Search

The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.

We describe the status of a new time-dependent simulation capability for dense plasmas. The backbone of this multi-institutional effort – the Cimarron Project – is the massively parallel molecular dynamics (MD) code “ddcMD,” developed at Lawrence Livermore National Laboratory. The project’s focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low-Z elements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This paper summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision, describes two new experimental efforts that play a central role in our validation work, highlights some significant results obtained to date, outlines concepts now being explored to deal more efficiently with the very disparate dynamical timescales that arise in fusion plasmas, and provides a careful comparison of quantum effects on electron trajectories predicted by more elaborate dynamical methods.

BlueGene/L (BG/L), developed through a partnership between IBM and Lawrence Livermore National Laboratory (LLNL), is currently the world's largest system both in terms of scale, with 131,072 processors, and absolute performance, with a peak rate of 367 Tflop/s. BG/L has led the last four Top500 lists with a Linpack rate of 280.6 Tflop/s for the full machine installed at LLNL and is expected to remain the fastest computer in the next few editions. However, the real value of a machine such as BG/L derives from the scientific breakthroughs that real applications can produce by successfully using its unprecedented scale and computational power. In this paper, we describe our experiences with eight large scale applications on BG/ L from several application domains, ranging from molecular dynamics to dislocation dynamics and turbulence simulations to searches in semantic graphs. We also discuss the challenges we faced when scaling these codes and present several successful optimization techniques. All applications show excellent scaling behavior, even at very large processor counts, with one code even achieving a sustained performance of more than 100 Tflop/s, clearly demonstrating the real success of the BG/L design.

Molecular dynamics simulations are presented for the stopping of a charged ion in an electron gas. Full Coulomb collisional processes are included, and the resulting particle wake and energy deposition profiles are examined. The present study is extensible to multicomponent plasmas, for evaluating parameters like dE/dx, straggling, blooming, and energy splits.

Hot dense radiative (HDR) plasmas common to inertial confinement fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validations of the models used for describing HDR plasmas are difficult to perform. Direct numerical simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation, but previous work either relies on the collisionless approximation or ignores radiation. We present a first attempt at a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.

We have recently carried out exploratory dynamic experiments where the samples were subjected to prescribed thermodynamic paths. In typical dynamic compression experiments, the samples are thermodynamically limited to the principal Hugoniot or quasi-isentrope. With recent developments in a functionally graded material impactor, we can prescribe and shape the applied pressure profile with similarly shaped, nonmonotonic impedance profile in the impactor. Previously inaccessible thermodynamic states beyond the quasi-isentropes and Hugoniot can now be reached in dynamic experiments with these impactors. In the light gas gun experiments on copper reported here, we recorded the particle velocities of the Cu–LiF interfaces and have employed hydrodynamic simulations to relate them to the thermodynamic phase diagram. Peak pressures for these experiments are on the order of megabars, and the time scales range from nanoseconds to several microseconds. The strain rates of these quasi-isentropic experiments are approximately 104–106s−1 in samples with thicknesses of up to 5mm. Though developed at a light gas gun facility, such shaped pressure profiles are also feasible using laser ablation or magnetically driven compression techniques and allow for previously unexplored directions to be taken in high pressure physics.

Superconducting YBa2Cu3O7 thin films have been prepared by using a magnetron sputtering system in the single‐source mode. Samples deposited on [100] single‐crystal MgO with and without a Au buffer layer all show high transition temperatures (82–87 K). The use of a Au buffer layer significantly improves the superconducting properties, particularly the Meissner effect and critical current density (3.3×106 A/cm2 at T=2 K and 3.5×104 A/cm2 at T=77 K). The Au films remain metallic after high‐temperature annealing in an oxygen atmosphere. We propose to use Au buffer layers as current shunts to protect superconducting films and devices.