Related papers: Derangement model of ligand-receptor binding
The phenomenon of residential segregation was captured by Schelling's famous segregation model where two types of agents are placed on a grid and an agent is content with her location if the fraction of her neighbors which have the same…
The complicated ways in which electrons interact in many-body systems such as molecules and materials have long been viewed through the lens of local electron correlation and associated correlation functions. However, quantum information…
A goodness-of-fit test for the fitting of a parametric model to data obtained from a detector with finite resolution and limited acceptance is proposed. The parameters of the model are found by minimization of a statistic that is used for…
We determine a general upper bound for the steady-state entanglement achievable by continuous feedback for systems of any number of bosonic degrees of freedom. We apply such a bound to the specific case of parametric interactions - the most…
We investigate both analytically and by numerical simulation the kinetics of a microscopic model of hard rods adsorbing on a linear substrate, a model which is relevant for compaction of granular materials. The computer simulations use an…
We examine the real space renormalization group method of finding \textit{excited eigenstate} (RSRG-X) of the XX spin-1/2 chain, from entanglement perspectives. Eigenmodes of entanglement Hamiltonian, especially the maximally entangled mode…
The entanglement of two qubits, each defined as an effective two-level, spin 1/2 system, is investigated for the case that the qubits interact via a Heisenberg XY interaction and are subject to decoherence due to population relaxation and…
In this paper we propose and analyze a distributed algorithm for achieving globally optimal decisions, either estimation or detection, through a self-synchronization mechanism among linearly coupled integrators initialized with local…
The multiparticle entanglement in the Lipkin-Meshkov-Glick model has been discussed extensively in this paper. Measured by the global entanglement and its generalization, our calculation shows that the multiparticle entanglement can…
We investigate system-environment correlations based on the exact dynamics of a qubit and its environment in the framework of pure decoherence (phase damping). We focus on the relation of decoherence and the build-up of system-reservoir…
Protein fibril accumulation at interfaces is an important step in many physiological processes and neurodegenerative diseases as well as in designing materials. Here we show, using $\beta$-lactoglobulin fibrils as a model, that semiflexible…
Transient bonds between fast linkers and slower particles are widespread in physical and biological systems. In spite of their diverse structure and function, a commonality is that the linkers diffuse on timescales much faster compared to…
This paper develops an active sensing framework for designing the transmit and receive beamformers of a multiple-input multiple-output (MIMO) radar system. In the proposed technique, the beamformers are adaptively designed in each sensing…
We consider the quantum dynamics of a many-fermion system in $\mathbb R^d$ with an ultraviolet regularized pair interaction as previously studied in [M. Gebert, B. Nachtergaele, J. Reschke, and R. Sims, Ann. Henri Poincar\'e 21.11 (2020)].…
This paper presents efficient algorithms for solving the problem of aligning a protein structure template to a query amino-acid sequence, known as protein threading problem. We consider the problem as a special case of graph matching…
Using the negativity as an entanglement measure, we investigate the possible amount of remotely prepared entanglement. For two identical isotropic states on two-qudit systems 12 and 34, we calculate the average amount of entanglement…
We observe the emergence of a disorder-induced insulating state in a strongly interacting atomic Fermi gas trapped in an optical lattice. This closed quantum system free of a thermal reservoir realizes the disordered Fermi-Hubbard model,…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
In this PhD thesis, several aspects regarding maximal entanglement are analyzed. In the first chapter, Bell Inequalities are analyzed from an operational perspective as well as novel Bell inequalities are obtained together with their…
Binding affinity optimization is crucial in early-stage drug discovery. While numerous machine learning methods exist for predicting ligand potency, their comparative efficacy remains unclear. This study evaluates the performance of…