Related papers: Definition of Systematic, Approximately Separable …
A general polarizable embedded (PE) quantum mechanics/molecular mechanics scheme for periodic systems is presented, describing mutual polarization of the two subsystems. The QM system, described with density functional theory (DFT), is…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set…
This work introduces a new class of symmetric matrix structures, called harmonic structures, which enable the generation of all possible directed transitions $(x_i, x_{i+1})$ over a set of $n$ symbols, without internal repetitions. Unlike…
Scalable quantum technologies will require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems. It is a challenging task to find a suitable elementary building block,…
Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for…
In this work, we explore the quantum chemical foundations of descriptors for molecular similarity. Such descriptors are key for traversing chemical compound space with machine learning. Our focus is on the Coulomb matrix and on the smooth…
The efficiency of atomic simulations of materials and molecules can rapidly deteriorate when large free energy barriers exist between local minima. We propose smooth basin classification, a universal method to define reaction coordinates…
In this work, we reconsider the study of 2D materials involving double lattice structures associated with periodic polygons. In tessellated periodic representation, it appears two periodic polygons of $k$ sides of unequal side lengths at…
In the framework of density functional theory (DFT) simulations of molecules and materials, anharmonic terms of the potential energy surface are commonly computed numerically, with an associated cost that rapidly increases with the size of…
Kernel matrices are ubiquitous in computational mathematics, often arising from applications in machine learning and scientific computing. In two or three spatial or feature dimensions, such problems can be approximated efficiently by a…
We demonstrate, using examples from $2$ and $3$-dimensions, a systematic method of finding all possible periodic arrangements of a given molecule or molecules such that the arrangements have the symmetry of a given space group. The…
Large-scale atomistic simulations can produce extreme volumes of information in the form of long trajectories. Reliably and automatically extracting key information from such datasets remains a formidable challenge, especially as it…
Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
In molecular structure data, SMILES (Simplified Molecular Input Line Entry System) strings are used to analyze molecular structure design. Numerical feature representation of SMILES strings is a challenging task. This work proposes a…
The most fundamental model of a molecule is a cloud of unordered atoms, even without chemical bonds that can depend on thresholds for distances and angles. The strongest equivalence between clouds of atoms is rigid motion, which is a…
Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties.…
Context. Due to our increasing knowledge on the Galactic and stellar neighborhood of the Solar System, modern long-period comet motion studies have to take into account both stellar perturbations and the overall Galactic potential. Aims.…
Semidefinite programs (SDPs) are a class of optimisation problems that find application in numerous areas of physics, engineering and mathematics. Semidefinite programming is particularly suited to problems in quantum physics and quantum…