Related papers: Cluster-scaling, chaotic order and coherence in DN…
Networks or graphs can easily represent a diverse set of data sources that are characterized by interacting units or actors. Social networks, representing people who communicate with each other, are one example. Communities or clusters of…
We consider complex clustered networks with a gradient structure, where sizes of the clusters are distributed unevenly. Such networks describe more closely actual networks in biophysical systems and in technological applications than…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
We observe regular patterns emerging across multiple length scales with high-concentration DNA solutions in microfluidic pillar arrays at low Reynolds numbers and high Deborah. Interacting vortices between pillars lead to long-range order…
Clustered solutions in oscillator networks provide an important insight into how a system might diversify from a synchronous solution into spatiotemporal complex solutions. They can therefore form a link between fully synchronized and…
Clustering, as an unsupervised technique, plays a pivotal role in various data analysis applications. Among clustering algorithms, Spectral Clustering on Euclidean Spaces has been extensively studied. However, with the rapid evolution of…
Clustering plays an important role in the structure of nuclei, especially for light nuclei in the $p$-shell. In nuclear cluster models these degrees of freedom are introduced explicitly. In the Resonating Group Method or in the Generator…
We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their…
Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements…
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…
We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a…
We study the impact of interaction of nodes in a layer of a multiplex network on the dynamical behavior and cluster synchronization of these nodes in other layers. We find that nodes interactions in one layer affects the cluster…
In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring learning dataset of already known genes. The fact that unsupervised gene-detection is possible closely connected to…
Clusters appear in nature in a diversity of contexts, involving distances as long as the cosmological ones, and down to atoms and molecules and the very small nuclear size. They also appear in several other scenarios, in particular in…
Nowadays there is a multitude of measures designed to capture different aspects of network structure. To be able to say if the structure of certain network is expected or not, one needs a reference model (null model). One frequently used…
The adoption of probabilistic models for the best individuals found so far is a powerful approach for evolutionary computation. Increasingly more complex models have been used by estimation of distribution algorithms (EDAs), which often…
In order to study the resonance spectra of chaotic cavities subject to some damping (which can be due to absorption or partial reflection at the boundaries), we use a model of damped quantum maps. In the high-frequency limit, the…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
Micro-scale flow in cylindrical geometries can harness chaotic advection to perform complex thermally activated biochemical reactions such as the polymerase chain reaction (PCR). We have applied a 3D computational fluid dynamics model to…
Quantum circuits that generate coherent superpositions of stochastic processes are key to many downstream quantum-accelerated tasks, such as risk analysis, importance sampling, and DNA sequencing. However, traditional methods for designing…