Related papers: Collective mode mining from molecular dynamics sim…
. The choice of a suitable random matrix model of a complex system is very sensitive to the nature of its complexity. The statistical spectral analysis of various complex systems requires, therefore, a thorough probing of a wide range of…
Several enhanced sampling methods such as umbrella sampling or metadynamics rely on the identification of an appropriate set of collective variables. Recently two methods have been proposed to alleviate the task of determining efficient…
The study of molecular polaritons beyond simple quantum emitter ensemble models (e.g., Tavis-Cummings) is challenging due to the large dimensionality of these systems (the number of molecular emitters is $N\approx 10^{6}-10^{10}$) and the…
Given a set of collective variables, a method is proposed to obtain the associated conjugated collective momenta and masses starting from a microscopic time-dependent mean-field theory. The construction of pairs of conjugated variables is…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
Understanding the molecular vibrations underlying each of the unknown infrared emission (UIE) bands (such as those found at 3.3, 3.4, 3.5, 6.2, 6.9, 7.7, 11.3, 15.8, 16.4, 18.9 mm) observed in or towards astronomical objects is a vital link…
Statistical moments of the intensity distributions are used as molecular descriptors. They are used as a basis for defining similarity distances between two model spectra. Parameters which carry the information derived from the comparison…
We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…
Since fullerene formation occurs under conditions where direct observation of atomic-scale reactions is not possible, modeling is the only way to reveal atomistic mechanisms which can lead to selection of abundant fullerene isomers (like…
Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation…
Mode clustering is a nonparametric method for clustering that defines clusters using the basins of attraction of a density estimator's modes. We provide several enhancements to mode clustering: (i) a soft variant of cluster assignment, (ii)…
We obtain exact analytic expressions for a class of functions expressed as integrals over the Haar measure of the unitary group in d dimensions. Based on these general mathematical results, we investigate generic dynamical properties of…
The model quantum system of fermions in a one dimensional harmonic oscillator potential is investigated by a molecular dynamics method at constant temperature. Although in quantum mechanics the equipartition theorem cannot be used like in…
In-depth studies of sociotechnical systems are largely limited to single instances. Network surveys are expensive, and platforms vary in important ways, from interface design, to social norms, to historical contingencies. With single…
We formulate a general method for the study of semiclassical-like dynamics in stable regions of a mixed phase-space, in order to theoretically study the dynamics of quantum accelerator modes. In the simplest case, this involves determining…
A general theory of electronic excitations in aggregates of molecules coupled to intramolecular vibrations and the harmonic environment is developed for simulation of the third-order nonlinear spectroscopy signals. The model is applied in…
Understanding and simulating how a quantum system interacts and exchanges information or energy with its surroundings is a ubiquitous problem, one which must be carefully addressed in order to establish a coherent framework to describe the…
Systems of active particles can show a large variety of collective behavior. In theory, two aspects determine the collective behavior: the model at the particle level and the parameter regime. While many studies consider a single model and…
There are many atomistic simulation methods with very different costs, accuracies, transferabilities, and numbers of empirical parameters. I show how statistical model selection can compare these methods fairly, even when they are very…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…