In traditional molecular dynamics (MD) simulations, atoms and coarse-grained particles are modeled as point masses interacting via isotropic potentials. For studies where particle shape plays a vital role, more complex models are required. In this paper we describe a spectrum of approaches for modeling aspherical particles, all of which are now available (some recently) as options within the LAMMPS MD package. Broadly these include two classes of models. In the first, individual particles are aspherical, either via a pairwise anisotropic potential which implicitly assigns a simple geometric shape to each particle, or in a more general way where particles store internal state which can explicitly define a complex geometric shape. In the second class of models, individual particles are simple points or spheres, but rigid body constraints are used to create composite aspherical particles in a variety of complex shapes. We discuss parallel algorithms and associated data structures for both kinds of models, which enable dynamics simulations of aspherical particle systems across a wide range of length and time scales. We also highlight parallel performance and scalability and give a few illustrative examples of aspherical models in different contexts.
The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to ''achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life.'' While more information about the program can be found at the GTL website (www.doegenomestolife.org), this paper provides an overview of one of the five GTL projects funded, ''Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling.'' This project is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to elucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO(2) are important terms in the global environmental response to anthropogenic atmospheric inputs of CO(2) and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. The project includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the Genomes to Life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. Furthermore, given that the ultimate goal of this effort is to develop a systems-level of understanding of how the Synechococcus genome affects carbon fixation at the global scale, we will develop and apply a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, because the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats, we have also established a companion computational infrastructure to support this effort as well as the Genomes to Life program as a whole.
Prokaryotic single-cell microbes are the simplest of all self-sufficient living organisms. Yet microbes create and use much of the molecular machinery present in more complex organisms, and the macro-molecules in microbial cells interact in regulatory, metabolic, and signaling pathways that are prototypical of the reaction networks present in all cells. We have developed a simple simulation model of a prokaryotic cell that treats proteins, protein complexes, and other organic molecules as particles which diffuse via Brownian motion and react with nearby particles in accord with chemical rate equations. The code models protein motion and chemistry within an idealized cellular geometry. It has been used to simulate several simple reaction networks and compared to more idealized models which do not include spatial effects. In this report we describe an initial version of the simulation code that was developed with FY03 funding. We discuss the motivation for the model, highlight its underlying equations, and describe simulations of a 3-stage kinase cascade and a portion of the carbon fixation pathway in the Synechococcus microbe.
Chemically Induced Surface Evolution with Level-Sets--ChISELS--is a parallel code for modeling 2D and 3D material depositions and etches at feature scales on patterned wafers at low pressures. Designed for efficient use on a variety of computer architectures ranging from single-processor workstations to advanced massively parallel computers running MPI, ChISELS is a platform on which to build and improve upon previous feature-scale modeling tools while taking advantage of the most recent advances in load balancing and scalable solution algorithms. Evolving interfaces are represented using the level-set method and the evolution equations time integrated using a Semi-Lagrangian approach [1]. The computational meshes used are quad-trees (2D) and oct-trees (3D), constructed such that grid refinement is localized to regions near the surface interfaces. As the interface evolves, the mesh is dynamically reconstructed as needed for the grid to remain fine only around the interface. For parallel computation, a domain decomposition scheme with dynamic load balancing is used to distribute the computational work across processors. A ballistic transport model is employed to solve for the fluxes incident on each of the surface elements. Surface chemistry is computed by either coupling to the CHEMKIN software [2] or by providing user defined subroutines. This report describes the theoretical underpinnings, methods, and practical use instruction of the ChISELS 1.0 computer code.
As current experimental and simulation methods cannot determine the mobility of flat boundaries across the large misorientation phase space, we have developed a computational method for imposing an artificial driving force on boundaries. In a molecular dynamics simulation, this allows us to go beyond the inherent timescale restrictions of the technique and induce non-negligible motion in flat boundaries of arbitrary misorientation. For different series of symmetric boundaries, we find both expected and unexpected results. In general, mobility increases as the grain boundary plane deviates from (111), but high-coincidence and low-angle boundaries represent special cases. These results agree with and enrich experimental observations.
The kinetic Monte Carlo method and its variants are powerful tools for modeling materials at the mesoscale, meaning at length and time scales in between the atomic and continuum. We have completed a 3 year LDRD project with the goal of developing a parallel kinetic Monte Carlo capability and applying it to materials modeling problems of interest to Sandia. In this report we give an overview of the methods and algorithms developed, and describe our new open-source code called SPPARKS, for Stochastic Parallel PARticle Kinetic Simulator. We also highlight the development of several Monte Carlo models in SPPARKS for specific materials modeling applications, including grain growth, bubble formation, diffusion in nanoporous materials, defect formation in erbium hydrides, and surface growth and evolution.
Resistive memory crossbars can dramatically reduce the energy required to perform computations in neural algorithms by three orders of magnitude when compared to an optimized digital ASIC [1]. For data intensive applications, the computational energy is dominated by moving data between the processor, SRAM, and DRAM. Analog crossbars overcome this by allowing data to be processed directly at each memory element. Analog crossbars accelerate three key operations that are the bulk of the computation in a neural network as illustrated in Fig 1: vector matrix multiplies (VMM), matrix vector multiplies (MVM), and outer product rank 1 updates (OPU)[2]. For an NxN crossbar the energy for each operation scales as the number of memory elements O(N2) [2]. This is because the crossbar performs its entire computation in one step, charging all the capacitances only once. Thus the CV2 energy of the array scales as array size. This fundamentally better than trying to read or write a digital memory. Each row of any NxN digital memory must be accessed one at a time, resulting in N columns of length O(N) being charged N times, requiring O(N3) energy to read a digital memory. Thus an analog crossbar has a fundamental O(N) energy scaling advantage over a digital system. Furthermore, if the read operation is done at low voltage and is therefore noise limited, the read energy can even be independent of the crossbar size, O(1) [2].