Trajectory of a sodium counter-ion (in purple) superimposed on a short nucleobase sequence of DNA. The trajectory, taken from a 1.6 nanosecond molecular dynamics simulation at room temperature of DNA in water, illustrates the high mobility of the counter-ions.

Uzi Landman, Robert N. Barnett, Charles L. Cleveland, Hannu Hakkinen, and W. David Luedtke, Georgia Institute of Technology

Research Objectives
This project focuses on development, implementation, and use of quantum and classical modeling and simulation methodologies on high-performance computational platforms for investigating microscopic physical and chemical processes and mechanisms underlying the generation and properties of novel materials in various forms and degrees of aggregation, under equilibrium and nonequilibrium conditions or subject to extreme environments. These investigations aim at discovering and elucidating size-dependent evolutionary patterns of materials properties, bridging the molecular, cluster, and condensed-phase regimes.

Computational Approach
We use large-scale classical molecular dynamics (particularly in nanotribology studies) and tested many-body interactions. We also use ab initio quantum molecular dynamics (in conjunction with norm-conserving nonlocal pseudopotentials and a plane-wave basis) based on local-spin density functional theory (LSD) with the inclusion of generalized exchange-correlation gradient corrections (GGA). In these ab initio simulations, the dynamics of the ions evolve on the concurrently calculated electronic ground state Born-Oppenheimer (BO) potential energy surface, using the BO-LSD-MD method formulated by us, with the codes rewritten for parallel computations with the assistance of Andrew Canning at NERSC.

Accomplishments
Investigations of the exactly solvable excitation spectra of two-electron quantum dots with a parabolic confinement, for different values of the parameter RW expressing the relative magnitudes of the interelectron repulsion and the zero-point kinetic energy, revealed for large RW a rovibrational spectrum associated with a linear trimeric rigid molecule composed of the two electrons and the infinitely heavy confining dot.

The properties of neutral and anionic PdN clusters were investigated with spin-density-functional calculations. The ground-state structures are three dimensional for N larger then 3 and magnetic with a spin triplet for N larger then 2 and smaller then 7, and a spin nonet for N equals 13 neutral clusters. Structural and spin isomers were determined and an anomalous increase of the magnetic moment with temperature is predicted for a Pd7 ensemble. Vertical electron detachment and ionization energies were calculated and the former agrees well with measured values for anionic PdN clusters.

Electron hole (radical cation) migration in DNA, where the quantum transport of an injected charge is gated in a correlated manner by the thermal motions of the hydrated counter-ions, was investigated. Classical molecular dynamics simulations in conjunction with large-scale first-principles electronic structure calculations revealed that different counter-ion configurations lead to formation of states characterized by varying spatial distributions and degrees of charge-localization. Comparative UV light-induced cleavage experiments on native B-DNA oligomers and on ones modified to contain counter-ion (Na⁺)-starved bridges between damage-susceptible hole-trapping sites (GG steps), show in the latter a reduction in damage at the distal step, indicating a reduced mobility of the hole across the modified bridge in correspondence with the theoretical predictions.

Significance
This research is significant both to the formulation and development of computational methodologies and to their employment in investigations of challenging physical and chemical problems in the areas of cluster science, nanostructures, and nanotribology.

Publications
R. N. Barnett, C. L. Cleveland, A. Joy, U. Landman, and G. B. Schuster, "Charge migration in DNA: Ion-gated transport," Science 294, 567 (2001).

M. Moseler, H. Hakkinen, R. N. Barnett, and U. Landman, "Structure and magnetism of neutral and anionic palladium clusters," Phys. Rev. Lett. 86, 2545 (2001).

C. Yannouleas and U. Landman, "Collective and independent-particle motion in two-electron artificial atoms," Phys. Rev. Lett. 85, 1726 (2000).