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A new scheme for numerical integration of motion for classical systems composed of rigid polyatomic molecules is proposed. The scheme is based on a matrix representation of the rotational degrees of freedom. The equations of motion are…
Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…
This article describes a volumetric approach for procedural shape modeling and a new Procedural Shape Modeling Language (PSML) that facilitates the specification of these models. PSML provides programmers the ability to describe shapes in…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
The growing amount of data produced by simulations and observations of space physics processes encourages the use of methods rooted in Machine Learning for data analysis and physical discovery. We apply a clustering method based on…
We consider discrete dynamical systems and lattice models in statistical mechanics from the point of view of their symmetry groups. We describe a C program for symmetry analysis of discrete systems. Among other features, the program…
Properties of a given symmetry group G are very important in investigation of a physical system invariant under its action. In the case of finite spin systems (magnetic rings, some planar macromolecules) the symmetry group is isomorphic…
Plasmons are likely to play an important role in integrated photonic ciruits, because they strongly interact with light and can be confined to subwavelength scales. These plasmons can be guided and controlled by plasmonic waveguides, which…
Intramolecular symmetry-adapted perturbation theory (ISAPT) is a method to compute and decompose the noncovalent interaction energy between two molecular fragments A and B connected via a linker C. The existing ISAPT algorithm displays…
The Particle-in-Cell (PIC) simulation has been a widely used method for studying plasma physics. However, fully three-dimensional PIC simulations always require huge computational resources. For problems with near azimuthal symmetry, recent…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
We propose a series of methods to represent the evolution of a field of science at different levels: namely micro, meso and macro levels. We use a previously introduced asymmetric measure of paradigmatic proximity between terms that enables…
We investigate the use of invariant polynomials in the construction of data-driven interatomic potentials for material systems. The "atomic body-ordered permutation-invariant polynomials" (aPIPs) comprise a systematic basis and are…
A novel electromagnetic particle-in-cell algorithm has been developed for fully kinetic plasma simulations on unstructured (irregular) meshes in complex body-of-revolution geometries. The algorithm, implemented in the BORPIC++ code,…
With the surge of multi- and manycores, much research has focused on algorithms for mapping and scheduling on these complex platforms. Large classes of these algorithms face scalability problems. This is why diverse methods are commonly…
We introduce symmetric arithmetic circuits, i.e. arithmetic circuits with a natural symmetry restriction. In the context of circuits computing polynomials defined on a matrix of variables, such as the determinant or the permanent, the…
Integrals to calculate generalised magnetic coordinates from an input magnetic flux function asymptotically close to the separatrix are presented, and implemented in the GPEC/DCON code suite. These integrals allow characterisation of the…
Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in…
Using the notion of aggregation work, we construct a system of differential equations for the aggregation number of micelles which is a function of the parameters of micellization (parametric equations). There are explicit solutions for two…