You are here

Scalable Systems Software Activity

FWP/Project Description: 

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.

Principal Investigators:
Mark Gordon

Chemical Analysis of Nanodomains

FWP/Project Description: 

Project Leader(s): Emily Smith

Principal Investigators: Ning Fang, Jacob Petrich, Emily Smith


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 reactions 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

Chemical Physics

FWP/Project Description: 

Project Leader(s): James Evans, Mark Gordon

Principal Investigators: James Evans, Mark Gordon, Klaus Ruedenberg, Theresa Windus

Key Scientific Personnel: Da-Jiang Liu, Michael Schmidt.


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

Homogeneous and Interfacial Catalysis in 3D Controlled Environment

FWP/Project Description: 

Project Leader(s): Marek Pruski

Principal Investigators: Andreja Bakac, Marek Pruski, Aaron Sadow, Igor Slowing

Key Scientific Personnel: Takeshi Kobayashi, Oleg Pestovsky


This collaborative research effort is geared toward bringing together the best features of homogeneous and heterogeneous catalysis for developing new catalytic principles. Novel silica-based, single-site mesoporous catalysts with controlled, nanostructured morphology and surface properties will be prepared. The control of specific chemical properties, spatial distribution, and concentrations of various catalytic functional groups on the pore walls will be achieved. The catalytic activity of these single-site heterogeneous catalysts will be examined. Detailed mechanistic studies of such systems will be carried out in an effort to recognize the key factors that determine selectivity, reactivity and kinetics of both homogeneous and heterogeneous catalytic reactions.

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

Mass Spectrometric Imaging of Plant Metabolites

FWP/Project Description: 

Project Leader(s): Basil Nikolau

Principal Investigators: Robert Houk, Young-Jin Lee, Basil Nikolau


We are developing mass spectrometric imaging techniques to map metabolite distributions within plant tissues, and eventually among individual plant cells. Such details will ultimately lead to a predictive understanding of the mechanisms that multicellular organisms use to regulate metabolic processes. By studying the diversity of the cuticular waxes, we hope to gain detailed insight into their biosynthesis as a function of genetics, tissue type, development, and environment. A laser beam will be used to interrogate sequentially micrometer areas of a plant by vaporizing the surface contents of the tissue into a mass spectrometer. Rastering of the laser beam over the tissue will produce a laterally resolved image of the various substances within different structures of the plant. Repeated vaporization at the same focused point of a plant structure will produce a depth profile of the components. We plan to generate ions directly from the plant tissue by designing novel additives as pseudo-matrixes.

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


FWP/Project Description: 

This research project aims to develop a nanoparticle technology for efficient and economical extraction methods for harvesting suitable chemical compounds, such as triglycerides, neutral lipids, and fatty acids, from microalgae for biodiesel production and single-step conversion to biodiesel.  Our proposal involves the use of nanoparticles to perform the following two stages, with superior efficiency in terms of yield, simplicity of processing and energy consumption.

  1. Simple, selective and efficient extraction of fatty acids by recyclable mesoporous nanoparticles possessing large surface areas and volumes and adjustable pore size.
  2. One step conversion of the extracted fatty acids into biodiesel by reusable, highly reactive nanoparticle based catalyst (Catilin method).


This research was supported by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy under grant Grant No. DE-FG26-0NT08854 through the Ames Laboratory. The Ames Laboratory is operated for the U.S. Department of Energy, Office of Basic Energy Sciences by Iowa State University under Contract No. DE-AC02-07CH11358.
This project concluded September 30, 2012.

Principal Investigators:
Young-Jin Lee, Marek Pruski

Key Scientific Personnel:
Igor Slowing

Theoretical/Computational Tools for Energy-Relevant Catalysis

FWP/Project Description: 

Project Leader(s): James Evans, Mark Gordon

Principal Investigators: James Evans, Mark Gordon


This project will develop new strategies for and integrated combinations of electronic structure analysis and statistical mechanical, coarse-grained, and multi-scale modeling approaches to treat energy-relevant heterogeneous catalytic systems. Currently, there is a lack of effective molecular-level modeling for overall catalytic reaction processes and a critical need to incorporate high-level energetics for predictivity. Essential to these efforts will be the development of novel new approaches in not only theoretical chemistry and materials science (BES), but also computational science and applied mathematics (ASCR).  Applications motivating the work include analysis of catalysis in mesoporous oxides and catalysis on metal surfaces and supported metal nanoclusters.

This research is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences and by the U.S. Department of Energy, Office of Advanced Scientific Computing Research 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

Bioinspired Materials

FWP/Project Description: 
Project Leader(s):
Principal Investigators:
Mufit Akinc, Surya Mallapragada, Marit Nilsen-Hamilton, Ruslan Prozorov, Alex Travesset, David Vaknin 
Postdoctoral Research Associates:
Wenjie Wang

The goal of this highly-interdisciplinary project is the synthesis and characterization of bioinspired hierarchical self-assembling polymer-inorganic nanocomposites. It seeks to answer the following questions:

  • What are the general design rules for bioinspired self-assembled polymer nanocomposites? To answer this question, a highly synergistic combination of theory and experiment will be implemented.
  • What experimental techniques or approaches can be developed or combined to probe the assembly at multiple length scales?

This work yields a robust and modular method for developing bioinspired hierarchical materials, with control over the formation as well as placement of an inorganic phase in the nanocomposite structure. This, in turn, leads to development of novel hybrid materials, lightweight and energy efficient, with potential for applications in fuel cells, spintronics, quantum computing, or magnetic actuators. This closely knit group, involving biochemists, chemists, materials scientists, engineers, and physicists, provides a unique skill set for this work; the success of their synergy has already been demonstrated by their bioinspired synthesis of magnetic nanoparticles.

Subtasks in this Project are:

  • Development of multiscale self-assembling bioinspired hybrid materials using bottom-up approaches. We design hierarchically self-assembling templates (synthetic polymers as well as protein- and peptide-based templates), and use bioinspired methods for room temperature synthesis of several energy-relevant hybrid materials with hierarchical order that are difficult to synthesize otherwise. (S. Mallapragada, M. Nilsen-Hamilton, M. Akinc, T. Prozorov, G. Kraus)
  • Development of techniques to probe assembly at multiple length scales and properties of these nanocomposites. We use a combination of solid-state NMR, scattering, and electron microscopy techniques to investigate the nanostructure and composition, and other characterization techniques to investigate the magneto-mechanical properties of these hybrid materials. (K. Schmidt-Rohr, B. Narasimhan, D. Vaknin)
  • Development of computational methods for understanding general design rules for self-assembled polymer nanocomposites. We develop and implement molecular simulations, using high performance computational approaches as a powerful tool to understand the underlying principles of self-assembly of complex structures, phase transformation between competing phases, as well as the response of a self assembled system to external stimuli. (A. Travesset-Casas, M. Lamm)

Complex Hydrides—A New Frontier for Future Energy Applications

FWP/Project Description: 
Project Leader(s):
Vitalij Pecharsky

Principal Investigators:
Scott Chumbley, Duane Johnson, Marek Pruski

Hydrogen storage is one of the enabling technologies required to guarantee a successful future transition from fossil to hydrogen based fuels. The proposed multidisciplinary research effort draws on considerable experimental and modeling experience and expertise existing at the Ames Laboratory in order to achieve a fundamental understanding of the relationships between the chemical composition, bonding, structure, microstructure, properties and performance of novel hydrogen-rich solid systems. We seek solids that mimic the structure of methane and ammonia, where four or three hydrogen atoms encapsulate a single carbon or nitrogen atom forming neutral CH4 and NH3 molecules as opposed to conventional metal hydrides where a single hydrogen atom is encapsulated by several metal atoms.  Mechanochemistry and thermochemistry coupled with advanced characterization, theory, modeling, and simulations are used to understand composition-structure-processing-property relationships in complex materials systems consisting of light-metal hydride compounds and their derivatives.

The specific objectives are to address issues that will advance basic science of complex hydrides and open up possibili¬ties for their future use by drawing on the experience and expertise of principal investigators in materials science, physics and chemistry of com¬plex hydrides, X-ray diffraction (XRD), high-resolution solid-state nuclear magnetic resonance (NMR), electron microscopy, and first-principles theory and modeling.  Our goals are:

  • Examine both mechanical energy- and thermal energy-driven phase transformations in chosen model hydride systems at and away from thermodynamic equilibrium.
  • Establish the nature of the products and intermediates using state-of-the-art characterization methods.
  • Identify events critical to achiev¬ing reversibility of hydrogen at mild conditions in model systems.
  • Integrate experiment with first-principles theory to provide a fundamental under¬standing of the nature of hydrogen bonding and formation, structure, and stability of the model systems, the effects of mechanical energy, temperature, and pressure in controlling the na¬ture of hydrogen-metal bonds.
  • Refine and extend the current understanding of the mechanisms of solid-state transforma¬tions from a few known hydrides to complex hydride-hydrogen systems by examining how chemical and structural modifications affect dehydrogenation/hydrogenation behaviors of selected model systems.
  • Create a knowledge base relating composition, structure and properties of model hydrides by investigating the effects of varying stoichiometry and processing history on their crystal and microscopic structures, chemical, thermodynamic and physical properties.
  • Develop predictive tools suitable to guide the discovery of materials at the atomic scale and tuning proc¬essing strategies to control the nano-, meso- and microscopic structures.

Complex States, Emergent Phenomena & Superconductivity in Intermetallic & Metal-like Compounds

FWP/Project Description: 


Project Leader(s):
Paul Canfield

Principal Investigators:
Sergey Bud'ko, Yuji Furukawa, David Johnston, Adam Kaminski, Vladimir Kogan, Ruslan Prozorov, Makariy Tanatar

The specific scientific question to be addressed by this FWP is: how can we develop, discover, understand and ultimately control and predictably modify new and extreme examples of complex states, emergent phenomena, and superconductivity? Over the next review period we will study materials manifesting specifically clear or compelling examples (or combinations) of superconductivity, strongly correlated electrons, quantum criticality, and exotic, bulk magnetism because of their potential to lead to revolutionary steps forward in our understanding of their complex, and potentially energy relevant, properties. For example, part of our effort will focus on the understanding and control of FeAs‐based superconductors as well as searching for other examples of novel, or high temperature, superconductivity. This work will be leveraged via highly collaborative interactions between the scientists within this FWP as well as through extensive collaborations with other Ames Laboratory FWPs, other DOE laboratories, and other universities and labs throughout the world. Experiment and theory will be implemented synergistically. The experimental work will consist of new materials development and crystal growth, combined with detailed and advanced measurements of microscopic, thermodynamic, transport, and spectroscopic properties, as well as electronic structure, at extremes of pressure, temperature, magnetic field and resolution. The theoretical work will focus on modeling transport, thermodynamic and spectroscopic properties using world‐leading, phenomenological approaches to superconductors and modern quantum many‐body theory.

To accomplish our goals, three highly interacting classes of research operate both in series and in parallel:

  • Design and Growth: (Canfield, Bud’ko, Johnston, Kogan)
  • Advanced Characterization: (Bud’ko, Furukawa, Kaminski, Prozorov, Tanatar)
  • Theory and Modeling: (Kogan, Johnston, Prozorov)


Subscribe to The Ames Laboratory RSS