Related papers: Linking in domain-swapped protein dimers
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…
We study spectral and transport properties of one-dimensional tight-binding $\mathcal{PT}$-symmetric chains with alternating couplings. Based on the transfer matrix method, we have analytically developed the expressions for the transmission…
We explore the ground-state physics of two-dimensional spin-$1/2$ $U(1)$ quantum link models, one of the simplest non-trivial lattice gauge theories with fermionic matter within experimental reach for quantum simulations. Whereas in the…
Protein molecules can be approximated by discrete polygonal chains of amino acids. Standard topological tools can be applied to the smoothening of the polygons to introduce a topological classification of proteins, for example, using the…
We present a one-dimensional tight-binding chain of two-level systems coupled only through common dissipative Markovian reservoirs. This quantum chain can demonstrate anomalous thermodynamic behavior contradicting Fourier law. Population…
We observe the low-lying excitations of a molecular dimer formed by two electrons in a GaAs semiconductor quantum dot in which the number of confined electrons is tuned by optical illumination. By employing inelastic light scattering we…
Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate three-dimensional structures is one of the remarkable examples of biological self-organization. We investigated native state structures of…
Protein domains are highly conserved functional units of proteins. Because they carry functionally significant information, the majority of the coding disease variants are located on domains. Additionally, domains are specific units of the…
Central to understanding membrane bound cell signaling is to quantify how the membrane ultra-structure consisting of transient spatial domains modulates signaling and how the signaling influences this ultra-structure. Yet, measuring the…
Machine learning methods are being actively considered as a new tool of describing many body physics. However, so far, their capabilities has been only demonstrated in previously studied models, such as e.g. Ising model. Here, we consider a…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…
We examine the ground state and the excitations of an one-dimensional Heisenberg spin 1/2 antiferromagnet with alternating dimers and four-spin plaquettes (dimer-plaquette chain). The properties of the system depend on the competing dimer…
The statistical mechanics of a ribbon polymer made up of two semiflexible chains is studied using both analytical techniques and simulation. The system is found to have a crossover transition at some finite temperature, from a type of short…
We develop a linked cluster method to calculate the spectral weights of many-particle excitations at zero temperature. The dynamical structure factor is expressed as a sum of exclusive structure factors, each representing contributions from…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric G\=o-like models with a coarse-grained C$_\alpha$ chain representation. We…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Entangled ring polymers, along with blends of ring and linear polymers, continue to be a topic of great interest and debate due to the conflicting experimental results in the literature as well as the difficulty of producing entangled…
The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction…