Related papers: Single-Molecule Morphology of Topologically Digest…
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked…
Assemblies of ring DNA and proteins, such as kinetoplast DNA (kDNA) and the chainmail-like network of the HK97 bacteriophage capsid, form "Olympic" topologies that govern the dynamics of gene-regulatory proteins, cellular metabolites, and…
All life forms are miraculous, but some are more inexplicable than others. Trypanosomes are by far one of the most puzzling organisms on Earth: their mitochondrial genome, also called kinetoplast DNA (kDNA) forms an Olympic-ring-like…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…
We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a…
A complexity-theoretic approach to studying biological networks is proposed. A simple graph representation is used where molecules (DNA, RNA, proteins and chemicals) are vertices and relations between them are directed and signed…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
We study networks constructed from gene expression data obtained from many types of cancers. The networks are constructed by connecting vertices that belong to each others' list of K-nearest-neighbors, with K being an a priori selected…
Neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems. Here, we investigate the viscoelasticity of DNA nanostar…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
A complex network is a condensed representation of the relational topological framework of a complex system. A main reason for the existence of such networks is the transmission of items through the entities of these complex systems. Here,…
In this work we present a computational study of the Kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation…
The interplay between topology and dynamics in complex networks is a fundamental but widely unexplored problem. Here, we study this phenomenon on a prototype model in which the network is shaped by a dynamical variable. We couple the…
We evolve network topology of an asymmetrically connected threshold network by a simple local rewiring rule: quiet nodes grow links, active nodes lose links. This leads to convergence of the average connectivity of the network towards the…
Triply-periodic networks (TPNs), like the well-known gyroid and diamond network phases, abound in soft matter assemblies, from block copolymers (BCPs), lyotropic liquid crystals and surfactants to functional architectures in biology. While…