Related papers: Receptor-ligand rebinding kinetics in confinement
Hydrodynamic interactions between particles confined in a liquid-filled linear channel are known to be screened beyond a distance comparable to the channel width. Using a simple analytical theory and lattice-Boltzmann simulations, we show…
In this paper we study a simple stochastic version of the Hopfield-Ninio kinetic proofreading model. The model is characterized by means of two parameters, the unbinding time, which depends on the binding energy between a ligand and a…
Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…
We present the results of molecular dynamics computer simulations of a binary Lennard-Jones liquid confined between two parallel rough walls. These walls are realized by frozen amorphous configurations of the same liquid and therefore the…
The existence of stable links and knots is demonstrated in three-dimensional, bistable, chemical media. The reaction-diffusion medium segregates into regions of high and low concentration separated by sharp interfaces. The interfaces repel…
Droplet deposition onto a hydrophobic surface is studied experimentally and numerically. A wide range of droplet sizes can result from the same syringe, depending strongly on the needle retraction speed. Three regimes are identified…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
Cells in multicellular organisms adhere to the extracellular matrix through two-dimensional clusters spanning a size range from very few to thousands of adhesion bonds. For many common receptor-ligand systems, the ligands are tethered to a…
Predicting protein-ligand binding affinity is an essential part of computer-aided drug design. However, generalisable and performant global binding affinity models remain elusive, particularly in low data regimes. Despite the evolution of…
We derive the boundary condition for a subdiffusive particle interacting with a reactive boundary with finite reaction rate. Molecular crowding conditions, that are found to cause subdiffusion of larger molecules in biological cells, are…
After discussing the relevance of statistical physics in molecular recognition processes, we present a schematic model for ligand-receptor association based on an Ising chain. We discuss the possible behaviors of the affinity when the…
Molecular communication (MC) allows nanomachines to communicate and cooperate with each other in a fluid environment. The diffusion-based MC is popular but is easily constrained by the transmit distance due to the severe attenuation of…
Spatial organization in metabolic pathways can arise from the interplay between enzymatic reaction kinetics and diffusion-driven instabilities. In this work we investigate how reversible enzyme--substrate binding influences pattern…
The study of the interactions of living adherent cells with mechanically stable (visco)elastic materials enables understanding and exploiting physiological phenomena mediated by cell-extracellular communication. However, insight on the…
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 analyze the influence of boundary conditions on numerical simulations of the diffusive properties of a two dimensional granular gas. We show in particular that periodic boundary conditions introduce unphysical correlations in time which…
We review the standard lock and key (LK) model for binding small ligands to larger adsorbent molecule. We discuss three levels of the traditional LK model for binding. Within this model the binding constant or the Gibbs energy of the…
Side chain flexibility is an important factor in ligand binding. In order to determine the extent to which side chain flexibility is involved in ligand binding, a knowledge-based approach was taken. A database composed of examples of…
The standard setup for single-file diffusion is diffusing particles in one dimension which cannot overtake each other, where the dynamics of a tracer (tagged) particle is of main interest. In this article we generalise this system and…
To adapt their behaviour in changing environments, cells sense concentrations by binding external ligands to their receptors. However, incorrect ligands may bind nonspecifically to receptors, and when their concentration is large, this…