Publications

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This document summarizes the work done in our three-year LDRD project titled 'Physics of Intense, High Energy Radiation Effects.' This LDRD is focused on electrical effects of ionizing radiation at high dose-rates. One major thrust throughout the project has been the radiation-induced conductivity (RIC) produced by the ionizing radiation. Another important consideration has been the electrical effect of dose-enhanced radiation. This transient effect can produce an electromagnetic pulse (EMP). The unifying theme of the project has been the dielectric function. This quantity contains much of the physics covered in this project. For example, the work on transient electrical effects in radiation-induced conductivity (RIC) has been a key focus for the work on the EMP effects. This physics in contained in the dielectric function, which can also be expressed as a conductivity. The transient defects created during a radiation event are also contained, in principle. The energy loss lead the hot electrons and holes is given by the stopping power of ionizing radiation. This information is given by the inverse dielectric function. Finally, the short time atomistic phenomena caused by ionizing radiation can also be considered to be contained within the dielectric function. During the LDRD, meetings about the work were held every week. These discussions involved theorists, experimentalists and engineers. These discussions branched out into the work done in other projects. For example, the work on EMP effects had influence on another project focused on such phenomena in gases. Furthermore, the physics of radiation detectors and radiation dosimeters was often discussed, and these discussions had impact on related projects. Some LDRD-related documents are now stored on a sharepoint site (https://sharepoint.sandia.gov/sites/LDRD-REMS/default.aspx). In the remainder of this document the work is described in catergories but there is much overlap between the atomistic calculations, the continuum calculations and the experiments.

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Biomolecular simulations have traditionally benefited from increases in the processor clock speed and coarse-grain inter-node parallelism on large-scale clusters. With stagnating clock frequencies, the evolutionary path for performance of microprocessors is maintained by virtue of core multiplication. Graphical processing units (GPUs) offer revolutionary performance potential at the cost of increased programming complexity. Furthermore, it has been extremely challenging to effectively utilize heterogeneous resources (host processor and GPU cores) for scientific simulations, as underlying systems, programming models and tools are continually evolving. In this paper, we present a parametric study demonstrating approaches to exploit resources of heterogeneous systems to reduce time-to-solution of a production-level application for biological simulations. By overlapping and pipelining computation and communication, we observe up to 10-fold application acceleration in multi-core and multi-GPU environments illustrating significant performance improvements over code acceleration approaches, where the host-to-accelerator ratio is static, and is constrained by a given algorithmic implementation. © 2010 IEEE.

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LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

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We have performed molecular dynamics simulations of cascade damage in the gadolinium pyrochlore Gd{sub 2}Zr{sub 2}O{sub 7}, comparing results obtained from traditional methodologies that ignore the effect of electron-ion interactions with a 'two-temperature model' in which the electronic subsystem is modeled using a diffusion equation to determine the electronic temperature. We find that the electron-ion interaction friction coefficient {gamma}{sub p} is a significant parameter in determining the behavior of the system following the formation of the primary knock-on atom (here, a U{sup 3+} ion). The mean final U{sup 3+} displacement and the number of defect atoms formed is shown to decrease uniformly with increasing {gamma}{sub p}; however, other properties, such as the final equilibrium temperature and the oxygen-oxygen radial distribution function show a more complicated dependence on {gamma}{sub p}.

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Application performance is determined by a combination of many choices: hardware platform, runtime environment, languages and compilers used, algorithm choice and implementation, and more. In this complicated environment, we find that the use of mini-applications - small self-contained proxies for real applications - is an excellent approach for rapidly exploring the parameter space of all these choices. Furthermore, use of mini-applications enriches the interaction between application, library and computer system developers by providing explicit functioning software and concrete performance results that lead to detailed, focused discussions of design trade-offs, algorithm choices and runtime performance issues. In this paper we discuss a collection of mini-applications and demonstrate how we use them to analyze and improve application performance on new and future computer platforms.

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A molecular-scale interpretation of interfacial processes is often downplayed in the analysis of traditional water treatment methods. However, such an approach is critical for the development of enhanced performance in traditional desalination and water treatments. Water confined between surfaces, within channels, or in pores is ubiquitous in technology and nature. Its physical and chemical properties in such environments are unpredictably different from bulk water. As a result, advances in water desalination and purification methods may be accomplished through an improved analysis of water behavior in these challenging environments using state-of-the-art microscopy, spectroscopy, experimental, and computational methods.

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We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

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We present all-atom molecular dynamics simulations of biologically realistic transmembrane potential gradients across a DMPC bilayer. These simulations are the first to model this gradient in all-atom detail, with the field generated solely by explicit ion dynamics. Unlike traditional bilayer simulations that have one bilayer per unit cell, we simulate a 170 mV potential gradient by using a unit cell consisting of three salt-water baths separated by two bilayers, with full three-dimensional periodicity. The study shows that current computational resources are powerful enough to generate a truly electrified interface, as we show the predicted effect of the field on the overall charge distribution. Additionally, starting from Poisson's equation, we show a new derivation of the double integral equation for calculating the potential profile in systems with this type of periodicity.

The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. In turn, the large-scale protein change then activates G-proteins and signal amplification throughout the cell. The nature of this change, involving a coupling between a local process and larger changes throughout the protein, may be important for many membrane proteins. In addition, functional work has shown that this coupling occurs with different efficiency in different lipid settings. To begin to understand the nature of the efficiency of this coupling in different lipid settings, we present a molecular dynamics study of rhodopsin in an explicit dioleoyl-phosphatidylcholine bilayer. Our system was simulated for 40ns and provides insights into the very early events of the visual cascade, before the full transition and activation have occurred. In particular, we see an event near 10ns that begins with a change in hydrogen bonding near the retinal and that leads through a series of coupled changes to a shift in helical tilt. This type of event, though rare on the molecular dynamics time-scale, could be an important clue to the types of coupling that occur between local and large-scale conformational change in many membrane proteins. © 2003 Elsevier Ltd. All rights reserved.

This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.