Global optimization of additive potential energy functions: predicting binary Lennard-Jones clusters.

We present a method for minimizing additive potential-energy functions. Our hidden-force algorithm can be described as an intricate multiplayer tug-of-war game in which teams try to break an impasse by randomly assigning some players to drop their ropes while the others are still tugging until a partial impasse is reached, then, instructing the dropouts to resume tugging, for all teams to come to a new overall impasse. Utilizing our algorithm in a non-Markovian parallel Monte Carlo search, we found 17 new putative global minima for binary Lennard-Jones clusters in the size range of 90-100 particles. The method is efficient enough that an unbiased search was possible; no potential-energy surface symmetries were exploited. All new minima are comprised of three nested polyicosahedral or polytetrahedral shells when viewed as a nested set of Connolly surfaces (though the shell structure has previously gone unscrutinized, known minima are often qualitatively similar). Unlike known minima, in which the outer and inner shells are comprised of the larger and smaller atoms, respectively, in 13 of the new minima, the atoms are not as clearly separated by size. Furthermore, while some known minima have inner shells stabilized by larger atoms, four of the new minima have outer shells stabilized by smaller atoms.

Transition from collisional to kinetic regimes in large-scale reconnection layers.

Using fully kinetic simulations with a Fokker-Planck collision operator, it is demonstrated that Sweet-Parker reconnection layers are unstable to plasmoids (secondary islands) for Lundquist numbers beyond S greater, similar 1000. The instability is increasingly violent at higher Lundquist numbers, both in terms of the number of plasmoids produced and the super-Alfvénic growth rate. A dramatic enhancement in the reconnection rate is observed when the half-thickness of the current sheet between two plasmoids approaches the ion inertial length. During this transition to kinetic scales, the reconnection electric field rapidly exceeds the runaway limit, resulting in the formation of electron-scale current layers that are unstable to the continual formation of new plasmoids.

Three-dimensional dynamics of collisionless magnetic reconnection in large-scale pair plasmas.

Using the largest three-dimensional particle-in-cell simulations to date, collisionless magnetic reconnection in large-scale electron-positron plasmas without a guide field is shown to involve complex interaction of tearing and kink modes. The reconnection onset is patchy and occurs at multiple sites which self-organize to form a single, large diffusion region. The diffusion region tends to elongate in the outflow direction and become unstable to secondary kinking and formation of "plasmoid-rope" structures with finite extent in the current direction. The secondary kink folds the reconnection current layer, while plasmoid ropes at times follow the folding of the current layer. The interplay between these secondary instabilities plays a key role in controlling the time-dependent reconnection rate in large-scale systems.

Mechanism of Na+/H+ antiporting.

Na+/H+ antiporters are central to cellular salt and pH homeostasis. The structure of Escherichia coli NhaA was recently determined, but its mechanisms of transport and pH regulation remain elusive. We performed molecular dynamics simulations of NhaA that, with existing experimental data, enabled us to propose an atomically detailed model of antiporter function. Three conserved aspartates are key to our proposed mechanism: Asp164 (D164) is the Na+-binding site, D163 controls the alternating accessibility of this binding site to the cytoplasm or periplasm, and D133 is crucial for pH regulation. Consistent with experimental stoichiometry, two protons are required to transport a single Na+ ion: D163 protonates to reveal the Na+-binding site to the periplasm, and subsequent protonation of D164 releases Na+. Additional mutagenesis experiments further validated the model.

The midpoint method for parallelization of particle simulations.

The evaluation of interactions between nearby particles constitutes the majority of the computational workload involved in classical molecular dynamics (MD) simulations. In this paper, we introduce a new method for the parallelization of range-limited particle interactions that proves particularly suitable to MD applications. Because it applies not only to pairwise interactions but also to interactions involving three or more particles, the method can be used for evaluation of both nonbonded and bonded forces in a MD simulation. It requires less interprocessor data transfer than traditional spatial decomposition methods at all but the lowest levels of parallelism. It gains an additional practical advantage in certain commonly used interprocessor communication networks by distributing the communication burden more evenly across network links and by decreasing the associated latency. When used to parallelize MD, it further reduces communication requirements by allowing the computations associated with short-range nonbonded interactions, long-range electrostatics, bonded interactions, and particle migration to use much of the same communicated data. We also introduce certain variants of this method that can significantly improve the balance of computational load across processors.

Theory of laser acceleration of light-ion beams from interaction of ultrahigh-intensity lasers with layered targets.

Experiments at the LANL Trident facility demonstrated the production of monoenergetic ion beams from the interaction of an ultraintense laser with a target comprising a heavy ion substrate and thin layer of light ions. An analytic model is obtained that predicts how the mean energy and quality of monoenergetic ion beams and the energy of substrate ions vary with substrate material and light-ion layer composition and thickness. Dimensionless parameters controlling the dynamics are derived and the model is validated with particle-in-cell simulations and experimental data.