Related papers: A Protocol for the Atomic Capture of Multiple Mole…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
Informally, a chemical reaction network is "atomic" if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational…
Computing the electronic structure of molecules with high precision is a central challenge in the field of quantum chemistry. Despite the enormous success of approximate methods, tackling this problem exactly with conventional computers is…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
Many forms of programmable matter have been proposed for various tasks. We use an abstract model of self-organizing particle systems for programmable matter which could be used for a variety of applications, including smart paint and…
Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our…
The adsorption of a single multi-block $AB$-copolymer on a solid planar substrate is investigated by means of computer simulations and scaling analysis. It is shown that the problem can be mapped onto an effective homopolymer adsorption…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
Quantum computing leverages the quantum resources of superposition and entanglement to efficiently solve computational problems considered intractable for classical computers. Examples include calculating molecular and nuclear structure,…
In the last few years there has been a lot of interest in quantum repeater protocols using only atomic ensembles and linear optics. Here we show that the local generation of high-fidelity entangled pairs of atomic excitations, in…
Quantum chemical studies of reactivity involve calculations on a large number of molecular structures and comparison of their energies. Already the set-up of these calculations limits the scope of the results that one will obtain, because…
We report the quantum computing of reacting flows by simulating the Hamiltonian dynamics. The scalar transport equation for reacting flows is transformed into a Hamiltonian system, mapping the dissipative and non-Hermitian problem in…
Near-term large quantum computers are not able to operate as a single processing unit. It is therefore required to partition a quantum circuit into smaller parts, and then each part is executed on a small unit. This approach is known as…
Atom tracing is essential for understanding the fate of labeled atoms in biochemical reaction networks, yet existing computational methods either simplify label correlations or suffer from combinatorial explosion. We introduce a…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended…
Samples with few hundred atoms within a few micrometer sized region of space are large enough to provide efficient cooperative absorption and emission of light, and small enough to ensure strong dipole-dipole interactions when atoms are…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Accurate prediction of molecular properties in complex chemical systems is crucial for accelerating material discovery and chemical innovation. However, current computational methods often struggle to capture the intricate compositional…
We propose to use a new platform - ultracold polar molecules - for quantum computing with switchable interactions. The on/off switch is accomplished by selective excitation of one of the "0" or "1" qubits - long-lived molecular states - to…