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Ab initio simulations are combined with in situ infrared spectroscopy to unveil the molecular transport of H$_2$, CO$_2$, and H$_2$O in the metal organic framework MOF-74-Mg. Our study uncovers---at the atomistic level---the major factors…
Energy functionals of the Green's function can simultaneously provide spectral and thermodynamic properties of interacting electrons' systems. Though powerful in principle, these formulations need to deal with dynamical…
An optical absorption spectrum constitutes one of the most fundamental material characteristics, with relevant applications ranging from material identification to energy harvesting and optoelectronics. However, the database of both…
It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e., regardless of the protein in question it closely follows one universal curve. The present study, including 135 proteins analyzed with…
We have applied Google's TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of alpha-helix and beta-sheet provide some characteristic…
Several dissociated and two non-dissociated adsorption structures of the phenol molecule on the Si(001)-(2 \times 1) surface are studied using density functional theory with various exchange and correlation functionals. The relaxed…
The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
Advances in time resolved spectroscopy have provided new insight into the energy transmission in natural photosynthetic complexes. Novel theoretical tools and models are being developed in order to explain the experimental results. We…
Effects of coupling between an molecular exciton and a surface plasmon (exciton-plasmon coupling) on the luminescence properties of the molecule and the surface plasmons are investigated using nonequilibrium Green's function method.…
The recent progress of linear-scaling or O(N) methods in the density functional theory (DFT) is remarkable. We expect that first-principles molecular dynamics (FPMD) simulations based on DFT can now treat more realistic and complex systems…
In green plants, chlorophyll-a and chlorophyll-b are the predominant pigments bound to light-harvesting proteins. While the individual characteristics of these chlorophylls are well understood, the advantages of their coexistence remain…
We investigate the time evolution process of one selected (initially prepared by optical pumping) vibrational molecular state, coupled to all other intra-molecular vibrational states of the same molecule, and also to its environment.…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
We present a realistic model of the fragile glass former orthoterphenyl and the results of extensive molecular dynamics simulations in which we investigated its basic static and dynamic properties. In this model the internal molecular…
Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate…
The ExoMol database currently provides comprehensive line lists for modelling the spectroscopic properties of molecules in hot atmospheres. Extending the spectral range of the data provided to ultraviolet (UV) wavelengths brings into play…
Charge injection into a molecule on a metallic interface is a key step in many photo-activated reactions. The energy barrier for injection is paralleled with the lowest particle and hole addition energies. We employ Green's function…
Mean-field molecular dynamics based on path integrals is used to approximate canonical quantum observables for particle systems consisting of nuclei and electrons. A computational bottleneck is the sampling from the Gibbs density of the…
The Bethe-Salpeter equation (BSE) combined with the Green's function GW method has successfully transformed into a robust computational tool to describe light-matter interactions and excitation spectra for molecules, solids, and materials…