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A Mathematical Analysis of Atomistic-to-Continuum (AtC) Multiscale Approaches

Description: We development a general framework for information-passing and concurrent discrete to continuum scale bridging and applied it to biological, electro-mechanical and thermo-electrical systems. Funds were used for partial support of two post-doctoral research associates (Aiqin Li, Dawei Zhang) and three graduate students (Renge Li, Mohan Nuggehally, Joseph Riendeau).
Date: February 24, 2009
Creator: Fish, Jacob & Shephard, Mark
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics

Description: The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research p… more
Date: February 21, 2008
Creator: Wallace, Susan S.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Cleanup Verification Package for the118-F-2 Burial Ground

Description: This cleanup verification package documents completion of remedial action, sampling activities, and compliance with cleanup criteria for the 118-F-2 Burial Ground. This burial ground, formerly called Solid Waste Burial Ground No. 1, was the original solid waste disposal site for the 100-F Area. Eight trenches contained miscellaneous solid waste from the 105-F Reactor and one trench contained solid waste from the biology facilities.
Date: February 21, 2008
Creator: Anselm, J. M. Capron and K. A.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

2007 Plant Metabolic Engineering Gordon Conference and Graduate Research Seminar

Description: Plant Metabolic Engineering is an emerging field that integrates a diverse range of disciplines including plant genetics, genomics, biochemistry, chemistry and cell biology. The Gordon-Kenan Graduate Research Seminar (GRS) in Plant Metabolic Engineering was initiated to provide a unique opportunity for future researcher leaders to present their work in this field. It also creates an environment allowing for peer-review and critical assessment of work without the intimidation usually associated … more
Date: September 15, 2008
Creator: Grotewold, Erich
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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2007 Archaea: Ecology, Metabolism and Molecular Biology

Description: The Archaea are a fascinating and diverse group of prokaryotic organisms with deep roots overlapping those of eukaryotes. The focus of this GRC conference, 'Archaea: Ecology Metabolism & Molecular Biology', expands on a number of emerging topics highlighting the evolution and composition of microbial communities and novel archaeal species, their impact on the environment, archaeal metabolism, and research that stems from sequence analysis of archaeal genomes. The strength of this conference lie… more
Date: September 18, 2008
Creator: Gray, Imke Schroeder Nancy Ryan
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department

Discovering and validating biological hypotheses from coherent patterns in functional genomics data

Description: The area of transcriptomics analysis is among the more established in computational biology, having evolved in both technology and experimental design. Transcriptomics has a strong impetus to develop sophisticated computational methods due to the large amounts of available whole-genome datasets for many species and because of powerful applications in regulatory network reconstruction as well as elucidation and modeling of cellular transcriptional responses. While gene expression microarray data… more
Date: August 12, 2008
Creator: Joachimiak, Marcin Pawel
Item Type: Refine your search to only Presentation
Partner: UNT Libraries Government Documents Department
open access

The Trichoplax Genome and the Nature of Placozoans

Description: Placozoans are arguably the simplest free-living animals, possibly evoking an early stage in metazoan evolution, yet their biology is poorly understood. Here we report the sequencing and analysis of the {approx}98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome exhibits cons… more
Date: August 1, 2008
Creator: Srivastava, Mansi; Begovic, Emina; Chapman, Jarrod; Putnam, Nicholas H.; Hellsten, Uffe; Kawashima, Takeshi et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Computational Biology, Advanced Scientific Computing, and Emerging Computational Architectures

Description: This CRADA was established at the start of FY02 with $200 K from IBM and matching funds from DOE to support post-doctoral fellows in collaborative research between International Business Machines and Oak Ridge National Laboratory to explore effective use of emerging petascale computational architectures for the solution of computational biology problems. 'No cost' extensions of the CRADA were negotiated with IBM for FY03 and FY04.
Date: June 27, 2007
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Heterogeneous processes at the intersection of chemistry and biology: A computational approach

Description: Heterogeneous processes hold the key to understanding many problems in biology and atmospheric science. In particular, recent experiments have shown that heterogeneous chemistry at the surface of sea-salt aerosols plays a large role in important atmospheric processes with far reaching implications towards understanding of the fate and transport of aerosolized chemical weapons (i.e. organophosphates such as sarin and VX). Unfortunately, the precise mechanistic details of the simplest surface enh… more
Date: February 11, 2008
Creator: Kuo, I W & Mundy, C J
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Three-Dimensional Aberration-Corrected Scanning Transmission Electron Microscopy for Biology

Description: Recent instrumental developments have enabled greatly improved resolution of scanning transmission electron microscopes (STEM) through aberration correction. An additional and previously unanticipated advantage of aberration correction is the greatly improved depth sensitivity that has led to the reconstruction of a three-dimensional (3D) image from a focal series. In this chapter the potential of aberration-corrected 3D STEM to provide major improvements in the imaging capabilities for biologi… more
Date: January 1, 2007
Creator: De Jonge, Niels; Sougrat, Rachid; Pennycook, Stephen J; Peckys, Diana B & Lupini, Andrew R
Item Type: Refine your search to only Book
Partner: UNT Libraries Government Documents Department
open access

Non-destructive Identification of Individual Leukemia Cells by Optical Trapping Raman Spectroscopy

Description: Currently, a combination of technologies is typically required to assess the malignancy of cancer cells. These methods often lack the specificity and sensitivity necessary for early, accurate diagnosis. Here we demonstrate using clinical samples the application of laser trapping Raman spectroscopy as a novel approach that provides intrinsic biochemical markers for the noninvasive detection of individual cancer cells. The Raman spectra of live, hematopoietic cells provide reliable molecular fing… more
Date: March 5, 2007
Creator: Chan, J W; Taylor, D S; Lane, S; Zwerdling, T; Tuscano, J & Huser, T
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Toxin studies using an integrated biophysical and structural biology approach.

Description: Clostridial neurotoxins, such as botulinum and tetanus, are generally thought to invade neural cells through a process of high affinity binding mediated by gangliosides, internalization via endosome formation, and subsequent membrane penetration of the catalytic domain activated by a pH drop in the endosome. This surface recognition and internalization process is still not well understood with regard to what specific membrane features the toxins target, the intermolecular interactions between b… more
Date: March 1, 2005
Creator: Last, Julie A.; Schroeder, Anne E.; Slade, Andrea Lynn; Sasaki, Darryl Yoshio; Yip, Christopher M. (University of Toronto, Toronto, Ontario, Canada) & Schoeniger, Joseph S. (Sandia National Laboratories, Livermore, CA)
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Reaction chemistry and ligand exchange at cadmium selenide nanocrystal surfaces

Description: Chemical modification of nanocrystal surfaces is fundamentally important to their assembly, their implementation in biology and medicine, and greatly impacts their electrical and optical properties. However, it remains a major challenge owing to a lack of analytical tools to directly determine nanoparticle surface structure. Early nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) studies of CdSe nanocrystals prepared in tri-n-octylphosphine oxide (1) and tri-n-octylpho… more
Date: December 2, 2008
Creator: Owen, Jonathan; Park, Jungwon; Trudeau, Paul-Emile & Alivisatos, A. Paul
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Counting constituents in molecular complexes by fluorescence photon antibunching

Description: Modern single molecule fluorescence microscopy offers new, highly quantitative ways of studying the systems biology of cells while keeping the cells healthy and alive in their natural environment. In this context, a quantum optical technique, photon antibunching, has found a small niche in the continuously growing applications of single molecule techniques to small molecular complexes. Here, we review some of the most recent applications of photon antibunching in biophotonics, and we provide a … more
Date: April 17, 2007
Creator: Fore, S; Laurence, T; Hollars, C & Huser, T
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Lawrence Livermore National Laboratory Workshop Characterization of Pathogenicity, Virulence and Host-Pathogen Interactions

Description: The threats of bio-terrorism and newly emerging infectious diseases pose serious challenges to the national security infrastructure. Rapid detection and diagnosis of infectious disease in human populations, as well as characterizing pathogen biology, are critical for reducing the morbidity and mortality associated with such threats. One of the key challenges in managing an infectious disease outbreak, whether through natural causes or acts of overt terrorism, is detection early enough to initia… more
Date: August 30, 2006
Creator: Krishnan, A.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Aberration-Coreected Electron Microscopy at Brookhaven National Laboratory

Description: The last decade witnessed the rapid development and implementation of aberration correction in electron optics, realizing a more-than-70-year-old dream of aberration-free electron microscopy with a spatial resolution below one angstrom [1-9]. With sophisticated aberration correctors, modern electron microscopes now can reveal local structural information unavailable with neutrons and x-rays, such as the local arrangement of atoms, order/disorder, electronic inhomogeneity, bonding states, spin c… more
Date: April 1, 2008
Creator: Zhu, Y. & Wall, J.
Item Type: Refine your search to only Book
Partner: UNT Libraries Government Documents Department
open access

Final Technical Report

Description: Our team of investigators from MIT (Michael Laub) and Stanford (Harley McAdams and Lucy Shapiro) conducted a multi-faceted, systematic experimental analysis of the 106 Caulobacter two-component signal transduction system proteins (62 histidine kinases and 44 response regulators) to understand how they coordinate cell cycle progression, metabolism, and response to environmental changes. These two-component signaling proteins were characterized at the genetic, biochemical, and genomic levels. The… more
Date: December 29, 2008
Creator: Laub, Michael
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

New developments for the site-specific attachment of protein to surfaces

Description: Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physic… more
Date: May 12, 2005
Creator: Camarero, J A
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Protein Microarrays--Without a Trace

Description: Many experimental approaches in biology and biophysics, as well as applications in diagnosis and drug discovery, require proteins to be immobilized on solid supports. Protein microarrays, for example, provide a high-throughput format to study biomolecular interactions. The technique employed for protein immobilization is a key to the success of these applications. Recent biochemical developments are allowing, for the first time, the selective and traceless immobilization of proteins generated b… more
Date: April 5, 2007
Creator: Camarero, J A
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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The Development of New User Research Capabilities in Environmental Molecular Science: Workshop Report

Description: On August 1, and 2, 2006, 104 scientists representing 40 institutions including 24 Universities and 5 National Laboratories gathered at the W.R. Wiley Environmental Molecular Sciences Laboratory, a National scientific user facility, to outline important science challenges for the next decade and identify major capabilities needed to pursue advanced research in the environmental molecular sciences. EMSL’s four science themes served as the framework for the workshop. The four science themes are 1… more
Date: October 31, 2006
Creator: Felmy, Andrew R.; Baer, Donald R.; Fredrickson, Jim K.; Gephart, Roy E. & Rosso, Kevin M.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Genomic Prospecting for Microbial Biodiesel Production

Description: Biodiesel is defined as fatty acid mono-alkylesters and is produced from triacylglycerols. In the current article we provide an overview of the structure, diversity and regulation of the metabolic pathways leading to intracellular fatty acid and triacylglycerol accumulation in three types of organisms (bacteria, algae and fungi) of potential biotechnological interest and discuss possible intervention points to increase the cellular lipid content. The key steps that regulate carbon allocation an… more
Date: March 20, 2008
Creator: Lykidis, Athanasios; Lykidis, Athanasios & Ivanova, Natalia
Item Type: Refine your search to only Book
Partner: UNT Libraries Government Documents Department
open access

Laser Safety for the Experimental Halls at SLAC_s Linac Coherent Light Source (LCLS)

Description: The LCLS at the SLAC National Accelerator Laboratory will be the world's first source of an intense hard x-ray laser beam, generating x-rays with wavelengths of 1nm and pulse durations less than 100fs. The ultrafast x-ray pulses will be used in pump-probe experiments to take stop-motion pictures of atoms and molecules in motion, with pulses powerful enough to take diffraction images of single molecules, enabling scientists to elucidate fundamental processes of chemistry and biology. Ultrafast c… more
Date: January 15, 2009
Creator: Woods, Michael; Anthony, Perry; Barat, Ken; Gilevich, Sasha; Hays, Greg & White, William E.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology

Description: Antisense oligodeoxynucleotide (ODN) inhibition emerges as an effective means for probing gene function in plant cells. Employing this method we have established the importance of the SUSIBA2 transcription factor for regulation of starch synthesis in barley endosperm, and arrived at a model for the role of the SUSIBAs in sugar signaling and source-sink commutation during cereal endosperm development. In this addendum we provide additional data demonstrating the suitability of the antisense ODN … more
Date: January 15, 2008
Creator: Jansson, Christer; Sun, Chuanxin; Ghebramedhin, Haile; Hoglund, Anna-Stina & Jansson, Christer
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Chemical Force Microscopy of Chemical and Biological Interactions

Description: Interactions between chemical functionalities define outcomes of the vast majority of important events in chemistry, biology and materials science. Chemical Force Microscopy (CFM)--a technique that uses direct chemical functionalization of AFM probes with specific functionalities--allows researchers to investigate these important interactions directly. We review the basic principles of CFM, some examples of its application, and theoretical models that provide the basis for understanding the exp… more
Date: January 2, 2006
Creator: Noy, A
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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