Related papers: Hamiltonian dynamics and distributed chaos in DNA
Chaos and complexity entail an entropic and computational obstruction to describing a system, and thus are intrinsically difficult to characterize. In this paper, we consider time evolution by Gaussian Unitary Ensemble (GUE) Hamiltonians…
Biological networks have been recently found to exhibit many topological properties of the so-called complex networks. It has been reported that they are, in general, both highly skewed and directed. In this paper, we report on the dynamics…
Conventional spectral probes of quantum chaos require eigenvalues, and sometimes, eigenvectors of the quantum Hamiltonian. This involves computationally expensive diagonalization procedures. We test whether an unsupervised neural network…
This paper summarises a numerical investigation of how the usual manifestations of chaos and regularity for flows in time-independent Hamiltonians can be alterred by a systematic time-dependence of the form arising naturally in an expanding…
Stable chaos is a generalization of the chaotic behaviour exhibited by cellular automata to continuous-variable systems and it owes its name to an underlying irregular and yet linearly stable dynamics. In this review we discuss analogies…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
We consider scenarios where the dynamics of a quantum system are partially determined by prior local measurements of some interacting environmental degrees of freedom. The resulting effective system dynamics are described by a disordered…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
This paper studies distributional chaos in non-autonomous discrete systems generated by given sequences of maps in metric spaces. In the case that the metric space is compact, it is shown that a system is Li-Yorke{\delta}-chaotic if and…
We developed a powerful computational approach to elaborate on onset mechanisms of deterministic chaos due to complex homoclinic bifurcations in diverse systems. Its core is the reduction of phase space dynamics to symbolic binary…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Analytical expressions for the width and conductance peak distributions of irregularly shaped quantum dots in the Coulomb blockade regime are presented in the limits of conserved and broken time-reversal symmetry. The results are obtained…
We study time evolution of a subsystem's density matrix under unitary evolution, generated by a sufficiently complex, say quantum chaotic, Hamiltonian, modeled by a random matrix. We exactly calculate all coherences, purity and…
In this work, we study a class of hybrid dynamical systems called hybrid gene regulatory networks (HGRNs) which was proposed to model gene regulatory networks. In HGRNs, there exist well-behaved trajectories that reach a fixed point or…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
In generic Hamiltonian systems with a mixed phase space chaotic transport may be directed and ballistic rather than diffusive. We investigate one particular model showing this behaviour, namely a spatially periodic billiard chain in which…
We demonstrate the presence of chaos in stochastic simulations that are widely used to study biodiversity in nature. The investigation deals with a set of three distinct species that evolve according to the standard rules of mobility,…
Continuous-time systems with switch-like behaviour occur in chemical kinetics, gene regulatory networks and neural networks. Networks with hard switching, as a limiting case of smooth sigmoidal switching, retain the richest possible range…
We speak of chaos in quantum systems if the statistical properties of the eigenvalue spectrum coincide with predictions of random-matrix theory. Chaos is a typical feature of atomic nuclei and other self-bound Fermi systems. How can the…