i-PI 2.0: A universal force engine for advanced molecular simulations
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Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...
We characterize the transition structure at the Si(100)-SiO2 interface by addressing the inverse ion-scattering problem. We achieve sensitivity to Si displacements at the interface by carrying out ion-scattering measurements in the channeling geometry for ...
Atomistic simulations have provided much insight into grain boundary (GB) structures and mechanisms which are important in understanding the properties of materials. In this paper, the Sigma 3{1 1 2}, Sigma 3{1 1 1} and Sigma 5{0 1 3} (coincidence site lat ...
The core structures of screw and edge dislocations on the basal and prism planes in Mg, and the associated gamma surfaces, were studied using an ab initio method and the embedded-atom-method interatomic potentials developed by Sun et al and Liu et al. The ...
In order to compute the thermodynamic weights of the different metastable conformations of a molecule, we want to approximate the molecule’s Boltzmann distribution π in a reasonable time. This is an essential issue in computational drug design. The energy l ...
A simplified formulation of the harmonic reaction path Hamiltonian (RPH) approach is used to calculate mode specific tunneling splittings and stereomutation times in (CH3OH)-C-12 and (CH3OH)-C-13. The experimental torsional spectrum is very well reproduced ...
The ab initio mol. dynamics method is extended to treat exchange of electrons between mols. and a reservoir at fixed chem. potential. The method is based on a rigorously grand-canonical d. functional approach using sep. potential energy surfaces for each o ...
Magnetic impurities in solids cause manifold changes in their macroscopic properties, such as anomalous low temperature resistance due to Kondo screening, reduction of the superconducting transition temperature due to local suppression of the order paramet ...
We use infrared-visible double-resonance overtone excitation to prepare HOCl molecules in single, well-characterized rotational levels of the high OH stretching states v(OH) = 7 and v(OH) = 8. This work extends our recent studies on HOCl dissociation dynam ...
We present a method for calcg. multidimensional free energy surfaces within the limited time scale of a first-principles mol. dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This sim ...
