COMPONENTIZING NETPIPE AND INTERFACING WITH GAMESS. RICHARD
WANG (Carnegie Mellon University, Pittsburgh, PA, 15213)
MASHA SOSONKINA (Ames Laboratory, Ames, IA, 50011)
Common Component
Architecture (CCA) allows programs written in different languages
and having different interfaces to interoperate with minimal
effort. As a result, complex applications with enhanced functionalities
may be constructed, so that they run more efficiently and readily
facilitate scientific progress. NetPIPE and GAMESS, developed
at Iowa State University and Ames Laboratory, have been used
to demonstrate this outcome when brought together by CCA. GAMESS
is a scientific application that can be used to solve a variety
of quantum chemistry computations. NetPIPE is a network evaluation
program that sends messages back and forth between two a network
nodes. A NetPIPE component has been created and connected with
GAMESS components using a CCA framework to provide GAMESS with
the knowledge of network resources availability. First, NetPIPE
analyzes the current network state and checks whether it is in
line with the full capacity for the given network. Second, NetPIPE's
findings, GAMESS configures its communication protocols. The
aim is to show that GAMESS will run more efficiently when tuned
to network conditions as analyzed by NetPIPE in the preprocessing
stage. In general, experiments underscore the premise of the
component design that scientific applications can execute more
efficiently and tackle more complex problems when implemented
as components and interconnected within a component framework.
Crystallographic Descriptors of a Metal Surface along a Fracture Line. RYAN GLAMM (Ohio State University, Columbus, OH, 43210)
BARBARA K. LOGRASSO (Ames Laboratory, Ames, IA, 50011)
This work investigated
the feasibility of using electron back scattered diffraction
(EBSD) to associate, or differentiate, metal fracture fragments.
The objective of this work was to determine an empirical basis
for the hypothesis that a minimum sequence of grains can be used
to identify a metal fracture line beyond a reasonable doubt.
Crystallographic misorientations between individual grains were
determined using EBSD along several lines (point-to-origin vectors)
of metal crystals within the microstructure of a 304 stainless
steel. From a given starting crystal, a grid of vectors was used
to do relative referencing comparison of the grain orientation
profiles along each vector. A radial grid was used with 5° spacing
between vectors at a radius of 11.5 times the average grain diameter.
Misorientation angle between grains was calculated by averaging
the misorientation angles within a single grain and referencing
this average misorientation angle back to the origin grain. The
average vector matched 2.6±2 grains with adjacent vectors out
of 16.9±7 grains characterized per vector. In point by point
matching, vectors placed 5° apart had 83±11% of data points match
in the first 2.5 grains away from the origin, with that falling
to 36±10% in the last 2.5 grains characterized in the vector.
The extent of point to point matching confirms that this method
can properly identify when similar or dissimilar profiles are
being compared. This leads to the conclusion that a relatively
low number of grains need to be analyzed to uniquely characterize
a fracture line by relative crystallographic orientations. It
also opens the possibility to a more extensive statistical review
of concepts and data.
Developing EPIMODEL2: A Computer Program for Teaching Population Growth Modeling. DANIEL HEIDFELD (Michigan Technological
University, Houghton, MI, 49931)
FORREST W. NUTTER JR. (Ames Laboratory, Ames, IA, 50011)
EPIMODEL is
a computer teaching program that is currently being used in more
than 40 universities worldwide to teach students biological concepts
concerning population growth modeling. EPIMODEL has become outdated
because it was originally created in Quick BASIC for MS-DOS.
Therefore, the goal of this project was to rewrite EPIMODEL using
a computer language that would support Windows™. The programming
language Java was chosen to develop EPIMODEL2 because Java is
capable of operating on many platforms, including Windows™. EPIMODEL2
was programmed with the aid of various online manuals to develop
algorithms that implement features within the Java environment.
EPIMODEL2 was designed to mimic all of the features of the old
version of EPIMODEL, but the new program implements a Graphical
User Interface (GUI). The new program, EPIMODEL2, is a valuable
and more versatile replacement for the outdated version, and
the development of a new version in Java successfully accomplished
the goal of this internship.
Exploration of using Starch as a Recovery Agent for Catalytic Iodine. BEN SIKORA (Colorado School of Mines, Golden, CO, 80401)
JOHN VERKADE (Ames Laboratory, Ames, IA, 50011)
Currently a
method for conjugating soybean oil is being developed that uses
Iodine as a catalyst. To help conjugated soybean oil be more
economically comparable to other oils, on the industrial scale,
Iodine must be able to be recycled. A survey of a variety of
starches and mixtures of these starches with water at various
concentrations has been conducted to obtain optimum conditions
for the removal of Iodine from Hexanes, and subsequent recovery
from the starch. When potato starch was used it was found that
it worked best when only wetted. The wetted potato starch gave
the fastest absorption time of Iodine out of Hexanes, but posed
problems when trying to drive the Iodine back out of the starch
by thermal decomposition of the starch-Iodine complex. "V" modified
starch was found to work without an outside solvent, such as
water. This helped make the removal process of Iodine much simpler
by removing the need to separate another liquid from the process.
The results obtained for driving Iodine out of the starch were
different from literature insight in the fact that literature
suggests that Iodine will leave the starch under thermodynamic
activation. Some complications are still perplexing and require
future investigation, such as the best process to remove the
Iodine from the starch back into the Hexanes for recycling.
Kinetics Of Dissociation Of Molecular Oxygen From A Superoxorhodium Complex. MAGDALENA FURCZON (Moraine Valley Community College, Palos HIlls, IL, 60459)
ANDREJA BAKAC (Ames Laboratory, Ames, IA, 50011)
Reduced transition
metal complexes react with molecular oxygen to generate superoxometal
species which are important in both biological and industrial
oxidations with O2.
It has been shown previously that a macrocyclic cobalt complex
binds oxygen only weakly and was therefore not a good candidate
as a catalyst for oxidations with O2.
The goal of the current project is to determine the rate of oxygen
dissociation from the rhodium analogue, which is expected to
bind oxygen more strongly. The superoxorhodium complex L(H2O)RhOO2+ (L = hexamethylcyclam) was prepared from O2 and
photochemically generated L(H2O)Rh2+.
The reverse of this reaction is homolysis, the topic of our study.
After removal of free oxygen, the equilibrium is shifted to the
left, and the newly generated L(H2O)Rh2+ removed
in a reaction with either L(H2O)RhOO2+ or an externally added scavenger, such as hydrogen peroxide
(H2O2).
The kinetics of disappearance of L(H2O)RhOO2+ were measured spectrophotometrically. It was found that the
dissociation of O2 from L(H2O)RhOO2+ takes several hours (khomolysis = 2 x 10-4 s-1), whereas that from L(H2O)CoOO2+ requires
only 100 microseconds for completion (khomolysis = 2 x 104 s-1). The 108-fold difference
between the two metals is outstanding and will be exploited in
future work on rhodium-catalyzed oxidations with molecular oxygen.
New Algorithms for the Network Protocol Independent Performance Evaluator. CALEB KLAPP (Westminster College, Fulton, MO, 65251) TROY BENJEGERDES (Ames Laboratory, Ames, IA, 50011)
The Network
Protocol Independent Performance Evaluator, (NetPIPE) has been
in development for over 5 years. As the website http://www.scl.ameslab.gov/netpipe/
describes it, “NetPIPE is a protocol independent performance
tool that visually represents the network performance under a
variety of conditions. It performs simple ping-pong tests, bouncing
messages of increasing size between two processes, whether across
a network or within an SMP system. Message sizes are chosen at
regular intervals, and with slight perturbations, to provide
a complete test of the communication system.” The original NetPIPE
program was designed with a single-pass algorithm using exponentially
increasing message sizes that exits when a time limit to transfer
a message was reached. In order to improve on this design, a
multi-stage algorithm was implemented. This new program uses
a pan and scan method to accurately derive a representative equation
for bandwidth at all message sizes. Some preliminary tests have
been performed on well behaved networks where the accuracy of
the program's calculations can be assessed. Comparing the experimental
data with the curve generated by the program has provided strong
evidence that the program produces valid performance information
as well as statistical analyses of the network performance data
which was not available with previous implementations.
Novel Coarsening of Pb Nanostructures on Si(111) 7 X 7. CHARLES
PYE (University of Kansas, Lawrence, KS, 66044) MICHAEL TRINGIDES (Ames Laboratory, Ames, IA, 50011)
This work investigated
the feasibility of using electron back scattered diffraction
(EBSD) to associate, or differentiate, metal fracture fragments.
The objective of this work was to determine an empirical basis
for the hypothesis that a minimum sequence of grains can be used
to identify a metal fracture line beyond a reasonable doubt.
Crystallographic misorientations between individual grains were
determined using EBSD along several lines (point-to-origin vectors)
of metal crystals within the microstructure of a 304 stainless
steel. From a given starting crystal, a grid of vectors was used
to do relative referencing comparison of the grain orientation
profiles along each vector. A radial grid was used with 5° spacing
between vectors at a radius of 11.5 times the average grain diameter.
Misorientation angle between grains was calculated by averaging
the misorientation angles within a single grain and referencing
this average misorientation angle back to the origin grain. The
average vector matched 2.6±2 grains with adjacent vectors out
of 16.9±7 grains characterized per vector. In point by point
matching, vectors placed 5° apart had 83±11% of data points match
in the first 2.5 grains away from the origin, with that falling
to 36±10% in the last 2.5 grains characterized in the vector.
The extent of point to point matching confirms that this method
can properly identify when similar or dissimilar profiles are
being compared. This leads to the conclusion that a relatively
low number of grains need to be analyzed to uniquely characterize
a fracture line by relative crystallographic orientations. It
also opens the possibility to a more extensive statistical review
of concepts and data.
Structural and Functional Studies of Multidrug Binding Protein, AcrR. DENAE CLAMPITT (Western Illinois University, Macomb, IL, 61455)
EDWARD YU (Ames Laboratory, Ames, IA, 50011)
This project
addresses fundamental questions regarding the nature of multi-ligand
recognition in transcriptional regulators. The primary target
is the Escherichia coli AcrR
repressor that regulates the multidrug transporter AcrB. The
215-residue AcrR consists of two domains, the C-terminal multi-ligand
binding and the N-terminal DNA binding domains. Upon binding
a wide variety of structurally diverse ligands in the C-terminal
region, it triggers conformational change at the N-terminal domain,
prohibiting the binding of AcrR to its target DNA. The sum result
is the over-expression of the AcrB transporter, which, in turn,
promotes efflux from the cell, thus protecting it from toxic
substances. How can AcrR and other transcriptional repressors
recognize a variety of toxic chemicals? To gain insight into
the mechanism that AcrR uses to recognize multi-ligand, we crystallized
the AcrR protein, and studied its function using circular dichroism
and tryptophan fluorescence measurements. We also measured the
binding affinities of rhodamine-6G, ciprofloxacin, and ethidium
bromide with AcrR. As AcrR is capable of recognizing a variety
of toxic chemicals, this research has the potential to contribute
to the development of protein-based chemical sensors.
Synthesis of Magnetic Nanoparticles. DEANNA
JONES (Brigham Young University
- Idaho, Rexburg, ID, 83440)
SURYA MALLAPRAGADA (Ames Laboratory, Ames, IA, 50011)
In this work,
a novel biomimetic synthesis was explored to form magnetic nanocrystalline
iron and iron-cobalt oxides in-vitro. Magnetite and mixed iron-cobalt
oxide nanocrystals were synthesized via a room-temperature co-precipitation
method in the presence of a recombinant, iron-binding protein
Mms6. This protein is thought to be involved in the biomineralization
and the formation of uniform magnetite nanoparticles in magnetotactic
bacteria. Synthesis was performed in aqueous polymeric gels to
slow down the diffusion rates of the reagents to better mimic
biological conditions. These gels included: agarose gel, thermoresponsive
Pluronic F127 gel and thermo and pH-responsive pentablock copolymer.
The resulting nanocrystalline magnetic particles were comprehensively
studied using Transmission Electron Microscopy, Electron Diffraction
Methods, X-ray Photoelectron Spectroscopy; and magnetization
measurements. The oxide particles were found to be crystalline
and superparamagnetic. They had a wide size distribution, depending
on the media and whether or not Mms6 was present. This method
provides a bioinspired route to nanomaterials synthesis and it
is now being tested in synthesis of mixed iron-ruthenium oxides.
Thermoset Composites from Bio-based Oils and Spent Germ from Ethanol Production. JEFFREY BAKER (Pennsylvania State University, State College, PA, 16801)
DR. RICHARD C. LAROCK (Ames Laboratory, Ames, IA, 50011)
Thermoset composites
have been prepared by the use of a bio-based resin and spent
germ filler, which is a byproduct from a wet ethanol production
plant. The bio-based resin is prepared by the free radical co-polymerization
of tung oil (TNG), methacrylonitrile (MAN), divinylbenzene (DVB),
and initiated with cumene hydroperoxide (CHP). This bio-based
resin is pre-cured for a few hours before being mixed with the
spent germ, the filler, upon which the mixture is cured under
mechanical pressure, and then post cured in an oven. The resulting
composite material consists of roughly a 1:1 ratio of resin to
spent germ. The crosslinked thermosets are dark brown in color,
hard and brittle, and have a slight burnt odor. Thermal and mechanical
analysis of the composites has been performed via thermogravimetric
analysis (TGA) and tensile testing. Results from the TGA show
that the composites have a multiple stage degradation with unstable
intermediates ranging from 239 – 304 ºC and 465 – 478 ºC. The
tensile tests show on average the modulus values range from 915 – 1375
MPa and the toughness values range from 0.02 – 0.05 MPa
