Related papers: Topological interactions in DNA catenanes
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
DNA is an essential molecule central to the survival and propagation of life, it was imperative to investigate possible electromagnetic properties inherent to it, such as the existence of any non-trivial interactions of this molecule with…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
We analyze the coherent dynamics of excitons in three dimensional topologically disordered networks with traps. If the interactions between the nodes of the network are long ranged, i.e., algebraically decaying as a function of the distance…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Polymer entanglements lead to complicated topological constraints and interactions between neighbouring chains in a dense solution or melt. Entanglements can be treated in a mean field approach, within the famous reptation model, since they…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
We study expanding circle maps interacting in a heterogeneous random network. Heterogeneity means that some nodes in the network are massively connected, while the remaining nodes are only poorly connected. We provide a probabilistic…
Using tools and concepts from contact topology we show that non-vanishing twist implies conservation of the layer structure in cholesteric liquid crystals. This leads to a number of additional topological invariants for cholesteric…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
Complex networks are used to depict topological features of complex systems. The structure of a network characterizes the interactions among elements of the system, and facilitates the study of many dynamical processes taking place on it.…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
We present a novel, self-consistent and robust theoretical model to investigate elastic interactions between topological defects in liquid crystal shells. Accounting for the non-concentric nature of the shell in a simple manner, we are able…
Atomically precise graphene nanoribbons (GNRs) have emerged as promising candidates for nanoelectronic applications due to their widely tunable energy band gaps resulting from lateral quantum confinement and edge effects. Here we report on…
We study the interaction between two cracks propagating quasistatically during the tearing of a thin brittle sheet. We show that the cracks attract each other following a path described by a power law resulting from the competition between…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
The dynamics of a single chain tethered to an interface and in contact with a cross-linked network is examined numerically. When the network is put in contact with the tethered chain, the chain moves with dynamics that are highly…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Experimental realizations of such systems include colloids grafted with complementary single-stranded DNA (ssDNA), and particles…
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…
Evolutionary mechanism in a self-organized system cause some functional changes that force to adapt new conformation of the interaction pattern between the components of that system. Measuring the structural differences one can retrace the…