Related papers: Topological interactions in systems of mutually in…
In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby…
We study one-dimensional, interacting, gapped fermionic systems described by variants of the Peierls-Hubbard model and characterize their phases via a topological invariant constructed out of their Green's functions. We demonstrate that the…
Simulations in which a globular ring polymer with delocalized knots is separated in two interacting loops by a slipping link, or in two non-interacting globuli by a wall with a hole, show how the minimal crossing number of the knots…
Here we analyze the topology of the network formed by the minima and transition states on the potential energy landscape of small clusters. We find that this network has both a small-world and scale-free character. In contrast to other…
The dual role played by symmetry in many-body physics manifests itself through two fundamental mechanisms: spontaneous symmetry breaking and topological symmetry protection. These two concepts, ubiquitous in both condensed matter and high…
Given discrete degrees of freedom (spins) on a graph interacting via an energy function, what can be said about the energy local minima and associated inherent structures? Using the lid algorithm in the context of a spin glass energy…
Ring polymers are prevalent in natural and engineered systems, including circular bacterial DNA, crown ethers for cation chelation, and mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and…
Previous efforts in complex networks research focused mainly on the topological features of such networks, but now also encompass the dynamics. In this Letter we discuss the relationship between structure and dynamics, with an emphasis on…
In this work a new strategy is proposed in order to build analytic and microscopic models of fluctuating polymer rings subjected to topological constraints. The topological invariants used to fix these constraints belong to a wide class of…
Many real-world complex systems including human interactions can be represented by temporal (or evolving) networks, where links activate or deactivate over time. Characterizing temporal networks is crucial to compare such systems and to…
We consider membranes adhered through specific receptor-ligand bonds. Thermal undulations of the membrane induce effective interactions between adhesion sites. We derive an upper bound to the free energy that is independent of interaction…
We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain…
In polymer physics it is typically assumed that excluded volume interactions are effectively screened in polymer melts. Hence, chains could be described by an effective random walk without excluded volume interactions. In this letter, we…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
Topological effects typically discussed in the context of quantum physics are emerging as one of the central paradigms of physics. Here, we demonstrate the role of topology in energy transport through dimerized micro- and nano-mechanical…
We theoretically study the emergence of topological magnons in electron-magnon coupled systems. The magnon dispersion in a ferromagnet usually possesses an effective time reversal symmetry in the absence of Dzyaloshinskii-Moriya (DM)…
We present our recent work on stochastic particle systems on complex networks. As a noninteracting system we first consider the diffusive motion of a random walker on heterogeneous complex networks. We find that the random walker is…
In the last twenty years network science has proven its strength in modelling many real-world interacting systems as generic agents, the nodes, connected by pairwise edges. Yet, in many relevant cases, interactions are not pairwise but…
We numerically examine the nonlinear rubber elasticity of topologically constrained polymer networks. We propose a simple and effective model based on Graessley and Pearson's topological model (GP model) for describing the topological…
A system of $N$ interacting objects with internal degrees of freedom is considered. Derivation of system of equations for the description of two interacting objects with spin is given. Relations between the parameters describing subsystems…