Related papers: Roadmap for Molecular Benchmarks in Nonadiabatic D…

To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…

In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…

Electron transfer is an important and fundamental process in chemistry, biology and physics, and has received significant attention in recent years. Perhaps one of the most intriguing questions concerns with the realization of the…

We introduce a novel computational framework for excited-states molecular quantum dynamics simulations driven by quantum computing-based electronic-structure calculations. This framework leverages the fewest-switches surface-hopping method…

Strong coupling of molecules to the vacuum field of micro cavities can modify the potential energy surfaces opening new photophysical and photochemical reaction pathways. While the influence of laser fields is usually described in terms of…

We present a general concept to accelerate non-relativistic charged particles. Our concept employs an adiabatically-tapered dielectric-lined waveguide which supports accelerating phase velocities for synchronous acceleration. We propose an…

All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…

The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a models' dynamics over a large parameter space…

Mathematical modelling is a widely used approach to understand and interpret clinical trial data. This modelling typically involves fitting mechanistic mathematical models to data from individual trial participants. Despite the widespread…

The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…

Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…

Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…

A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…

Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as…

The standard wave function approach for the treatment of neutrino oscillations fails in situations where quantum ensembles at a finite temperature with or without an interacting background plasma are encountered. As a first step to treat…

Proteins are made of atoms constantly fluctuating, but can occasionally undergo large-scale changes. Such transitions are of biological interest, linking the structure of a protein to its function with a cell. Atomic-level simulations, such…

We extend the DeePMD neural network architecture to predict electronic structure properties necessary to perform non-adiabatic dynamics simulations. While learning the excited state energies and forces follows a straightforward extension of…

In this paper we will present SDeval, a software project that contains tools for creating and running benchmarks with a focus on problems in computer algebra. It is built on top of the Symbolic Data project, able to translate problems in…

The molecular energies of chemical systems have been successfully calculated on quantum computers, however, more attention has been paid to the dynamic process of chemical reactions in practical application, especially in catalyst design,…