Femtosecond bond breaking and charge dynamics in ultracharged amino acids.

Historically, structure determination of nanocrystals, proteins, and macromolecules required the growth of high-quality crystals sufficiently large to diffract X-rays efficiently while withstanding radiation damage. The development of the X-ray free-electron laser has opened the path toward high resolution single particle imaging, and the extreme intensity of the X-rays ensures that enough diffraction statistics are collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event. In this study, we use first-principles based methods to study the impact of radiation induced ionization of six amino acids on the reconstruction process. In particular, we study the fragmentation and charge rearrangement to elucidate the time scales involved and the characteristic fragments occurring.

Lattice dynamics and chemical bonding in Sb2Te3 from first-principles calculations.

Pressure effects on the lattice dynamics and the chemical bonding of the three-dimensional topological insulator, Sb2Te3, have been studied from a first-principles perspective in its rhombohedral phase. Where it is possible to compare, theory agrees with most of the measured phonon dispersions. We find that the inclusion of relativistic effects, in terms of the spin-orbit interaction, affects the vibrational features to some extend and creates large fluctuations on phonon density of state in high frequency zone. By investigations of structure and electronic structure, we analyze in detail the semiconductor to metal transition at ∼2 GPa followed by an electronic topological transition at a pressure of ∼4.25 GPa.

First principles molecular dynamics without self-consistent field optimization.

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.

Extended Lagrangian Born-Oppenheimer molecular dynamics in the limit of vanishing self-consistent field optimization.

We present an efficient general approach to first principles molecular dynamics simulations based on extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The reduction of the optimization requirement reduces the computational cost to a minimum, but without causing any significant loss of accuracy or long-term energy drift. The optimization-free first principles molecular dynamics requires only one single diagonalization per time step, but is still able to provide trajectories at the same level of accuracy as "exact," fully converged, Born-Oppenheimer molecular dynamics simulations. The optimization-free limit of extended Lagrangian Born-Oppenheimer molecular dynamics therefore represents an ideal starting point for robust and efficient first principles quantum mechanical molecular dynamics simulations.

Dynamical stability of body center cubic iron at the Earth's core conditions.

Here, using self-consistent ab initio lattice dynamical calculations that go beyond the quasiharmonic approximation, we show that the high-pressure high-temperature bcc-Fe phase is dynamically stable. In this treatment the temperature-dependent phonon spectra are derived by exciting all the lattice vibrations, in which the phonon-phonon interactions are considered. The high-pressure and high-temperature bcc-Fe phase shows standard bcc-type phonon dispersion curves except for the transverse branch, which is overdamped along the high symmetry direction Gamma-N, at temperatures below 4,500 K. When lowering the temperature down to a critical value T(C), the lattice instability of the bcc structure is reached. The pressure dependence of this critical temperature is studied at conditions relevant for the Earth's core.

Phonon lifetimes from first-principles self-consistent lattice dynamics.

Phonon lifetime calculations from first principles usually rely on time-consuming molecular dynamics calculations, or density functional perturbation theory where the zero-temperature crystal structure is assumed to be dynamically stable. Here is presented a new and effective method for calculating phonon lifetimes from first principles. This method is not limited to crystallographic phases stable at 0 K and provides a scheme more effective than most corresponding molecular dynamics calculations. The method is based on the recently developed self-consistent ab initio lattice dynamical method and is here tested by calculating the bcc phase phonon lifetimes of Li, Na, Ti and Zr as representative examples.

Entropically stabilized local dipole formation in lead chalcogenides.

We report the observation of local structural dipoles that emerge from an undistorted ground state on warming, in contrast to conventional structural phase transitions in which distortions emerge on cooling. Using experimental and theoretical probes of the local structure, we demonstrate this behavior in binary lead chalcogenides, which were believed to adopt the ideal, undistorted rock-salt structure at all temperatures. The behavior is consistent with a simple thermodynamic model in which the emerging dipoles are stabilized in the disordered state at high temperature due to the extra configurational entropy despite the fact that the undistorted structure has lower internal energy. Our findings shed light on the anomalous electronic and thermoelectric properties of the lead chalcogenides. Similar searches may show that the phenomenon is more widespread.