Related papers: Derangement model of ligand-receptor binding
A balance is described with Langmuir binding of weights to each side. This simple physical system, when coupled with a previously derived equation for the equivalent displacement of weight that perturbs the equilibrium of a balance, models…
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component…
Specific interactions between receptors and their target ligands in the presence of non-target ligands are crucial for biological processes such as T cell ligand discrimination. To discriminate between the target and non-target ligands,…
We analyze the stability of micro-domains of ligand-receptor bonds that mediate the adhesion of biological model membranes. After evaluating the effects of membrane fluctuations on the binding affinity of a single bond, we characterize the…
Motivated by modern applications of light detection and ranging (LIDAR), we study the model of an optical receiver based on an avalanche photo-diode (APD), followed by electronic circuitry for detection of reflected optical signals and…
The most important function of proteins may well be to bind to other biomolecules. It has long been felt that kinetic rates of bond formation and dissociation between soluble receptors and ligands might account for most features of the…
In this paper, we study the effect of dependence on detecting a class of signals in Ising models, where the signals are present in a structured way. Examples include Ising Models on lattices, and Mean-Field type Ising Models…
The adhesion of biological membranes is controlled by various types of receptor and ligand molecules. In this letter, we present a statistical-mechanical model for membranes that interact via receptor/ligand bonds of two different lengths.…
Thread-like structures are pervasive across scales, from polymeric proteins to root systems to galaxy filaments, and their characteristics can be readily investigated in the network formalism. Yet, network links usually represent only parts…
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…
Rebinding of dissociated ligands from cell surface proteins can confound quantitative measurements of dissociation rates important for characterizing the affinity of binding interactions. This can be true also for in vitro techniques such…
We investigate the theoretical foundations of the simulated tempering method and use our findings to design efficient algorithms. Employing a large deviation argument first used for replica exchange molecular dynamics [Plattner et al., J.…
A deep equilibrium model (DEQ) is implicitly defined through an equilibrium point of an infinite-depth weight-tied model with an input-injection. Instead of infinite computations, it solves an equilibrium point directly with root-finding…
We numerically investigate the necessary ingredients for reentrant behavior in the phase diagram of physical systems. Studies on the possibly simplest model that exhibits reentrance, the two-dimensional random bond Ising model, show that…
We study a mathematical model for deformation of glued elastic bodies in 2D or 3D, which is a linear elasticity system with adhesive force on the glued surface. We reveal a variational structure of the model and prove the unique existence…
We address the experimental determination of entanglement for systems made of a pair of polarization qubits. We exploit quantum estimation theory to derive optimal estimators, which are then implemented to achieve ultimate bound to…
Entanglement swapping is a key primitive for distributing entanglement across nodes in quantum networks. In standard protocols, the outcome of the intermediate measurement determines the resulting state, making the process inherently…
Accurate measurements of kinetic rate constants for interacting biomolecules is crucial for understanding the mechanisms underlying intracellular signalling pathways. The magnitude of binding rates plays a very important molecular…
We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin…
We study entanglement in dimerized Heisenberg systems. In particular, we give exact results of ground-state pairwise entanglement for the four-qubit model by identifying a Z_2 symmetry. Although the entanglements cannot identify the…