 300 ns, which we show is sufficient for reservoir computing. We then characterize the dependence of computational performance on system parameters to find the best operating point of the reservoir. When the best parameters are chosen, the reservoir is able to classify short input patterns with performance that decreases over time. In particular, we show that four distinct input patterns can be classified for 70 ns, even though the inputs are only provided to the reservoir for 7.5 ns.
Much research effort has been devoted to developing methods for reconstructing the links of a network from dynamics of its nodes. Many current methods require the measurements of the dynamics of all the nodes be known. In real-world problems, it is common that either some nodes of a network of interest are unknown or the measurements of some nodes are unavailable. These nodes, either unknown or whose measurements are unavailable, are called hidden nodes. In this paper, we derive analytical results that explain the effects of hidden nodes on the reconstruction of bidirectional networks. These theoretical results and their implications are verified by numerical studies.
We consider the one-dimensional totally asymmetric simple exclusion model (TASEP model) with open boundary conditions and present the analytical computations leading to the exact formula for distance clearance distribution, i.e. probability density for a clear distance between subsequent particles of the model. The general relation is rapidly simplified for middle part of the one-dimensional lattice using the large $N$ approximation. Both the analytical formulas and their approximations are successfully compared with the numerical representation of the TASEP model. Furthermore, we introduce the pertinent estimation for so-called spectral rigidity of the model. The results obtained are sequentially discussed within the scope of vehicular traffic theory.
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