Related papers: Linear Polycatenanes from Kinetoplast Edge Loops
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 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…
The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The evolution, replication and self-assembly of this structure…
Recent experiments have elucidated the physical properties of kinetoplasts, which are chain-mail-like structures found in the mitochondria of trypanosome parasites formed from catenated DNA rings. Inspired by these studies, we use Monte…
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…
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.…
Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
Formation of random network of DNA strands is simulated on a two-dimensional triangular lattice. We investigate the size distribution of pores in the network. The results are interpreted within theory of percolation on Bethe lattice.
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…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
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…
Collagen networks provide the main structural component of most tissues and represent an important ingredient for bio-mimetic materials for bio-medical applications. Here we study the mechanical properties of stiff collagen networks derived…
Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and heavily crosslinked. Relating their large-scale dynamics to properties of their…
The elasticity of DNA catenanes, i.e. multiply linked DNA rings, is investigated using the Gauss invariant as a minimal model for topology conservation. An effective elastic free energy as a function of the distance $R$ between segments…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…
Inspired by experiments on topologically linked DNA networks, we consider the connectivity of Borromean networks, in which no two rings share a pairwise-link, but groups of three rings form inseparable triplets. Specifically, we focus on…
We study the micromechanics of collagen-I gel with the goal of bridging the gap between theory and experiment in the study of biopolymer networks. Three-dimensional images of fluorescently labeled collagen are obtained by confocal…