Related papers: Linking in domain-swapped protein dimers
Polymers are an effective test-bed for studying topological constraints in condensed matter due to a wide array of synthetically-available chain topologies. When linear and ring polymers are blended together, emergent rheological properties…
Topological invariants such as winding numbers and linking numbers appear as charges of topological solitons in diverse nonlinear physical systems described by a unit vector field defined on two and three dimensional manifolds. While the…
We establish a one-to-one correspondence between one-sided and two-sided regular systems of conditional probabilities on the half-line that preserves the associated chains and Gibbs measures. As an application, we determine uniqueness and…
Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors.…
Recent electronic transport experiments using metallic contacts attached to proteins identified some 'stylized facts' which contradict conventional wisdom that increasing either the spatial distance between the electrodes or the temperature…
Confinement is an intriguing phenomenon prevalent in condensed matter and high-energy physics. Exploring its effect on the far-from-equilibrium criticality of quantum many-body systems is of great interest both from a fundamental and…
A linear spin wave analysis of dimerization of alternating Heisenberg system with spins $s_{1}$ and $s_{2}$ on linear chain as well as square lattice is presented. Among the several possible dimerized configurations considered in two…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
A directed graph $G$ is $\textit{intrinsically linked}$ if every embedding of that graph contains a non-split link $L$, where each component of $L$ is a consistently oriented cycle in $G$. A $\textit{tournament}$ is a directed graph where…
Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…
Mechanical unfolding of several domains of calmodulin and titin is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. It is shown that this simple model captures the experimentally observed…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
We study the effect of a coupling between two motor domains in highly-processive motor protein complexes. A simple stochastic discrete model, in which the two parts of the protein molecule interact through some energy potential, is…
Sufficiently strong inter-site interactions in extended-Hubbard and XXZ spin models result in dynamically-bound clusters at neighboring sites. We show that the dynamics of these clusters in two-dimensional lattices is remarkably different…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
We model proteins with intramolecular bonds, such as disulfide bridges, using the concept of bonded knots -- closed loops in three-dimensional space equipped with additional bonds that connect different segments of the knot. We extend the…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…