Related papers: A schematic model for molecular affinity and bindi…
In this work, we study and evaluate the impact of a periodic spin-lattice coupling in an Ising-like system on a 2D triangular lattice. Our proposed simple Hamiltonian considers this additional interaction as an effect of preferential phonon…
From understanding the sand on the beach to the foam on your beer, soft sphere simulations have been crucial to the study of the amorphous world around us. However, many of the materials we interact with on a daily basis aren't comprised of…
The Ising model is important in statistical modeling and inference in many applications, however its normalizing constant, mean number of active vertices and mean spin interaction -- quantities needed in inference -- are computationally…
How complex is an Ising model? Usually, this is measured by the computational complexity of its ground state energy problem. Yet, this complexity measure only distinguishes between planar and non-planar interaction graphs, and thus fails to…
Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
If we have a system of binary variables and we measure the pairwise correlations among these variables, then the least structured or maximum entropy model for their joint distribution is an Ising model with pairwise interactions among the…
The relaxation process of a diffusive ring becomes under-damped if the bias (so called affinity) exceeds a critical threshold value, aka delocalization transition. This is related to the spectral properties of the pertinent stochastic…
We describe the representation of the chemical affinity between the antigen-combining site of the immunoglobulin molecule and the antigen molecule as the probability of the two molecules existing in a bound state. Our model is based on the…
Predicting compound-protein affinity is critical for accelerating drug discovery. Recent progress made by machine learning focuses on accuracy but leaves much to be desired for interpretability. Through molecular contacts underlying…
The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…
Experimental advances in condensed matter physics and material science have enabled ready access to atomic-resolution images, with resolution of modern tools often sufficient to extract minute details of symmetry-breaking distortions such…
In this paper we study the effect of dependence on detecting a class of structured signals in Ferromagnetic Ising models. Natural examples of our class include Ising Models on lattices, and Mean-Field type Ising Models such as dense…
Motivation: The clinical efficacy of antibody therapeutics critically depends on high-affinity target engagement, yet laboratory affinity-maturation campaigns are slow and costly. In computational settings, most protein language models…
Several recent experiments in biology study systems composed of several interacting elements, for example neuron networks. Normally, measurements describe only the collective behavior of the system, even if in most cases we would like to…
Numerical data on scaling of the normalized Binder cumulant and the normalized correlation length are shown for the Thermodynamic limit regime, first for canonical Ising ferromagnet models and then for a range of Ising spin glass models. A…
Jamming is a phenomenon shared by a wide variety of systems, such as granular materials, foams, and glasses in their high density regime. This has motivated the development of a theoretical framework capable of explaining many of their…
Dynamic nonlinear (cubic) susceptibility in quantum d-dimensional Ising spin glass with short-range interactions is investigated on the basis of quantum droplet model and quantum-mechanical nonlinear response theory. Nonlinear response…
An improved linear model is developed for elasto-plastic and adhesive contact. New correlations are proposed and validated to estimate the key input parameters of the model, including contact stiffness, yield point, maximum pull-off force…
In this paper, we consider the problem of parameter sensitivity in models of complex dynamical systems through the lens of information geometry. We calculate the sensitivity of model behavior to variations in parameters. In most cases,…
We associate to each unit volume lattice of $\R^d$ the Ising model with bond variables equal to the inverse successive minima of that lattice. This induces the notion of a critical temperature for a random lattice for which integrability…