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The stable crystal structure of LiBeH(3) is predicted on the basis of ab initio total-energy calculations using density-functional theory and an extended database of candidate structures and using global optimizations based on an evolutionary algorithm. At the level of density-functional theory, a CaSiO(3)_1-type structure with space group P2(1)/c,(More)
The accurate modeling of protein dynamics in crystalline states holds keys to the understanding of protein dynamics relevant to functions. In this study, we used coarse-grained elastic network models (ENMs) to explore the atomic fluctuations of a protein structure that interacts with its crystalline environment, and evaluated the modeling results using the(More)
The sticking and scattering of O(2)Pt(111) has been studied by tight-binding molecular dynamics simulations based on an ab initio potential energy surface. We focus, in particular, on the sticking probability as a function of the angle of incidence and the energy and angular distributions in scattering. Our simulations provide an explanation for the(More)
A novel H(2) molecular adsorption state on metal surfaces has been detected by temperature-programmed desorption and electron energy loss spectroscopy experiments of the H(2)/Pd(210) system. The molecular nature of this state has been verified by isotope exchange experiments. This molecular state leads to a decrease of the surface work function while atomic(More)
Normal mode analysis (NMA) has been proven valuable in modeling slow conformational dynamics of biomolecular structures beyond the reach of direct molecular simulations. However, it remains computationally expensive to directly solve normal modes for large biomolecular systems. In this study, we have evaluated the accuracy and efficiency of two approximate(More)
The accurate modeling of protein dynamics in crystalline states is essential for the development of computational techniques for simulating protein dynamics under physiological conditions. Following a previous coarse-grained modeling study of atomic fluctuations in protein crystal structures, we have refined our modeling with all-atom representation and(More)
The standard approach to ab initio simulations of activated chemical processes is based on the harmonic-oscillator/rigid-rotor approximation to transition state theory. However, there is increasing evidence that these approximations fail for reactions involving loosely bound reactant and/or transitions states where entropy makes a significant contribution(More)
Periodic DFT and combined quantum mechanics/interatomic potential function (QM-pot) models were used to describe the interaction of CO with the Cu+ sites in FER. The CO stretching frequencies were calculated using omega(CO)(CCSD(T))/r(CO)(DFT) scaling method relating frequencies determined using a high-level quantum-chemical (coupled clusters) method for(More)
A periodic density functional theory (DFT) study of the isomerization reactions of toluene and xylene catalyzed by acidic mordenite is reported. Monomolecular isomerization reactions have been considered and analyzed. The different reaction pathways have been discussed in detail. The use of periodic structure calculations allows consideration and analysis(More)