Related papers: Derangement model of ligand-receptor binding
A quantum quench is the simplest protocol to investigate nonequilibrium many-body quantum dynamics. Previous studies on the entanglement properties of quenched quantum many-body systems mainly focus on the growth of entanglement entropy.…
Entanglement plays a prominent role in the study of condensed matter many-body systems: Entanglement measures not only quantify the possible use of these systems in quantum information protocols, but also shed light on their physics.…
Quantum many-body systems realise many different phases of matter characterised by their exotic emergent phenomena. While some simple versions of these properties can occur in systems of free fermions, their occurrence generally implies…
In this article, we study the kinetics of reversible ligand binding to receptors on a spherical cell surface using a self-consistent stochastic theory. Binding, dissociation, diffusion and rebinding of ligands are incorporated into the…
The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor…
Targeted drug delivery relies on two physical processes: the selective binding of a therapeutic particle to receptors on a specific cell membrane, followed by transport of the particle across the membrane. In this article, we address some…
We extend the Bell forced dissociation rate model to take account into dynamic disorder. The motivation of the present work is from the recent forced dissociation experiments of the adhesive receptor-ligand complexes, in which some…
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…
The reduced density matrix of many-body systems possessing an additive conserved quantity can be decomposed in orthogonal sectors which can be independently analyzed. Recently, these have been proven to equally contribute to entanglement…
Cells adapt to changing environments by sensing ligand concentrations using specific receptors. The accuracy of sensing is ultimately limited by the finite number of ligand molecules bound by receptors. Previously derived physical limits to…
Receptor-ligand binding is a critical first step in signal transduction and the duration of the interaction can impact signal generation. In mammalian cells, clustering of receptors may be facilitated by heterogeneous zones of lipids, known…
We consider a coupled bulk-surface system of partial differential equations with nonlinear coupling modelling receptor-ligand dynamics. The model arises as a simplification of a mathematical model for the reaction between cell surface…
We compute absolute binding affinities for two ligands bound to the FKBP protein using non-equilibrium unbinding simulations. The methodology is straight-forward, requiring little or no modification to many modern molecular simulation…
DNA-encoded library (DEL) screening has revolutionized the detection of protein-ligand interactions through read counts, enabling rapid exploration of vast chemical spaces. However, noise in read counts, stemming from nonspecific…
The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is…
We study experimentally accessible lower bounds on entanglement measures based on entropic uncertainty relations. Experimentally quantifying entanglement is highly desired for applications of quantum simulation experiments to fundamental…
Accurate prediction of protein-ligand binding affinity is crucial for rapid and efficient drug development. Recently, the importance of predicting binding affinity has led to increased attention on research that models the three-dimensional…
It is widely accepted that the dynamic of entanglement in presence of a generic circuit can be predicted by the knowledge of the statistical properties of the entanglement spectrum. We tested this assumption by applying a Metropolis-like…
Recent advancements in protein docking site prediction have highlighted the limitations of traditional rigid docking algorithms, like PIPER, which often neglect critical stochastic elements such as solvent-induced fluctuations. These…
Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…