Showing papers by "Roberto Car published in 2004"

Calculation of near-edge x-ray-absorption fine structure at finite temperatures: Spectral signatures of hydrogen bond breaking in liquid water

Abstract: We calculate the near-edge x-ray-absorption fine structure of H(2)O in the gas, hexagonal ice, and liquid phases using heuristic density-functional based methods. We present a detailed comparison of our results with experiment. The differences between the ice and water spectra can be rationalized in terms of the breaking of hydrogen bonds around the absorbing molecule. In particular the increase in the pre-edge absorption feature from ice to water is shown to be due to the breaking of a donor hydrogen bond. We also find that in water approximately 19% of hydrogen bonds are broken.

Thermal conductivity of crystalline quartz from classical simulations

Abstract: We calculate the thermal conductivity of crystalline $\ensuremath{\alpha}$- and $\ensuremath{\beta}$-quartz in the high-temperature range ($500\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ to $1100\phantom{\rule{0.3em}{0ex}}\mathrm{K}$) using nonequilibrium molecular dynamics simulations and an empirical interatomic potential. We find that finite-size effects associated with the nonequilibrium dynamics are not negligible, which implies that reliable results for the bulk thermal conductivity of quartz must be obtained by extrapolation to infinite sizes. The calculated thermal conductivity is nearly temperature independent over a wide range of temperature, in agreement with experiment.

First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bioinorganic systems.

Abstract: We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metalorganic systems. Our results show that accurate density-functional theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.

Current in Open Quantum Systems

Abstract: We show that a dissipative current component is present in the dynamics generated by a Liouville-master equation, in addition to the usual component associated with Hamiltonian evolution. The dissipative component originates from coarse graining in time, implicit in a master equation, and needs to be included to preserve current continuity. We derive an explicit expression for the dissipative current in the context of the Markov approximation. Finally, we illustrate our approach with a simple numerical example, in which a quantum particle is coupled to a harmonic phonon bath and dissipation is described by the Pauli master equation.

First-principles string molecular dynamics: An efficient approach for finding chemical reaction pathways

Abstract: A recently proposed approach, called “string method,” allows us to find minimum energy pathways connecting two metastable states of a system [W. E et al., Phys. Rev. B 66, 052301 (2002)]. So far this approach has been only used with empirical force field parametrizations of the atomic potential energy surface or in the context of macroscopic continuum models. Here we show that the string method can be efficiently combined with first-principles molecular dynamics to provide an accurate description of chemical reaction pathways and barriers. We illustrate the first-principles string molecular dynamics by applying it to the study of a surface chemical reaction, for which extensive experimental and theoretical works are available, namely, the adsorption of H2 on the reconstructed Si(100) surface.

Kinetic theory of quantum transport at the nanoscale

Abstract: We present a quantum-kinetic scheme for the calculation of non-equilibrium transport properties in nanoscale systems. The approach is based on a Liouville-master equation for a reduced density operator and represents a generalization of the well-known Boltzmann kinetic equation. The system, subject to an external electromotive force, is described using periodic boundary conditions. We demonstrate the feasibility of the approach by applying it to a double-barrier resonant tunneling structure.

Mapping potential energy surfaces

Abstract: A recently proposed dynamical method [A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002)] allows us to globally sample the free energy surface. This approach uses a coarse-grained non-Markovian dynamics to bias microscopic atomic trajectories. After a sufficiently long simulation time, the global free energy surface can be reconstructed from the non-Markovian dynamics. Here we apply this scheme to study the T=0 free energy surface, i.e., the potential energy surface in coarse-grained space. We show that the accuracy of the reconstructed potential energy surface can be dramatically improved by a simple postprocessing procedure with only minor computational overhead. We illustrate this approach by conducting conformational analysis on a small organic molecule, demonstrating its superiority over traditional unbiased approaches in sampling potential energy surfaces in coarse-grained space.

Strongly Non-Arrhenius Self-Interstitial Diffusion in Vanadium

Abstract: We study diffusion of self-interstitial atoms (SIAs) in vanadium via molecular-dynamics simulations. The ⟨111⟩-split interstitials are observed to diffuse one-dimensionally at low temperature, but rotate into other ⟨111⟩ directions as the temperature is increased. The SIA diffusion is highly non-Arrhenius. At $Tl600\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, this behavior arises from temperature-dependent correlations. At $Tg600\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, the Arrhenius expression for thermally activated diffusion breaks down when the migration barriers become small compared to the thermal energy. This leads to Arrhenius diffusion kinetics at low $T$ and diffusivity proportional to temperature at high $T$.

Longitudinal polarizability of long polymeric chains: quasi-one-dimensional electrostatics as the origin of slow convergence.

Abstract: The longitudinal linear polarizability alpha(N) of a stereoregular oligomer of size N is proportional to N in the large-N limit, provided the system is nonconducting in that limit. It has long been known that the convergence of alpha(N)/N to the asymptotic alpha(infinity) value is slow. We show that the leading term in the difference between alpha(N)/N and alpha(infinity) is of the order of 1/N. The difference [alpha(N)-alpha(N-1)], as well as alpha(center)(N) (when computationally accessible), also converge to alpha(infinity), but faster, the leading term being of the order of 1/N(2). We also present evidence that in these cases the power law convergence behavior is due to quasi-one-dimensional electrostatics, with one exception. Specifically, in molecular systems the difference between alpha(N)/N and alpha(infinity) has not just one but two sources of the O(1/N) term, with one being due to the aforementioned Coulomb interactions, and the second due to the short ranged exponentially decaying perturbations on chain ends. The major role of electrostatics in the convergence of the remainders is demonstrated by means of a Clausius-Mossotti-type classical model. The conclusions derived from the model are also shown to be applicable in molecular systems, by means of test-case ab initio calculations on linear stacks of H(2) molecules, and on polyacetylene chains. The implications of the modern theory of polarization for extended systems are also discussed.

Mechanism of the hydrogen/platinum(111) fuel cell

Abstract: We discuss our recently proposed mechanism for the electro-oxidation/reduction on Pt(111) surfaces (J. Electroanal. Chem. 2002, 537, 7) in the presence of sulfuric acid. The bisulfate ion has a large dipole moment and is strongly adsorbed on the positive electrode. Due to the large field gradients, the oxygen atoms of the adsorbed water molecules (and the dipoles) point down and bind to the on-top positions of the platinum substrate. As the electrode becomes more negative, the field gradient changes direction, and the water dipoles gradually reverse their orientation. At a certain critical value of the orientational parameter (which depends also on the bisulfate surface concentration), a two-dimensional honeycomb array of hydrogen bonded water molecules is formed. This is a new form of solid water, a true two-dimensional "ice". For these negative potentials, the stable structure has one of the hydrogen atoms of the water pointing down, and this means that it is adsorbed by the hollow site of the Pt lattice. To satisfy the stoichiometry of the hydrogen bonds, we need to adsorb one-third of the surface sites of H+ ions. The following reversible reaction occurs: (H5O2+)(3) + 6e(-) reversible arrow 6H + (H3O3-)(3). For the (111) surface of platinum and because of the geometrical matchup (the Pt-Pt distance is 2.77 Angstrom, and the water diameter is 2.76 Angstrom) this reaction occurs as a first-order transition, visible in the voltammogram as a sharp peak. From the [H+] concentration dependence of this sharp spike, we get an effective charge of 1.02 +/- 0.02 for the adsorbed moiety. High-accuracy quantum calculations on a five-layer platinum metal slab show that this compound is stable in the absence of bisulfate ions. The quantum calculations show also that the hydrogen atoms in the hollow positions are neutralized. Since there are two-thirds of the Pt sites in the hollow positions, our model gives a natural explanation to the well-known fact that the hydrogen yield is 2/3 on this surface. We have revised our theory to shift the turning point of the water molecules to the transition potential where the HER honeycomb phase is formed. The turning point is in general agreement with the recent laserinduced measurements of the potential of zero charge.

Density functional theory of dissipative systems

Abstract: Time-dependent density functional theory is extended to include dissipative systems evolving under a master equation, providing a Hamiltonian treatment for molecular electronics. For weak electric fields, the isothermal conductivity is shown to match the adiabatic conductivity, thereby recovering the Landauer result.

Erratum: Molecular dynamics study of the threshold displacement energy in vanadium [Phys. Rev. B 67, 134114 (2003)]

Abstract: Following manuscript publication, P. Vajda has brought to our attention the existence of experimental references on the threshold displacement energy in vanadium, 29,31–35 which were inadvertently missed in our literature review. Additionally, P. Vajda also brought to our attention our erroneous description of literature data as being experimentally obtained, when in fact they were produced by computer simulation. Thus, we present: (i) a modified version of Fig. 2 that includes the measured TDE values in vanadium along the low index k100l, k110l, andk111l directions due to Kenik and Mitchell; 29