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PyMOL, a cross-platform molecular graphics tool, has been widely used for three-dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories. It is also capable of editing molecules, ray tracing ...
We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibration ...
The overarching objective of this thesis is extending and adapting the set of computational tools available for describing molecular precursors of organic semiconductors. The research presented within develops adhering to three principle goals: (1) provide ...
Solid-liquid interfaces are ubiquitous. Despite the unquestioned relevance, many scientific research fields rely on simplified or macroscopic descriptions, discarding the molecular nature of the constituents. However, it is the specific molecular interacti ...
An average-atom (A-atom) embedded-atom-method potential for random multicomponent alloys at any composition is derived analytically and validated by comparing A-atom and true random alloys bulk and defect properties, in model Fe-Ni-Cr systems. The A-atom c ...
The electronic charge density plays a central role in determining the behavior of matter at the atomic scale, but its computational evaluation requires demanding electronic-structure calculations. We introduce an atom-centered, symmetry-adapted framework t ...
The layered transition metal dichalcogenides which show an inherent tendency towards charge density wave order are traditionally considered to realize rather two-dimensional electronic systems. However, recent theoretical and experimental results suggest t ...
Antihydrogen, a positron bound to an antiproton, is the simplest anti-atom. Its structure and properties are expected to mirror those of the hydrogen atom. Prospects for precision comparisons of the two, as tests of fundamental symmetries, are driving a vi ...
We combine classical and ring polymer molecular dynamics simulations with the molecular jump model to provide a molecular description of the nuclear quantum effects (NQEs) on water reorientation and hydrogen-bond dynamics in liquid H2O and D2O. We show tha ...
The application of local control theory combined with nonadiabatic ab initio molecular dynamics to study the photoinduced intramolecular proton transfer reaction in 4-hydroxyacridine was investigated. All calculations were performed within the framework of ...
