Related papers: Derangement model of ligand-receptor binding

We present TerraBind, a foundation model for protein-ligand structure and binding affinity prediction that achieves 26-fold faster inference than state-of-the-art methods while improving affinity prediction accuracy by $\sim$20\%. Current…

We revisit the problem of efficiently learning the underlying parameters of Ising models from data. Current algorithmic approaches achieve essentially optimal sample complexity when given i.i.d. samples from the stationary measure and the…

Ligand unbinding is mediated by the free energy change, which has intertwined contributions from both energy and entropy. It is important but not easy to quantify their individual contributions. We model hydrophobic ligand unbinding for two…

We introduce a protocol based on optimal control to drive many body quantum systems into long-lived entangled states, protected from decoherence by big energy gaps, without requiring any apriori knowledge of the system. With this approach…

Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…

We use recently developed strong-coupling expansion methods to study the two-particle spectra for the frustrated alternating Heisenberg model, consisting of an alternating nearest neighbor antiferromagnetic exchange and a uniform second…

We present several ordering mechanisms in diblock copolymers. For temperatures above the order-disorder temperature and in the weak segregation regime, a linear response theory is presented which gives the polymer density in the vicinity of…

Coherent enhancement is a powerful mechanism for improving the sensitivity of a wide range of detectors, but its practical use is often limited by the difficulty of preparing the required quantum states. We show that this difficulty has a…

Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…

We present a procedure inspired by dense coding, which enables a highly efficient transmission of information of a continuous nature. The procedure requires the sender and the recipient to share a maximally entangled state. We deal with the…

Entanglement does not correspond to any observable and its evaluation always corresponds to an estimation procedure where the amount of entanglement is inferred from the measurements of one or more proper observables. Here we address…

We study geometrical aspects of entanglement, with the Hilbert--Schmidt norm defining the metric on the set of density matrices. We focus first on the simplest case of two two-level systems and show that a ``relativistic'' formulation leads…

Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…

Recent work has shown that use of quantum feedback can significantly enhance both the speed and success rate of measurement-based remote entanglement generation, but it is generally unknown what feedback protocols are optimal for these…

Living cells often need to measure chemical concentrations that vary in time. To this end, they deploy many resources, e.g. receptors, downstream signaling molecules, time and energy. Here, we present a theory for the optimal design of a…

We study the boundary regularity properties and derive a priori pointwise supremum estimates of weak solutions and their derivatives in terms of suitable weighted $L^2$-norms for a class of degenerate parabolic equations that satisfy…

Separability problem, to decide whether a given state is entangled or not, is a fundamental problem in quantum information theory. We propose a powerful and computationally simple separability criterion, which allows us to detect the…

Using the density matrix renormalization group algorithm, we investigate the lattice model for spinless fermions in one dimension in the presence of a strong interaction and disorder. The phase sensitivity of the ground state energy is…

We describe the entanglement of two indistinguishable delocalized spin-$\frac{1}{2}$ particles in the simplest spatial configuration of three spatial modes with the constraint that at most one particle occupy each mode. It is show that this…

The problem of rigid body pose estimation is treated in discrete-time via discrete Lagrange-d'Alembert principle and discrete Lyapunov methods. The position and attitude of the rigid body are to be estimated simultaneously with the help of…