Related papers: Cluster-scaling, chaotic order and coherence in DN…
The affect of demographic stochasticity of a system of globally coupled chaotic maps is considered. A two-step model is studied, where the intra-patch chaotic dynamics is followed by a migration step that coupled all patches; the…
In order to analyze the effect of chaos or order on the rate of decoherence in a subsystem we aim to distinguish effects of the two types of dynamics from those depending on the choice of the wave packet. To isolate the former we introduce…
Nestedness characterizes the linkage pattern of networked systems, indicating the likelihood that a node is linked to the nodes linked to the nodes with larger degrees than it. Networks of mutualistic relationship between distinct groups of…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
We investigate the role of connection density in an adaptive network model of chaotic units that dynamically rewire based on their internal states and local coherence. By systematically varying the network's connectivity density, we uncover…
We give evidence that particles interacting via the simple, radially symmetric square-shoulder potential can self-organize in highly complex, low-symmetry lattices, forming thereby clusters, columns, or lamellae; only at high pressure…
$\alpha$-clustering study since the pioneering discovery of $^{12}$C+$^{12}$C molecular resonances half a century ago. Our knowledge on physics of nuclear molecules has increased considerably and nuclear clustering remains one of the most…
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…
We show that dynamical clustering, where a system segregates into distinguishable subsets of synchronized elements, and chimera states, where differentiated subsets of synchronized and desynchronized elements coexist, can emerge in networks…
Clustering is typically measured by the ratio of triangles to all triples, open or closed. Generating clustered networks, and how clustering affects dynamics on networks, is reasonably well understood for certain classes of networks…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
A statistical analysis of the spectrum of two particle - two hole doorway states in a finite nucleus is performed. On the unperturbed mean-field level sizable attractive correlations are present in such a spectrum. Including particle-hole…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
Data analysis and data mining are concerned with unsupervised pattern finding and structure determination in data sets. "Structure" can be understood as symmetry and a range of symmetries are expressed by hierarchy. Such symmetries directly…
We study the asymptotic behavior of multiscale stochastic spatial gene networks. Multiscaling takes into account the difference of abundance between molecules , and captures the dynamic of rare species at a mesoscopic level. We introduce an…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…