Multiscale molecular modelling: from electronic structure to dynamics of nanosystems and beyond

Abstract

Important contemporary biological and materials problems often depend on interactions that span orders of magnitude differences in spatial and temporal dimensions. This Perspective attempts to provide an introduction to such...

DADApy: Distance-based analysis of data-manifolds in Python

“…Another key difference between k NN and PA k estimators is that k NN assumes the density to be exactly constant in the neighborhood of each point, while PA k possesses an additional free parameter that allows to describe small density variations. The PA k density estimator can be used to reconstruct free energy surfaces, especially in high-dimensional spaces, 18 , 20 , 21 , 22 and it can also be used for a detailed analysis of the data, as in Offei-Danso et al., 23 where a distinct analysis of the data points with different densities lead to some physical insight about the system under study.…”

Simulation and analysis of the relaxation dynamics of a photochromic furylfulgide

“…One such approximation is to construct the PESs of the molecule with the use of a hybrid (or, multilayer) method. [63][64][65][66] In this approach, we would take advantage of the fact that the bulky alkyl substituents are not directly involved in low-lying excited electronic states, which are localised in the conjugated π-bonding system that extends over the furyl and the anhydride moieties. Hence, the alkyl groups can be treated at a lower level of approximation than the moieties which form part of the π-bonding system.…”

Coarse-Grained Modeling Using Neural Networks Trained on Structural Data

“…We note further that the transferability of the model with respect to solute concentration can be more important in CG simulations of nonhomogeneous systems under conditions of phase separation or aggregation. For example, one of the problems of CG modeling of self-assembly of lipids into aggregated structures is that effective pair interactions between the lipids depend on their concentration, 27 and it is different, (3) (1, 2, 3) − E (2) (1, 2) − E (2) (2, 3) − E (2) (1, 2), where E (3) (1, 2, 3) is the energy of three CG particles and E (2) (i, j) is the energy of each of the three particle pairs. The three-body component is shown as a density map of the position of the third particle when the first two particles are fixed at distances of 3.4, 4.5, and 6.3 Å, respectively.…”