Related papers: Structured Random Binding: a minimal model of prot…
Fracture processes in heterogeneous materials comprise a large number of disordered spatial degrees of freedom, representing the dynamical state of a sample over the entire domain of interest. This complexity is usually modeled directly,…
Borromean rings and Borromean binding, a class of intriguing phenomena as three objects are linked (bound) together while any two of them are unlinked (unbound), widely exist in nature and have been found in systems of biology, chemistry…
This paper studies the controllability of networked relative coupling systems (NRCSs), in which subsystems are of fixed high-order linear dynamics and coupled through relative variables depending on their neighbors, from a structural…
The abundance of data about social relationships allows the human behavior to be analyzed as any other natural phenomenon. Here we focus on balance theory, stating that social actors tend to avoid establishing cycles with an odd number of…
Theoretical work has shed light on the phase behavior of idealized mixtures of many components with random interactions. But typical mixtures interact through particular physical features, leading to a structured, non-random interaction…
Artificial neural networks used for reinforcement learning are structurally rigid, meaning that each optimized parameter of the network is tied to its specific placement in the network structure. It also means that a network only works with…
We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…
Models for near-rigid shape matching are typically based on distance-related features, in order to infer matches that are consistent with the isometric assumption. However, real shapes from image datasets, even when expected to be related…
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…
Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between…
The Restricted Boltzmann Machine (RBM), an important tool used in machine learning in particular for unsupervized learning tasks, is investigated from the perspective of its spectral properties. Starting from empirical observations, we…
Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81]…
Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…
It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other…
Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, gene expression, etc. Accurate prediction…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Understanding the structural origins of the properties of amorphous materials remains one of the most important challenges in structural science. In this study we demonstrate that local 'structural simplicity', embodied by the degree to…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
Quenched disorders can strongly influence the physical properties of quantum many-body systems. The real-space strong-disorder renormalization group (SDRG) analysis has shown that the spin-1/2 random Heisenberg chain is controlled by the…