Pacific Northwest National Laboratory

Ocean Dynamics in the GeoMIP G1 Suite of GCM Simulations
Hansi Singh, University of Washington
Practicum Year: 2014
Practicum Supervisor: Phillip Rasch, Chief Scientist for Climate Science, Atmospheric Sciences and Global Change, Pacific Northwest National Laboratory
Analyzed model output from the GeoMIP suite of climate models regarding the effect of geoengineering via solar radiation management on the ocean. Worked on attribution of the ocean response to the changes in the surface wind stress forcing.
Genetic algorithm-based inference of protein-protein interactions
Jeffrey Kilpatrick, Rice University
Practicum Year: 2010
Practicum Supervisor: Haluk Resat, Senior Research Scientist, Biological Sciences, Pacific Northwest National Laboratory
The complexity and robustness of biology is engineered in a similar fashion to many man-made large-scale systems: with a limited number of parts interacting in multiple contexts to achieve various goals. Proteins, which are themselves comprised of domains that often occur in many molecules and species, form the basis of this machinery. We extended a framework to infer protein-protein interactions by way of guessing the strength of domain-domain interactions using a genetic algorithm. We found that the procedure produces robust predictions, even when training with data from distantly related species.
Implementation of coupled-cluster linear response theory for molecular properties within NWChem
Jeff Hammond, University of Chicago
Practicum Year: 2006
Practicum Supervisor: Dr. Bert deJong, Senior Research Scientist, EMSL: MSCF Visualization & User Services, Pacific Northwest National Laboratory
The goal of this project was to add molecular property functionality to the high-accuracy methods within NWChem. Karol Kowalski and I implemented linear-response theory for CCSD and CCSDT dipole moments and dipole polarizabilities. This code allows the study of molecules previously inaccessible with these levels of theory. We are currently extending these developments in a number of directions, including QM/MM calculations of solvated molecules in collaboration with Marat Valiev and other kinds properties with Bert deJong.
Integration of models TNF and EGF signaling pathways in HMEC cells
Bree Aldridge, Massachusetts Institute of Technology
Practicum Year: 2004
Practicum Supervisor: Steven Wiley, Director, Biomolecular Systems, Systems Biology, Biomolecular Systems, Pacific Northwest National Laboratory
The purpose of the project was to lay the computational foundation for merging large scale signaling pathway models. The growing number of ODE-based models of signaling pathways being developed at PNNL and in academia creates the need to explore how to combine and compare large models. Over the course of the practicum, we re-formatted three large (500-1000 ODEs) models to be SMBL-exportable and graphically supported. To prepare exploring how the three models might be merged, a series of quantitative Western blots were performed. We established that before merging the models together, we need a mathematical representation of extracellular crosstalk. The Western blots also helped us clarify the downstream crosstalk between TNF and EGF receptor signaling. Collaborative work on this project is ongoing.
Microarray analysis of a crp regulatory mutant of Shewanella oneidensis
Amoolya Singh, University of California, Berkeley
Practicum Year: 2004
Practicum Supervisor: Jim Fredrickson, Laboratory Fellow, Biological Sciences Division, Pacific Northwest National Laboratory
This summer, I set out to learn the high-throughput experimental techniques that generate the biological data feeding my (theoretical) thesis work, and to study in detail the gene regulatory networks activated by environmental stress in various ecological niches. I focused on two strains of the model bacterium Shewanella oneidensis MR-1, one wild type and the other a crp regulatory mutant which, in addition to being defective in catabolite repression and carbon source selection, is also deficient in anaerobic respiration (Saffarini, Schultz et al. 2003). Both strains had been cultured in chemostats at PNNL in August 2003 with a variety of nutrient sources, electron acceptors, and oxygen concentrations.
Computer Simulations of The Active Site of Ras/Raf
Seung Lee, Massachusetts Institute of Technology
Practicum Year: 2003
Practicum Supervisor: David A. Dixon, Associate Director, Theory, Modeling and Simulation, Pacific Northwest National Laboratory
The Ras proteins are a family of the GTP-activated molecular switches that control signaling pathways for gene expression, cell proliferation and differentiation. The GDP-bound OFF (inactive) state can be activated by exchanging GDP with GTP. The GTP-bound ON (active) state can be turned off by hydrolysis of GTP to GDP. This hydrolysis rate can be increased by factors of up to 105 with the presence of GTPase activating proteins (GAPs). Mutations were found on Gln-61 of Ras proteins in 30% of human tumors. These mutations are characterized by decrease in hydrolysis rate and insensitivity to GAP. Ras also interacts with the well characterized effector protein Raf-1 to trigger the pathways for gene expression. We turn to numerical analyses, molecular dynamics and quantum mechanics, to elucidate the specific chemical interactions of these protein-protein complexes.
Evaluation of a Variety of Chemistry-transport Coupling Methods for Geochemical Groundwater Transport
Christopher Gesh, Texas A&M University
Practicum Year: 1995
Practicum Supervisor: Dr. Steven Yabusaki, , Environmental Research Center, Pacific Northwest National Laboratory
I helped evaluate the relative effectiveness of three methods for coupling the chemistry and transport code. I wrote several one dimensional codes for testing purposes and modified an existing three dimensional code. The methods we considered were global implicit, operator splitting and sequential iteration.
Odor Classification with Fuzzy ARTMAP
Lars Liden, Boston University
Practicum Year: 1995
Practicum Supervisor: Dr. Paul Keller, , Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory
The ability of an artificial neural network known as Fuzzy ARTMAP to classify and identify odors present in an enclosed environment was examined. Data collected from an array of widely-tuned tin-oxide sensors formed a distributed representation (or signature) for chemicals present in an enclosed environment. The Fuzzy ARTMAP network learned to correctly classify sensor activations into categories and identify which chemical or combination of chemicals was present.
A Parallel Implementation of the Car-Parrinello Algorithm
James Wiggs, University of Washington
Practicum Year: 1992
Practicum Supervisor: Dr. John Lafemina, , Materials and Interfaces, Pacific Northwest National Laboratory
The Car-Parrinello algorithm is a computationally expensive technique for doing ab-initio molecular dynamics and global energy minimization of a coupled ionic-electronic system. We have developed a portable parallel implementation of the algorithm to be used on such machines as the iPSC/860, the Intel Delta or Paragon, the CM-5, etc.