相关论文: Single-Molecule Morphology of Topologically Digest…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
Many complex systems can be described in terms of networks of interacting units. Recent studies have shown that a wide class of both natural and artificial nets display a surprisingly widespread feature: the presence of highly heterogeneous…
In biological evolution complex neural structures grow from a handful of cellular ingredients. As genomes in nature are bounded in size, this complexity is achieved by a growth process where cells communicate locally to decide whether to…
Two different types of directed networks are investigated, transcriptional regulation networks and neural networks. The directed network structure are studied and also shown to reflect the different processes taking place on the networks.…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well-documented example of sequence…
Motivated by the relevance of higher-order interactions in quantum physics and materials science at the nanoscale, recently a model has been introduced for new classes of networks that grow by the geometrically constrained aggregation of…
Internet, social media, neuronal or blood vessel are organized in complex networks. These networks are characterized by several quantities such as the underlying graph connectivity (topology), how they grow in time, scaling laws or by the…
The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent $\nu$ is topologically invariant and equal to the SAW…
In this article we investigate the topological changes undergone by trajectory networks as a consequence of progressive geographical infiltration. Trajectory networks, a type of knitted network, are obtained by establishing paths between…
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
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…
Atomic Force Microscopy analysis is employed to study the geometrical and topological properties of $3000$kbp DNA molecules fixed in mica substrates with $MgCl_{2}$. We found that the aggregates on the substrate surface for certain salt…
RNA molecules are single-stranded analogues of DNA that can fold into various structures which influence their biological function within the cell. RNA structures can be modelled combinatorially in terms of a certain type of graph called an…