Related papers: Derangement model of ligand-receptor binding
This article considers a class of disordered mean-field combinatorial optimization problems. We focus on the Gibbs measure, where the inverse temperature does not vary with the size of the graph and the edge weights are sampled from a…
We present a new scheme to efficiently establish entanglement between optical modes in a time-multiplexed coherent Ising machine (CIM) by means of nonlocal measurement and feedback. We numerically simulate and evaluate the generation of…
In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…
What entanglement is present in naturally occurring physical systems at thermal equilibrium? Most such systems are intractable and it is desirable to study simple but realistic systems which can be solved. An example of such a system is the…
We develop a recently-proposed mapping of the two-dimensional Ising model with random exchange (RBIM), via the transfer matrix, to a network model for a disordered system of non-interacting fermions. The RBIM transforms in this way to a…
We train machine learning algorithms to infer the entanglement structure of disordered long-range interacting quantum spin chains by learning from the strong disorder renormalisation group (SDRG) method. The system consists of…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
In a recent publication, we have discussed the effects of boundary conditions in finite quantum systems and their connection with symmetries. Focusing on the one-dimensional Hubbard Hamiltonian under twisted boundary conditions, we have…
Detection and quantification of entanglement in quantum resources are two key steps in the implementation of various quantum-information processing tasks. Here, we show that Bell-type inequalities are not only useful in verifying the…
The unbinding process of a protein-ligand complex of major biological interest was investigated by means of a computational approach at atomistic classical mechanical level. An energy minimisation-based technique was used to determine the…
We formulate a general family of entanglement criteria for multipartite systems. Fisher information criteria compare the sensitivity to unitary rotations with the variances of suitable local observables. Generalized squeezing-type criteria…
We propose a tensor network method for investigating strongly disordered systems that is based on an adaptation of entanglement renormalization [G. Vidal, Phys. Rev. Lett. 99, 220405 (2007)]. This method makes use of the strong disorder…
We consider a general class of two-dimensional spin systems, with continuous but not necessarily smooth, possibly long-range, $O(N)$-symmetric interactions, for which we establish algebraically decaying upper bounds on spin-spin…
Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability…
Some cells have to take decision based on the quality of surroundings ligands, almost irrespective of their quantity, a problem we name "absolute discrimination". An example of absolute discrimination is recognition of not-self by immune T…
This paper presents the methods that have participated in the SHREC 2022 contest on protein-ligand binding site recognition. The prediction of protein-ligand binding regions is an active research domain in computational biophysics and…
Recovering properties of correlation functions is typically challenging. On one hand, experimentally, it requires measurements with a temporal resolution finer than the system's dynamics. On the other hand, analytical or numerical analysis…
In this paper, we discuss the entanglement properties of graph-diagonal states, with particular emphasis on calculating the threshold for the transition between the presence and absence of entanglement (i.e. the separability point). Special…
We perform both analytical and numerical studies of the one-dimensional tight-binding Hamiltonian with stochastic uncorrelated on-site energies and non-fluctuating long-range hopping integrals . It was argued recently [A. Rodriguez at al.,…
The binding of a ligand molecule to a protein is often accompanied by conformational changes of the protein. A central question is whether the ligand induces the conformational change (induced-fit), or rather selects and stabilizes a…