Related papers: Linking in domain-swapped protein dimers
Motivated by the existence of mobile low-energy excitations like domain walls in one dimension or gauge-charged fractionalized particles in higher dimensions, we compare quantum dynamics in the presence of weak Markovian dephasing for a…
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular…
We investigate entanglement properties of mixtures of short-range spin-s dimer coverings in lattices of arbitrary topology and dimension. We show that in one spacial dimension nearest neighbour entanglement exists for any spin $s$.…
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins.…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
Simulations of knotting and unknotting in polymers or other filaments rely on random processes to facilitate topological changes. Here we introduce a method of \textit{topological steering} to determine the optimal pathway by which a…
Quantum phase transition in dimerized antiferromagnetic Heisenberg spin chain has been studied. A staircase structure in the variation of concurrence within strongly coupled pairs with that of external magnetic field has been observed…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
We present a novel dual-head deep learning architecture for protein-protein interaction modeling that enables simultaneous prediction of binding affinity ($\Delta G$) and mutation-induced affinity changes ($\Delta\Delta G$) using only…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Confinement is an ubiquitous phenomenon when matter couples to gauge fields, which manifests itself in a linear string potential between two static charges. Although gauge fields can be integrated out in one dimension, they can mediate…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…