Related papers: Linking in domain-swapped protein dimers
Two headed motor proteins, such as kinesin and dynein, hidrolyze environmental ATP in order to propel unidirectionally along cytoskeletal filaments such as microtubules. In the case of kinesin, protein heads bind primarily on the alpha…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
We investigate entanglement of spin pairs in alternating open spin chains in the equilibrium state in an external magnetic field. We calculate the reduced density matrix of spin pairs and estimate the concurrence with Wootter's criteria.…
Confinement properties of the $1+1$ Schwinger model can bestudied by computing the string tension between two charges. It is finite (vanishing) if the fermions are massive (massless) corresponding to the occurrence of confinement…
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…
For a family of integer-valued height functions defined over the faces of planar graphs, we establish a relation between the probability of connection by level sets and the spin-spin correlations of the dual $O(2)$ symmetric spin models…
We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
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…
We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely,…
Motivated by the hinge structure present in protein chains and other molecular conformations, we study the singularities of certain maps associated to body-and-hinge and panel-and-hinge chains. These are sequentially articulated systems…
Numerical studies of the reduced density matrix of a gapped spin-1/2 Heisenberg antiferromagnet on a two-leg ladder find that it has the same form as the Gibbs density matrix of a gapless spin-1/2 Heisenberg antiferromagnetic chain at a…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
We investigate the static and dynamic properties of dendrimers diffusing through a network of linear associative polymers using coarse-grained Brownian dynamics simulations. Both dendrimers and network chains are modelled as bead-spring…
The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral…
Recent findings suggest that shell protein distribution and morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component…