Related papers: Dynamic cluster-scaling in DNA
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional…
We study the formation of a colloidal gel by means of Molecular Dynamics simulations of a model for colloidal suspensions. A slowing down with gel-like features is observed at low temperatures and low volume fractions, due to the formation…
DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two…
Many real-world complex systems rely on cluster synchronization to function properly. A cluster of nodes exhibits synchronous behavior while others behave erratically. Predicting the emergence of these clusters and understanding the…
Clustering is one of the mayor collective phenomena observed in active matter. We study the overdamped motion of interacting active Brownian particles in two dimensions. An instability in the pair correlation function causes the onset of…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
The dynamical arrest of gels is the consequence of a well defined structural phase transition, leading to the formation of a spanning cluster of bonded particles. The dynamical glass transition, instead, is not accompanied by any clear…
Based on the competition between members of a hierarchy of length scales in complex multi-scale systems, it is shown how clustering of active quantities into concentrated sets, like bubbles in a Swiss cheese, is a generic property that…
$\alpha$-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…
Nucleonic matter displays a quantum liquid structure, but in some cases finite nuclei behave like molecules composed of clusters of protons and neutrons. Clustering is a recurrent feature in light nuclei, from beryllium to nickel. For…
In mammalian cells, repair centers for DNA double-strand breaks (DSBs) have been identified. However, previous researches predominantly rely on methods that induce specific DSBs by cutting particular DNA sequences. The clustering and its…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
Clustering is one of the most complex phenomena known to the structure of atomic nuclei. A comprehensive description of this ubiquitous phenomenon goes beyond standard shell model and cluster model frameworks. We argue that clustering is a…
We study the synchronization of coupled dynamical systems on a variety of networks. The dynamics is governed by a local nonlinear map or flow for each node of the network and couplings connecting different nodes via the links of the…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the…
A review is given on the studies of formation of light clusters and heavier fragments in heavy-ion collisions at incident energies from several tens of MeV/nucleon to several hundred MeV/nucleon, focusing on dynamical aspects and on…