Related papers: Coarse-Grained Geometric Quantum Dynamics in the T…
Molecular docking is a critical computational method in drug discovery used to predict the binding conformation and orientation of a ligand within a protein's binding site. Mapping this challenge onto a graph-based problem, specifically the…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…
An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables, the…
We establish and analyse the performance and resource requirements of an end-to-end fault-tolerant quantum algorithm for computing the absorption spectrum and population dynamics of photoexcited pyrazine. The quantum circuit construction…
Over the last two years, the canonical approach to quantum gravity based on connections and triads has been put on a firm mathematical footing through the development and application of a new functional calculus on the space of gauge…
We demonstrate that a numerical linked cluster expansion method is a powerful tool to calculate quantum dynamics. We calculate the dynamics of the magnetization and spin correlations in the two-dimensional transverse field Ising and XXZ…
Coarse-grained descriptions can be used to account for physical processes in which information is lost or not entirely accessible. In this paper, we start by proposing a connection between effective, coarse-grained descriptions of quantum…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We apply a temporal edge prediction model for weighted dynamic graphs to predict time-dependent changes in molecular structure. Each molecule is represented as a complete graph in which each atom is a vertex and all vertex pairs are…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
First-quantized, real-space formulations of quantum chemistry on quantum computers are appealing: qubit count scales logarithmically with spatial resolution, and Coulomb operators achieve quadratic instead of quartic computational scaling…
We study the non-equilibrium dynamics of the dissipative quantum East model via numerical tensor networks. We use matrix product states to represent evolution under quantum-jump unravellings for sizes beyond those accessible to exact…
We use machine learning to enable large-scale molecular dynamics (MD) of a correlated electron model under the Gutzwiller approximation scheme. This model exhibits a Mott transition as a function of on-site Coulomb repulsion $U$. The…
We introduce a new geometric framework for relativistic particle dynamics based on contact geometry and suitable for treating dissipative processes like particle decay. The dynamics is formulated on a nine--dimensional extended phase space…
Quantum collision models are receiving increasing attention as they describe many nontrivial phenomena in dynamics of open quantum systems. In a general scenario of both fundamental and practical interest, a quantum system repeatedly…
A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is…
Conical intersections are ubiquitous in chemistry and physics, often governing processes such as light harvesting, vision, photocatalysis, and chemical reactivity. They act as funnels between electronic states of molecules, allowing rapid…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…