Related papers: Linking in domain-swapped protein dimers
The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the…
Dynamic spin correlation function of the $S=1/2$ antiferromagnetic spin chain with alternating nearest neighbor and competing next nearest neighbor interactions is studied using the numerical diagonalization method. We find characteristics…
Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to…
Strongly interacting one-dimensional fermions form an effective spin chain in the absence of an external lattice potential. We show that the exchange coefficients of such a chain may be locally tuned by properly tailoring the transversal…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
We present a simple model for the underlying structure of protein-protein pairwise interaction graphs that is based on the way in which proteins attach to each other in experiments such as yeast two-hybrid assays. We show that data on the…
We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
Confinement is a ubiquitous mechanism in nature, whereby particles feel an attractive force that increases without bound as they separate. A prominent example is color confinement in particle physics, in which baryons and mesons are…
We explore the effect of random permanent cross-links on a system of directed polymers confined between two planes with their end-points free to slide on them. We treat the cross-links as quenched disorder and we use a semimicroscopic…
Vitrimers are polymer networks that can undergo bond exchange reactions. They dynamically rearrange their structures while maintaining their overall integrity, thus resulting in unique properties such as self-healing, reprocessability,…
The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong non-linear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that…
We predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term 'promiscuity' to describe such nonspecific binding.…
Quantum entanglement is one of the most fascinating types of correlation that can be shared only among quantum systems. The Heisenberg chain is one of the simplest quantum chains which exhibits a reach entanglement feature, due to the…
Recent magnetic tweezers experiments have reported systematic deviations of the twist response of double-stranded DNA from the predictions of the twistable worm-like chain model. Here we show, by means of analytical results and computer…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
Topological entanglements are abundant, and often detrimental, in polymeric systems in biology and materials science. Here we theoretically investigate the topological simplification of knots by diffusing slip-links (SLs), which may…