Related papers: A schematic model for molecular affinity and bindi…
We theoretically consider specific adhesion of a fluctuating membrane to a hard substrate via the formation of bonds between receptors attached to the substrate and ligands in the membrane. By integrating out the degrees of freedom of the…
The statistics of critical spin-spin correlation functions in Ising systems with non-frustrated disorder are investigated on a strip geometry, via numerical transfer-matrix techniques. Conformal invariance concepts are used, in order to…
The Ising model, in presence of an external magnetic field, is isomorphic to a model of localized interacting particles satisfying the Fermi statistics. By using this isomorphism, we construct a general solution of the Ising model which…
Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug design and protein design. Based on large scale data sets, we show that protein…
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 method for calculation of the correlation functions of the Ising-type systems with short-range interaction and with arbitrary value of spin is developed within cluster approximation. For the Ising model (spin $S^z=\pm1$) the expressions…
Finite 3D Ising ferromagnets are studied in periodic magnetic fields both by computer simulations and mean-field theoretical approaches. The phenomenon of stochastic resonance is revealed. The characteristic peak obtained for the…
We consider the three-dimensional Ising model slightly below its critical temperature, with boundary conditions leading to the presence of an interface. We show how the interfacial properties can be deduced starting from the particle modes…
Enormous enhancement in the viscosity of a liquid near its glass transition is generally connected to the growing many-body static correlations near the transition, often coined as `amorphous ordering'. Estimating the length scales of such…
A self-consistent model is developed to investigate attachment / detachment kinetics of two soft, deformable microspheres with irregular surface and coated with flexible binding ligands. The model highlights how the microscale binding…
We study the critical Ising model on the square lattice in bounded simply connected domains with + and free boundary conditions. We relate the energy density of the model to a fermionic observable and compute its scaling limit by discrete…
We study the two-filament insulin fibril's structure by incorporating recent simulation results and mechanical measurements. Our investigation suggests that the persistence length measurement correlates well with the previously proposed…
A class of random graphs is introduced and studied. The graphs are constructed in an algorithmic way from five motifs which were found in [Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., Alon U., Science, 2002, 298, 824-827].…
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…
We report an effective functional form for the spin-spin correlation function of the 2D Ising model as a function of temperature and field. Although the Ising model has been well studied, no analytical result for the spin-spin correlation…
Using explicit-water molecular dynamics (MD) simulations of a generic pocket-ligand model we investigate how chemical and shape anisotropy of small ligands influences the affinities, kinetic rates and pathways for their association to…
A spin-$s$ variable-range interacting Ising model may display qualitatively different behaviors depending on the fall-off rate of the interactions, as already seen in equilibrium studies of spin-1/2 systems. We propose a dynamical method…
We investigate the performance of neural networks in identifying critical behaviour in the 2D Ising model with next-to-nearest neighbour interactions. We train DNN and CNN based classifiers on the Ising model configurations with nearest…
A novel statistical model for the cooperative binding of monomeric ligands to a linear lattice is developed to study the interaction of ionic surfactant molecules with flexible polyion chain in dilute solution. Electrostatic binding of a…
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…