Related papers: A schematic model for molecular affinity and bindi…
Experiments have shown that elasticity of disordered filamentous networks with compliant crosslinks is very different from networks with rigid crosslinks. Here, we model and analyze filamentous networks as a collection of randomly oriented…
The Ising model is a model for pairwise interactions between binary variables that has become popular in the psychological sciences. It has been first introduced as a theoretical model for the alignment between positive (+1) and negative…
Ising models describe the joint probability distribution of a vector of binary feature variables. Typically, not all the variables interact with each other and one is interested in learning the presumably sparse network structure of the…
We consider the coarsening properties of a kinetic Ising model with a memory field. The probability of a spin-flip depends on the persistence time of the spin in a state. The more a spin has been in a given state, the less the spin-flip…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…
Modulation of the properties of AMPA receptors at the post-synaptic membrane is one of the main suggested mechanisms behind synaptic plasticity in the central nervous system of vertebrates. Electrophysiological recordings of single channels…
Ising models, and the physical systems described by them, play a central role in generating entangled states for use in quantum metrology and quantum information. In particular, ultracold atomic gases, trapped ion systems, and Rydberg atoms…
Neurons subject to a common non-stationary input may exhibit a correlated firing behavior. Correlations in the statistics of neural spike trains also arise as the effect of interaction between neurons. Here we show that these two situations…
To investigate the properties of $c=1$ matter coupled to $2$d{--}gravity we have performed large-scale simulations of two copies of the Ising Model on a dynamical lattice. We measure spin susceptibility and percolation critical exponents…
Form factor representation of the correlation function of the 2D Ising model on a cylinder is generalized to the case of arbitrary disposition of correlating spins. The magnetic susceptibility on a lattice, one of whose dimensions ($N$) is…
In order to investigate the effects of connectivity and proximity in the specific heat, a special class of exactly solvable planar layered Ising models has been studied in the thermodynamic limit. The Ising models consist of repeated…
Disordered fibre networks are ubiquitous in nature and have a wide range of industrial applications as novel biomaterials. Predicting their viscoelastic response is straightforward for affine deformations that are uniform over all length…
We consider the equilibrium dynamics of Ising spin models with multi-spin interactions on sparse random graphs (Bethe lattices). Such models undergo a mean field glass transition upon increasing the graph connectivity or lowering the…
This is the second in a series of three articles about recovering the full algebraic structure of a boundary conformal field theory (CFT) from the scaling limit of the critical Ising model in slit-strip geometry. Here we study the fusion…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
We introduce varying spin strengths to the Ising model, a central pillar of statistical physics. With inhomogeneous physical systems in mind, but also anticipating interdisciplinary applications, we present the model on network structures…
This paper reports numerical studies of a compressible version of the Ising spin glass in two dimensions. Compressibility is introduced by adding a term that couples the spin-spin interactions and local lattice deformations to the standard…
We study pairwise Ising models for describing the statistics of multi-neuron spike trains, using data from a simulated cortical network. We explore efficient ways of finding the optimal couplings in these models and examine their…
We study the elastic response of rigid, wire frame particles in concentrated, glassy suspensions to a step strain by applying the simple, geometric methods developed in part I. The wire frame particles are comprised of thin, rigid rods of…