Publications

  • Ebolavirus comparative genomics

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae....
  • The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations.

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 Å(2) at 25 °C. MD simulations with POPS lipid area constrained at different values were also performed...
  • Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community.

    Detailed characterization of post-translational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have...
  • Reactive Force Field Study of Li/C Systems for Electrical Energy Storage

    Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected...
  • Protein conformational populations and functionally relevant substates

    Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates...
  • A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors

    Bacterial chemoreceptors are widely used as a model system for elucidating the molecular mechanisms of transmembrane signalling and have provided a detailed understanding of how ligand binding by the receptor modulates the activity of its associated kinase CheA. However, the mechanisms by which conformational signals move between signalling elements within a receptor dimer and how they control kinase activity remain unknown. Here, using long molecular dynamics simulations, we show that the kinase-activating cytoplasmic tip of the chemoreceptor fluctuates between two stable conformations in a...
  • An open port sampling interface for liquid introduction atmospheric pressure ionization mass spectrometry

    Rationale A simple method to introduce unprocessed samples into a solvent for rapid characterization by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The continuous flow, self-cleaning open port sampling interface introduced here fills this void. Methods The open port sampling interface used a vertically aligned, co-axial tube arrangement enabling solvent delivery to the sampling end of the device through the tubing annulus and solvent aspiration down the center tube and into the ionization source of the mass spectrometer via...
  • Reduced carbon emission estimates from fossil fuel combustion and cement production in China

    Nearly three-quarters of the growth in global carbon emissions from the burning of fossil fuels and cement production between 2010 and 2012 occurred in China1, 2. Yet estimates of Chinese emissions remain subject to large uncertainty; inventories of China’s total fossil fuel carbon emissions in 2008 differ by 0.3 gigatonnes of carbon, or 15 per cent1, 3, 4, 5. The primary sources of this uncertainty are conflicting estimates of energy consumption and emission factors, the latter being uncertain because of very few actual measurements representative of the mix of Chinese...
  • Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum

    Consolidated bioprocessing (CBP) has the potential to reduce biofuel or biochemical production costs by processing cellulose hydrolysis and fermentation simultaneously without the addition of pre-manufactured cellulases. In particular, Clostridium thermocellum is a promising thermophilic CBP host because of its high cellulose decomposition rate. Here we report the engineering of C. thermocellum to produce isobutanol. Metabolic engineering for isobutanol production in C. thermocellum is hampered by enzyme toxicity during cloning, time-consuming pathway engineering...
  • Tunable Encapsulation Structure of Block Copolymer Coated Single-Walled Carbon Nanotubes in Aqueous Solution

    Nanosized and shape-tunable molecular building blocks can provide great opportunities for the fabrication of precisely controlled nanostructures. In this work, we have fabricated a molecular building block of single-walled carbon nanotubes (SWNTs) coated by PPO–PEO–PPO block copolymers whose encapsulation structure can be controlled via temperature or addition of small molecules. The structure and optical properties of SWNT block copolymers have been investigated by small-angle neutron scattering (SANS), ultraviolet–visible (UV–vis) spectroscopy, atomic force microscopy (AFM), and molecular...
  • ORNL identifies environmental indicators for sustainable production of algal biofuels

    For analyzing sustainability of algal biofuels, we identify 16 environmental indicators that fall into six categories: soil quality, water quality and quantity, air quality, greenhouse gas emissions, biodiversity, and productivity. Indicators are selected to be practical, widely applicable, predictable in response, anticipatory of future changes, independent of scale, and responsive to management. Major differences between algae and terrestrial plant feedstocks, as well as their supply chains for biofuel, are highlighted, for they influence the choice of appropriate sustainability indicators...
  • Imaging and Microanalysis of Thin Ionomer Layers by Scanning Transmission Electron Microscopy

    Optimized conditions for imaging and spectroscopic/elemental mapping of thin perfluorosulfonic acid (PFSA) ionomer layers in fuel cell electrodes by scanning transmission electron microscopy (STEM) have been investigated. The proper conditions were first identified using model systems of either Nafion ionomer-coated nanostructured thin film catalysts or thin films on nanoporous Si. These analysis conditions were then applied in a quantitative study of the ionomer through-layer loading for two differently-prepared electrode catalyst layers using electron energy loss (EELS) and energy...
  • Well-to-wheel analysis of direct and indirect use of natural gas in passenger vehicles

    The abundance of natural gas in the United States because of the number of existing natural gas reserves and the recent advances in extracting unconventional reserves has been one of the main drivers for low natural gas prices. A question arises of what is the optimal use of natural gas as a transportation fuel. Is it more efficient to use natural gas in a stationary power application to generate electricity to charge electric vehicles, compress natural gas for onboard combustion in vehicles, or re-form natural gas into a denser transportation fuel? This study investigates the well-to-wheels...
  • Dereplicating and Spatial Mapping of Secondary Metabolites from Fungal Cultures in Situ

    Ambient ionization mass spectrometry techniques have recently become prevalent in natural product research due to their ability to examine secondary metabolites in situ. These techniques retain invaluable spatial and temporal details that are lost through traditional extraction processes. However, most ambient ionization techniques do not collect mutually supportive data, such as chromatographic retention times and/or UV/vis spectra, and this can limit the ability to identify certain metabolites, such as differentiating isomers. To overcome this, the droplet–liquid microjunction–surface...
  • Identification of phases, symmetries and defects through local crystallography

    Advances in electron and probe microscopies allow 10 pm or higher precision in measurements of atomic positions. This level of fidelity is sufficient to correlate the length (and hence energy) of bonds, as well as bond angles to functional properties of materials. Traditionally, this relied on mapping locally measured parameters to macroscopic variables, for example, average unit cell. This description effectively ignores the information contained in the microscopic degrees of freedom available in a high-resolution image. Here we introduce an approach for local analysis of material structure...
  • Opto-nanomechanical spectroscopic material characterization

    The non-destructive, simultaneous chemical and physical characterization of materials at the nanoscale is an essential and highly sought-after capability. However, a combination of limitations imposed by Abbe diffraction, diffuse scattering, unknown subsurface, electromagnetic fluctuations and Brownian noise, for example, have made achieving this goal challenging. Here, we report a hybrid approach for nanoscale material characterization based on generalized nanomechanical force microscopy in conjunction with infrared photoacoustic spectroscopy. As an application, we tackle the outstanding...
  • The simultaneous determination of 235U and 239Pu using delayed neutron activation analysis

    Delayed neutron activation analysis (DNAA) remains one of the most sensitive methods of nondestructively determining fissile materials in a variety of sample matrices, provided that the samples contain only a single fissile component. This has historically been the limiting factor in many applications of DNAA, and often chemically destructive methods of analysis have needed to be utilized for many real-world samples. This work seeks to develop a method that will allow for DNAA to be utilized on samples containing multiple fissile components. Initial efforts, presented here, show that using a...
  • The optimum choice of gate width for neutron coincidence counting

    In the measurement field of international nuclear safeguards, passive neutron coincidence counting is used to quantify the spontaneous fission rate of certain special nuclear materials. The shift register autocorrelation analysis method is the most commonly used approach. However, the Feynman-Y technique, which is more commonly applied in reactor noise analysis, provides an alternative means to extract the correlation information from a pulse train. In this work we consider how to select the optimum gate width for each of these two time-correlation analysis techniques. The optimum is...
  • Autonomous radiation monitoring of small vessels

    Small private vessels are one avenue by which nuclear materials may be smuggled across international borders. While one can contemplate using the terrestrial approach of radiation portal monitors on the navigable waterways that lead to many ports, these systems are ill-suited to the problem. They require vehicles to pass at slow speeds between two closely-spaced radiation sensors, relying on the uniformity of vehicle sizes to space the detectors, and on proximity to link an individual vehicle to its radiation signature. In contrast to roadways where lanes segregate vehicles, and motion is...
  • Californium Recovery from Palladium Wire.

    The recovery of 252Cf from palladium-252Cf cermet wires was investigated to determine the feasibility of implementation into the cermet wire production operation at the Radiochemical Engineering Development Center at Oak Ridge National Laboratory. The dissolution of Pd wire in 8 M HNO3 and trace amounts of HCl was studied at both ambient and elevated temperatures. These studies showed that it took days to dissolve the wire at ambient temperature and only 2 hours at 60°C. Adjusting the ratio of the volume of solvent to the mass of the wire segment from 0.176 mL/mg down to 0.019...
  • Californium Purification and Electrodeposition

    The staff at the Radiochemical Engineering Development Center, located at Oak Ridge National Laboratory, produced a 6.3 ± 0.4 GBq (1.7 ± 0.1 Ci) 252Cf source for the Californium Rare Isotope Breeder Upgrade (CARIBU) project at Argonne National Laboratory’s Argonne Tandem Linac Accelerator System. The source was produced by electrodeposition of a 252Cf sample onto a stainless steel substrate, which required material free from excess mass for efficient deposition. The resulting deposition was the largest reported 252Cf electrodeposition source ever produced. Several different chromatographic...
  • Synthesis and characterization of lanthanum phosphate nanoparticles as carriers for 223Ra and 225Ra for targeted alpha therapy

    Targeted alpha therapy (TAT) has the potential for killing micro-metastases with minimum collateral damage to surrounding healthy tissue. In-vivo generator radionuclides, such as223Ra, 225Ra, and 225Ac, are of special interest for radiotherapeutic applications as they emit multiple α-particles during their decay. Utilizing appropriate carriers capable of retaining both the parent radioisotope as well as daughter products is important for the effective delivery of the radioisotope to the tumor site while mitigating global in vivo radiotoxicity. In this work, LaPO4 core and core+2 shells...
  • Covariance Applications in Criticality Safety, Light Water Reactor Analysis, and Spent Fuel Characterization

    A new covariance data library based on ENDF/B-VII.1 was recently processed for the SCALE nuclear analysis code system. The multigroup covariance data are discussed here, along with testing and application results for critical benchmark experiments. The cross section covariance library, along with covariances for fission product yields and decay data, is used to compute uncertainties in the decay heat produced by a burned reactor fuel assembly.
  • Impact of Nuclear Data Uncertainties on Calculated Spent Fuel Nuclide Inventories and Advanced NDA Instrument Response

    The U.S. Department of Energy’s Next Generation Safe­guards Initiative Spent Fuel (NGSI‑SF) project is nearing the final phase of developing several advanced nondestructive assay (NDA) instruments designed to measure spent nucle­ar fuel assemblies for the purpose of improving nuclear safeguards. Current efforts are focusing on calibrating sev­eral of these instruments with spent fuel assemblies at two international spent fuel facilities. Modelling and simulation is expected to play an important role in predicting nuclide compositions, neutron and gamma source terms, and in­strument responses...
  • Efficient solution of the simplified Pn equations

    In this paper we show new solver strategies for the multigroup SPN equations for nuclear reactor analysis. By forming the complete matrix over space, moments, and energy, a robust set of solution strategies may be applied. Power iteration, shifted power iteration, Rayleigh quotient iteration, Arnoldi’s method, and a generalized Davidson method, each using algebraic and physics-based multigrid preconditioners, have been compared on the C5G7 MOX test problem as well as an operational pressurized water reactor model. Our results show that the most efficient approach is the generalized Davidson...