Personnel

Overview

The theoretical Chemical Physics program at Ames Laboratory supports integrated efforts in electronic structure theory and non-equilibrium statistical mechanical & multiscale modeling.  The primary focus is on the development and especially application of methods that enable the study of surface phenomena, heterogeneous catalysis, surface and bulk properties of solid clusters, solvent effects, and mechanisms in organometallic chemistry including solvents and relativistic effects.

Electronic structure theory efforts integrate development of fundamental theory by (expanding the capability for accurate treatment of large or complex systems of interest to DOE), with optimal strategies for computational implementation within GAMESS and NWChem. In particular, this includes development of embedding methods, effective fragment potential approaches, with special interest in liquid-solid interfaces, and a rigorous basis for semi-empirical tight-binding methods, all geared towards applications to various complex condensed phase systems.

The statistical mechanical & multiscale modeling studies often incorporate energetics from electronic structure analyses. A core focus is the modeling of chemisorption and heterogeneous catalysis on metal surfaces. We consider both reactions on extended surfaces (including multiscale studies of spatiotemporal behavior) and in nanoscale catalyst systems (including analysis of fluctuation effects). We also model transport and reaction processes at non-conducting surfaces and in mesoporous systems, and analyze fundamental behavior in general far-from-equilibrium reaction-diffusion systems.

 

This research is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences through the Ames Laboratory.  The Ames Laboratory is operated for the U.S. Department of Energy by Iowa State University under Contract No. DE-AC02-07CH11358.

Publications

2008
Bytautas L; Ruedenberg K . 2008. Correlation energy and dispersion interaction in the ab initio potential energy curve of the neon dimer. Journal of Chemical Physics. 128:214308. abstract
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2007
Bitter T; Ruedenberg K; Schwarz W H E . 2007. Toward a physical understanding of electron-sharing two-center bonds. I. General aspects. Journal of Computational Chemistry. 28:411-422. abstract
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Personnel

Overview

We seek to understand the basic principles that underlie energy-relevant chemical separations; develop analytical methods to improve the sensitivity, reliability, and productivity of analytical determinations; and to develop new approaches to analysis. Our research emphasizes instrumentation and technique development highly relevant to the main focus areas of the Separation and Analysis activities of the Division of Chemical Science, Geoscience and Biosciences within the DOE Office of Basic Energy Sciences.  

The goal of this research is to develop the next generation of imaging tools and methodologies for the analysis of phenomena that occur at nanometer length scales and picosecond time scales. The developed instrumentation and methodology will be applied to model systems of interest to the DOE mission, where fundamental insight can be gained with the high spatial and temporal resolution afforded by our developed methods: chemical reac tions in heterogeneous silica supported catalysts; the organization and dynamics of mixed model lipid bilayers and cell membranes; chromatographic interactions; and heterogeneous enzyme reactions. The methods we propose to develop are:

1. High resolution total internal reflection (TIR) Raman microspectroscopy and imaging
2. Sub-diffraction limited imaging, including differential interference contrast (DIC) microscopy, variable-angle evanescent-field (EFM) microscopy, and time-resolved stimulated emission depletion (STED) microscopy
3. Novel single molecule spectroscopies

 

This research is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences through the Ames Laboratory.  The Ames Laboratory is operated for the U.S. Department of Energy by Iowa State University under Contract No. DE-AC02-07CH11358.

Publications

2008
Li J W; Yeung E S . 2008. Real-Time Single-Molecule Kinetics of Trypsin Proteolysis. Analytical Chemistry. 80:8509-8513. abstract
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Sun W; Fang N; Trewyn B G; Tsunoda M; Slowing I I; Lin V S Y; Yeung E S . 2008. Endocytosis of a single mesoporous silica nanoparticle into a human lung cancer cell observed by differential interference contrast microscopy. Analytical and Bioanalytical Chemistry. 391:2119-2125. abstract
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Zhang Y; Phillips G J; Yeung E S . 2008. Quantitative imaging of gene expression in individual bacterial cells by chemiluminescence. Analytical Chemistry. 80:597-605. abstract
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Personnel

Overview

The Computational Science effort is focused on issues of development, use and performance of advanced parallel computer architectures.  This includes the development of advanced system and resource management software in collaboration with other groups around the country.  In addition, issues of network performance are addressed through the investigation of OS-bypass technologies on a variety of network hardware and operating system architectures.

Publications

Personnel

Overview

The new generation of complex physical models encountered today in DOE mission-critical applications often result in large sparse linear and least-squares systems of equations which are very difficult to solve.  Our goal is to investigate robust parallel reconditioning techniques for solving difficult large sparse linear systems, such as those that arise in circuit simulation, and the simulation of wave phenomena.  We have recently developed a solution technique based on a form of a multilevel implementation of complete-pivoting incomplete LU factorization.  The starting point for this research is to consider parallel implementations of this strategy.  We will also develop multilevel strategies for least-squares problems, which are similar in spirit to those of the Algebraic Recursive Multilevel Solvers.                   

Publications

2011
Carlson B C . 2011. Permutation symmetry for theta functions. Journal of Mathematical Analysis and Applications. 378:42-48. abstract
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Personnel

Overview

A multi-scale approach, from very high accuracy quantum chemistry methods, to coarse grained potentials that are derived directly from quantum mechanics, to large scale stochastic models will be developed and applied to important problems in bio-remediation, including the interactions of heavy metal complexes with proteins and their building blocks. To make this effort computationally viable, new parallel computing paradigms will be developed, including innovative methods that are designed to take advantage of new petascale hardware systems.

Publications

2012
Rios D; Schoendorff G; Van Stipdonk M J; Gordon M S; Windus T L; Gibson J K; de Jong W A . 2012. Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes. Inorganic Chemistry. 51:12768-12775. abstract
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Personnel

Overview

Researchers will arrive at a comprehensive and unified description of nuclei and their reactions that is grounded in the interactions between the constituent nucleons. Current phenomenological models of nuclear structure and reactions will be replaced with a well-founded microscopic theory delivering maximum predictive power with minimal, well quantified uncertainties.  A national effort will link theoretical physics and computational science together to develop forefront software for state-of-the-art architectures. A national capability will be built to calculate nuclear structure and low-energy nuclear cross sections, and assess their uncertainties, relevant to several DOE programs. Nuclear structure and reactions play an essential role in the science to be investigated at the Rare Isotope Accelerator (RIA) and in nuclear physics applications to the Science-Based Stockpile Stewardship program, next generation reactors, and threat reduction.  In order to build this capability, we will develop a multi-pronged program of theoretical, algorithmic, and computational developments that will deliver nuclear cross section information critical to DOE programs that is more accurate than is currently available. We anticipate an expansion of the computational techniques and methods we currently employ, and developments of new treatments, to take advantage of petascale architectures.

Publications

2009
He J; Watson L T; Sosonkina M . 2009. Algorithm 897: VTDIRECT95: Serial and Parallel Codes for the Global Optimization Algorithm DIRECT. Acm Transactions on Mathematical Software. 36:17. abstract
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Laghave N; Sosonkina M; Maris P; Vary J P . 2009. Benefits of Parallel I/O in Ab Initio Nuclear Physics Calculations. Computational Science - Iccs 2009, Part I. 5544:84-931030. abstract
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It is proposed to further the present understanding of circulating fluidized beds from the conceptual standpoint of kinetic theory.  The primary purpose is to provide a theoretical underpinning for the construction of computer codes to better understand and predict multiphase flow behavior in circulating fluidized beds, and, in particular, to provide theoretical estimates for the transport coefficient analogues that parameterize the computer simulations.

Publications

Personnel

Overview

High-performance applications executing on distributed systems achieve only a fraction of the peak aggregate performance of the underlying hardware and middleware.  This is due mainly to the mismatch between the way parallel computation and communication are organized into applications and the optimal way to use the processor, memory, and interconnect hardware.  Different programming models, language primitives, and supporting services are “single-box” systems to distributed systems with nodes located thousands of miles apart.  The purpose of the project is twofold: to achieve transparent tuning of high-performance applications to the communication subsystem while facilitating transition to future programming models, and to augment the newly developed and enhanced programming models with information about the communication environment.

Publications

2011
Liu F; Sosonkina M; Sato M; Matsuoka S; Sloot P M A; VanAlbada G D; Dongarra J . 2011. A Multilevel Parallelism Support for Multi-Physics Coupling. Proceedings of the International Conference on Computational Science. 4:261-270. abstract
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2010
Liu F; Sosonkina M; Bramley R . 2010. A New Approach: Component-Based Multi-physics Coupling through CCA-LISI. Computational Science and Its Applications - Iccsa 2010, Pt 2, Proceedings. 6017:503-518602. abstract
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2009
Asadchev A; Bode B M; Gordon M S . 2009. Performance of Electronic Structure Calculations on BG/L and XT4 Computers. Journal of Computational and Theoretical Nanoscience. 6:1290-1296. abstract
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Personnel

Overview

The development of emerging technologies such as molecular computing, nanotechnology, and next generation catalysts will continue to place increasing demands on chemical simulation software, requiring more capabilities and more sophisticated simulation environments.  Such software will be too complex for a single group, or even a single discipline to develop independently.  Coupling multiple physical models in one domain and coupling simulations across multiple time and length-scales will become the norm rather than the exception. These simulations will also run on more complicated and diverse hardware platforms, potentially with hundreds of thousands of processors and performance exceeding one petaFLOP/s.  This evolution will transform the way chemists must think about scientific problems, models and algorithms, software lifecycle and the use of computational resources.  Advances in chemical science critical to DOE and national challenges require adoption of new approaches for large-scale collaborative development and a flexible, community-based architecture. We propose to employ the infrastructure of the Common Component Architecture to develop interfaces among three of the most important computational chemistry codes in the world: General Atomic and Molecular Electronic Structure System (GAMESS), the Massively Parallel Quantum Chemistry program (MPQC) and Northwest Chem (NWChem).

Publications

2009
Crosby L D; Windus T L . 2009. Temperature Scaling Method for Markov Chains. Journal of Physical Chemistry A. 113:607-616. abstract
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Andreja Bakac Group

Reaserch Interests

Our research focuses on activation of oxygen in its various forms (molecular oxygen, peroxide, ozone) for oxidations of organic and inorganic substrates. Coordination and partial reduction of oxygen by transition metal complexes provides an exceptionally powerful activation method that is widely utilized in nature and somewhat less efficiently in the laboratory.