Related papers: Deciphering general characteristics of residues co…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
Data-driven schemes that associate molecular and crystal structures with their microscopic properties share the need for a concise, effective description of the arrangement of their atomic constituents. Many types of models rely on…
Some remarkable generic properties, related to isostaticity and potential energy minimization, of equilibrium configurations of assemblies of rigid, frictionless grains are studied. Isostaticity -the uniqueness of the forces, once the list…
We analyze the occurrence of in-plane anisotropy in the electronic, magnetic, elastic and transport properties of more than one thousand 2D materials from the C2DB database. We identify hundreds of anisotropic materials and classify them…
High-T_c superconductors in small magnetic fields directed away from the crystal symmetry axes have been found to exhibit inhomogeneous chains of flux lines (vortices), in contrast to the usual regular triangular flux-line lattice. We…
This paper explores the problem of class-agnostic anomaly detection (AD), where the objective is to train one class-agnostic AD model that can generalize to detect anomalies in diverse new classes from different domains without any…
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…
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers…
The aggregation or clustering of proteins and other macromolecules plays an important role in the formation of large-scale molecular assemblies within cell membranes. Examples include lipid rafts and postsynaptic domains (PSDs). PSDs are…
We consider the slow and athermal deformations of amorphous solids and show how the ensuing sequence of discrete plastic rearrangements can be mapped onto a directed network. The network topology reveals a set of highly connected regions…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
The boundaries of cooperative helix--coil transitions directly affect protein allostery and conformational dynamics, yet the physical origin of the persistent one-to-two-residue assignment ambiguity at these structural interfaces remains…
A database of minima and transition states corresponds to a network where the minima represent nodes and the transition states correspond to edges between the pairs of minima they connect via steepest-descent paths. Here we construct…
A dissipative stochastic sandpile model is constructed on one and two dimensional small-world networks with different shortcut densities $\phi$ where $\phi=0$ and $1$ represent a regular lattice and a random network respectively. In the…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
Assortative mixing in networks is the tendency for nodes with the same attributes, or metadata, to link to each other. It is a property often found in social networks manifesting as a higher tendency of links occurring between people with…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…