Multifractal analysis of nonhyperbolic coupled map lattices: application to genomic sequences

Vulnerability assessment of freeway network considering the probabilities and consequences from a perspective based on network cascade failure

Freeway networks are vulnerable to natural disasters and man-made disruptions. The closure of one or more toll stations of the network often causes a sharp decrease in freeway performance. Therefore, measuring the probability and consequences of vulnerability to identify critical parts in the network is crucial for road emergency management. Most existing techniques only measure the consequences of node closure and rarely consider the probability of node closure owing to the lack of an extensive historical database; moreover, they ignore highways outside the study area, which can lead to errors in topological analysis and traffic distribution. Furthermore, the negative effects produced by the operation of freeway tunnels in vulnerability assessment have been neglected. In this study, a framework for freeway vulnerability assessment that considers both the probability and consequences of vulnerability is proposed, based on the perspective of network cascade failure analysis. The cascade failure analysis is conducted using an improved coupled map lattice model, developed by considering the negative effects of tunnels and optimizing the rules of local traffic redistribution. The perturbation threshold and propagation time step of network cascade failure are captured to reflect the probabilities and consequences of vulnerability. A nodal vulnerability index is established based on risk assessment, and a hierarchical clustering method is used to identify the vulnerability classification of critical nodes. The freeway network of Fuzhou in China is utilized to demonstrate the effectiveness of the proposed approach. Specifically, the toll stations in the study area are classified into five clusters of vulnerability: extremely high, high, medium, low, and extremely low. Approximately 31% of the toll stations were classified as the high or extremely high cluster, and three extremely vulnerable freeway sections requiring different precautions were identified. The proposed network vulnerability analysis method provides a new perspective to examine the vulnerability of freeway networks.

Spatial constrains and information content of sub-genomic regions of the human genome

Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities of DNA sequences (exonic, intronic, intergenic, repeat, unique) with the purpose to ask questions regarding the segmental organization of the human genome within the size distribution of these sequences. For this we developed an integrated methodology that is based upon the reconstructed phase space theorem, the non-extensive statistical theory of Tsallis, ML techniques, and a technical index, integrating the generated information, which we introduce and named complexity factor (COFA). Our analysis revealed that the size distribution of the genomic regions within chromosomes are not random but follow patterns with characteristic features that have been seen through its complexity character, and it is part of the dynamics of the whole genome. Finally, this picture of dynamics in DNA is recognized using ML tools for clustering, classification, and prediction with high accuracy.

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The lengths of DNA subgenomic entities satisfied the Tsallis non-extensive statistics

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The size distribution of the subgenomic entities within chromosomes follow specific patterns

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A technical index COFA was introduced to characterize the degree of complexity

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The degree of complexity behavior in DNA is identifiable using ML approaches

Exhaled aerosol pattern discloses lung structural abnormality: a sensitivity study using computational modeling and fractal analysis

BACKGROUND

Exhaled aerosol patterns, also called aerosol fingerprints, provide clues to the health of the lung and can be used to detect disease-modified airway structures. The key is how to decode the exhaled aerosol fingerprints and retrieve the lung structural information for a non-invasive identification of respiratory diseases.

OBJECTIVE AND METHODS

In this study, a CFD-fractal analysis method was developed to quantify exhaled aerosol fingerprints and applied it to one benign and three malign conditions: a tracheal carina tumor, a bronchial tumor, and asthma. Respirations of tracer aerosols of 1 µm at a flow rate of 30 L/min were simulated, with exhaled distributions recorded at the mouth. Large eddy simulations and a Lagrangian tracking approach were used to simulate respiratory airflows and aerosol dynamics. Aerosol morphometric measures such as concentration disparity, spatial distributions, and fractal analysis were applied to distinguish various exhaled aerosol patterns.

FINDINGS

Utilizing physiology-based modeling, we demonstrated substantial differences in exhaled aerosol distributions among normal and pathological airways, which were suggestive of the disease location and extent. With fractal analysis, we also demonstrated that exhaled aerosol patterns exhibited fractal behavior in both the entire image and selected regions of interest. Each exhaled aerosol fingerprint exhibited distinct pattern parameters such as spatial probability, fractal dimension, lacunarity, and multifractal spectrum. Furthermore, a correlation of the diseased location and exhaled aerosol spatial distribution was established for asthma.

CONCLUSION

Aerosol-fingerprint-based breath tests disclose clues about the site and severity of lung diseases and appear to be sensitive enough to be a practical tool for diagnosis and prognosis of respiratory diseases with structural abnormalities.

Coupled intermittent maps modeling the statistics of genomic sequences: A network approach

The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long-range correlation features which are observed in the genomic sequences of higher eucaryotes. A weighted network approach to symbolic sequences is introduced, and it is shown that coupled intermittent polynomial maps produce degree and link size distributions with power-law exponents similar to the ones observed in real genomes. The proposed network approach to symbolic sequences is generic and can be applied to any symbol sequence (artificial or natural).

Detecting correlations among functional-sequence motifs

Sequence motifs are words of nucleotides in DNA with biological functions, e.g., gene regulation. Identification of such words proceeds through rejection of Markov models on the expected motif frequency along the genome. Additional biological information can be extracted from the correlation structure among patterns of motif occurrences. In this paper a log-linear multivariate intensity Poisson model is estimated via expectation maximization on a set of motifs along the genome of E. coli K12. The proposed approach allows for excitatory as well as inhibitory interactions among motifs and between motifs and other genomic features like gene occurrences. Our findings confirm previous stylized facts about such types of interactions and shed new light on genome-maintenance functions of some particular motifs. We expect these methods to be applicable to a wider set of genomic features.

Multifractal analysis of thermal denaturation based on the Peyrard-Bishop-Dauxois model

The theory of DNA dynamics is exceedingly complex and not easily explained. In the past two decades, by adapting methods of statistical physics, the dynamics of DNA in contact with a thermal bath is widely studied. In this paper, the thermal denaturation of DNA in the framework of the Peyrard-Bishop-Dauxois (PBD) model through the Rényi dimension is investigated. As a result, the Rényi dimension spectrum of the melting transition process reveals the multifractal nature of the dynamics of the Peyrard-Bishop-Dauxois model. Also, it can be concluded that the Rényi dimension (D(q)) at negative values of q is the characteristic signature of pre-melting and thermal denaturation of DNA. Furthermore, this approach is in excellent agreement with previous experimental studies.