Hydrogen and muonium in diamond: A path-integral molecular dynamics simulation

Isolated hydrogen, deuterium, and muonium in diamond have been studied by path-integral molecular dynamics simulations in the canonical ensemble. Finite-temperature properties of these point defects were analyzed in the range from 100 to 800 K. Interatomic interactions were modeled by a tight-binding potential fitted to density-functional calculations. The most stable position for these hydrogenic impurities is found at the C-C bond center. Vibrational frequencies have been obtained from a linear-response approach, based on correlations of atom displacements at finite temperatures. The results show a large anharmonic effect in impurity vibrations at the bond center site, which hardens the vibrational modes with respect to a harmonic approximation. Zero-point motion causes an appreciable shift of the defect level in the electronic gap, as a consequence of electron-phonon interaction. This defect level goes down by 70 meV when replacing hydrogen by muonium.Comment: 11 pages, 8 figure

Controlled collisions of a single atom and ion guided by movable trapping potentials

We consider a system composed of a trapped atom and a trapped ion. The ion charge induces in the atom an electric dipole moment, which attracts it with an r^{-4} dependence at large distances. In the regime considered here, the characteristic range of the atom-ion interaction is comparable or larger than the characteristic size of the trapping potential, which excludes the application of the contact pseudopotential. The short-range part of the interaction is described in the framework of quantum-defect theory, by introducing some short-range parameters, which can be related to the s-wave scattering length. When the separation between traps is changed we observe trap-induced shape resonances between molecular bound states and vibrational states of the external trapping potential. Our analysis is extended to quasi-one-dimensional geometries, when the scattering exhibit confinement-induced resonances, similar to the ones studied before for short-range interactions. For quasi-one-dimensional systems we investigate the effects of coupling between the center of mass and relative motion, which occurs for different trapping frequencies of atom and ion traps. Finally, we show how the two types of resonances can be employed for quantum state control and spectroscopy of atom-ion molecules.Comment: 17 pages, 16 figure

Semi-Classical Wavefunction Perspective to High-Harmonic Generation

We introduce a semi-classical wavefunction (SCWF) model for strong-field physics and attosecond science. When applied to high harmonic generation (HHG), this formalism allows one to show that the natural time-domain separation of the contribution of ionization, propagation and recollisions to the HHG process leads to a frequency-domain factorization of the harmonic yield into these same contributions, for any choice of atomic or molecular potential. We first derive the factorization from the natural expression of the dipole signal in the temporal domain by using a reference system, as in the quantitative rescattering (QRS) formalism [J. Phys. B. 43, 122001 (2010)]. Alternatively, we show how the trajectory component of the SCWF can be used to express the factorization, which also allows one to attribute individual contributions to the spectrum to the underlying trajectories

Critical examination of the inherent-structure-landscape analysis of two-state folding proteins

Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single topology of a two-state folding protein, and the simplifying assumptions of the method have not been examined. In this work, we construct the thermodynamics of four two-state folding proteins of different sizes and secondary structure by MD simulations using the ISL method, and critically examine possible limitations of the method. Our results show that the ISL approach correctly describes the thermodynamics function, such as the specific heat, on a qualitative level. Using both analytical and numerical methods, we show that some quantitative limitations cannot be overcome with enhanced sampling or the inclusion of harmonic corrections.Comment: published Physical Review E, vol. 80, 061907-1-11 (2009

Thermodynamics of liquids: standard molar entropies and heat capacities of common solvents from 2PT molecular dynamics

We validate here the Two-Phase Thermodynamics (2PT) method for calculating the standard molar entropies and heat capacities of common liquids. In 2PT, the thermodynamics of the system is related to the total density of states (DoS), obtained from the Fourier Transform of the velocity autocorrelation function. For liquids this DoS is partitioned into a diffusional component modeled as diffusion of a hard sphere gas plus a solid component for which the DoS(υ) → 0 as υ → 0 as for a Debye solid. Thermodynamic observables are obtained by integrating the DoS with the appropriate weighting functions. In the 2PT method, two parameters are extracted from the DoS self-consistently to describe diffusional contributions: the fraction of diffusional modes, f, and DoS(0). This allows 2PT to be applied consistently and without re-parameterization to simulations of arbitrary liquids. We find that the absolute entropy of the liquid can be determined accurately from a single short MD trajectory (20 ps) after the system is equilibrated, making it orders of magnitude more efficient than commonly used perturbation and umbrella sampling methods. Here, we present the predicted standard molar entropies for fifteen common solvents evaluated from molecular dynamics simulations using the AMBER, GAFF, OPLS AA/L and Dreiding II forcefields. Overall, we find that all forcefields lead to good agreement with experimental and previous theoretical values for the entropy and very good agreement in the heat capacities. These results validate 2PT as a robust and efficient method for evaluating the thermodynamics of liquid phase systems. Indeed 2PT might provide a practical scheme to improve the intermolecular terms in forcefields by comparing directly to thermodynamic properties