Related papers: An Efficient Integrator Scheme for Sampling the (Q…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
Preparing thermal (Gibbs) states is a common task in physics and computer science. Recent algorithms mimic cooling via system-bath coupling, where the cost is determined by mixing time, akin to classical Metropolis-like algorithms. However,…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
Computing properties of molecular systems rely on estimating expectations of the (unnormalized) Boltzmann distribution. Molecular dynamics (MD) is a broadly adopted technique to approximate such quantities. However, stable simulations rely…
A scheme for measuring complex temperature partition functions of Ising models is introduced. In the context of ordered qubit registers this scheme finds a natural translation in terms of global operations, and single particle measurements…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
We introduce a method that ensures efficient computation of one-dimensional quantum systems with long-range interactions across all temperatures. Our algorithm operates within a quasi-polynomial runtime for inverse temperatures up to…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Very recently, interferometric methods have been proposed to measure the full statistics of work performed on a driven quantum system [Dorner et al. Phys. Rev. Lett. 110 230601 (2013)] and [Mazzola et al. Phys. Rev. Lett. 110 230602…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
An investigation to optimize the application of the third-generation charge optimized many-body (COMB3) interatomic potential and associated input parameters was carried out through the study of solid-liquid interactions in classical…
By leveraging the Variational Quantum Eigensolver (VQE), the ``quantum equation of motion" (qEOM) method established itself as a promising tool for quantum chemistry on near term quantum computers, and has been used extensively to estimate…
A simple deterministic and time reversal invariant type of thermostat is proposed to be used for computer simulations of classical systems. It acts on collisions with the walls of the container exclusively. It maps the incoming and outgoing…
The accuracy of molecular simulations is fundamentally limited by the interatomic potentials that govern atomic interactions. Traditional potential development, which relies heavily on ab initio calculations, frequently struggles to…
The Stoermer-Verlet-leapfrog group of integrators commonly used in molecular dynamics simulations has long become a textbook subject and seems to have been studied exhaustively. There are, however, a few striking effects in performance of…
In this article, we focus on the sampling of the configurational Gibbs-Boltzmann distribution, that is, the calculation of averages of functions of the position coordinates of a molecular $N$-body system modelled at constant temperature. We…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…