John M Dzenitis

Lawrence Livermore National Laboratory, Livermore, California, United States

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Publications (32)55.65 Total impact

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    ABSTRACT: There is no abstract available for this article.
    Physics of Plasmas 12/2014; 21(12-12):129902. DOI:10.1063/1.4903459 · 2.25 Impact Factor
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    ABSTRACT: Inertial Confinement Fusion experiments at the National Ignition Facility (NIF) are designed to understand and test the basic principles of self-sustaining fusion reactions by laser driven compression of deuterium-tritium (DT) filled cryogenic plastic (CH) capsules. The experimental campaign is ongoing to tune the implosions and characterize the burning plasma conditions. Nuclear diagnostics play an important role in measuring the characteristics of these burning plasmas, providing feedback to improve the implosion dynamics. The Neutron Imaging (NI) diagnostic provides information on the distribution of the central fusion reaction region and the surrounding DT fuel by collecting images at two different energy bands for the primary (13-15 MeV) and downscattered (10-12 MeV) neutrons. From these distributions, the final shape and size of the compressed capsule can be estimated and the symmetry of the compression can be inferred. The first downscattered neutron images from imploding ICF capsules are shown in this paper.
    The European Physical Journal Conferences 11/2013; 59:13018. DOI:10.1051/epjconf/20135913018
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    ABSTRACT: A summary of data and results from the first neutron images produced by the National ignition Facility (NIF), Lawrence Livermore National Laboratory, Livermore, CA, USA are presented. An overview of the neutron imaging technique is presented, as well as a synopsis of data and measurements made to date. Data from directly driven, DT filled microballoons, as well as indirectly driven, cryogenically layered ignition experiments are presented. The data show that the primary cores from directly driven implosions are approximately twice as large, 64 ± 3 µm, as indirectly driven cores, 25 ± 4 and 29 ± 4 µm and more asymmetric, P2/P0 = 47% vs. -14% and 7%. Further, comparison with the size and shape of X-ray image data on the same implosions show good agreement, indicating X-ray emission is dominated by the hot regions of the implosions.
    The European Physical Journal Conferences 11/2013; 59:13017. DOI:10.1051/epjconf/20135913017
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    ABSTRACT: Directly laser driven and X-radiation driven DT filled capsules differ in the relationship between neutron and X-ray images. Shot N1102017, a directly driven DT-filled glass micro-balloon provided the first neutron images at the National Ignition Facility. As seen in implosions on the Omega laser, the neutron image can be enclosed inside time integrated X-ray images. HYDRA simulations show the X-ray image is dominated by emission from the hot glass shell while the neutron image arises from the DT fuel it encloses. In the absence of mix or jetting, X-ray images of a cryogenically layered THD fuel capsule should be dominated by emission from the hydrogen rather than the cooler plastic shell that is separated from the hot core by cold DT fuel. This cool, dense DT, invisible in X-ray emission, shows itself by scattering hot core neutrons. Germanium X-ray emission spectra and Ross pair filtered X-ray energy resolved images suggest that germanium doped plastic emits in the torus shaped hot spot, probably reducing the neutron yield.
    The European Physical Journal Conferences 11/2013; 59:04002. DOI:10.1051/epjconf/20135904002
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    ABSTRACT: We have fielded a neutron imaging system at the National Ignition Facility to collect images of fusion neutrons produced in the implosion of inertial confinement fusion experiments and scattered neutrons from (n,n') reactions of the source neutrons in the surrounding dense material. A description of the neutron imaging system is presented, including the pinhole array aperture, the line-of-sight collimation, the scintillator-based detection system and the alignment systems and methods. Discussion of the alignment and resolution of the system is presented. We also discuss future improvements to the system hardware.
    The European Physical Journal Conferences 11/2013; 59:13016. DOI:10.1051/epjconf/20135913016
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    ABSTRACT: One of the scientific goals of the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory, Livermore CA, is to obtain thermonuclear ignition by compressing 2.2 mm diameter capsules filed with deuterium and tritium to densities approaching 1000 g/cm3 and temperatures in excess of 4 keV. Thefusion reaction d + t --> n + a results in a 14.03 MeV neutron providing a source of diagnostic particles to characterize the implosion. The spectrum of neutrons emanating from the assembly may be used to infer the fusion yield, plasma ion temperature, and fuel areal density, all key diagnostic quantities of implosion quality. The neutron time-of-flight (nToF) system co-located along the Neutron Imaging System line-of-site, (NIToF), is a set of 4 scintillation detectors located approximately 27.3 m from the implosion source. Neutron spectral information is inferred using arrival time at the detector. The NIToF system is described below, including the hardware elements, calibration data, analysis methods, and an example of its basic performance characteristics.
    Proceedings of SPIE - The International Society for Optical Engineering 09/2013; DOI:10.1117/12.2030170 · 0.20 Impact Factor
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    ABSTRACT: Detection of pathogens and relevant genetic markers using their nucleic acid signatures is extremely common due to the inherent specificity genomic sequences provide. One approach for assaying a sample simultaneously for many different targets is the DNA microarray, which consists of several million short nucleic acid sequences (probes) bound to an inexpensive transparent substrate. Typically, complex samples hybridize to the microarray and the pattern of fluorescing probes on the microarray's surface identifies the detected targets. In the case of evolving or newly emergent organisms, a hybridization pattern can occur that differs from any previously known sources. When this happens it can be useful to recover the hybridized DNA from the binding locations of interest for sequencing. Here we present the novel utilization of a focused Infrared (IR) laser to heat user-selected spots on the DNA microarray surface, causing only localized dehybridization and recovery of the desired DNA into an elution buffer where it is available for subsequent amplification or sequencing. The introduction of a focused dehybridization method for spots of interest suppresses the amount of background DNA to be analyzed from downstream processes, and should reduce subsequent sequence assembly errors. This technique could also be applied to high-density protein microarrays where the desire to locally heat spots for release of bound molecules is desired.
    The Analyst 05/2013; DOI:10.1039/c3an00288h · 4.11 Impact Factor
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    ABSTRACT: The National Ignition Facility (NIF) is a 192-beam high energy laser designed for Inertial Confinement Fusion (ICF), and High Energy Density (HED) and basic science experiments. In order to achieve ignition with an ICF target, the beam and target alignment must be performed within very tight specifications. At the same time, in order to be able to conduct the wide range of HED and basic science experiments, the facility must be able to meet the tight tolerances for both main and offset backlighter beams and targets. To diagnose the ignition event, many different target diagnostics are employed, including optical, x-ray, and nuclear diagnostics. These target diagnostics must also be positioned accurately and reliably within very tight specifications in order to ensure good data is acquired. In this paper, we describe the strategy for beam, target, and diagnostic alignment at NIF.
    Proceedings of SPIE - The International Society for Optical Engineering 10/2012; DOI:10.1117/12.969066 · 0.20 Impact Factor
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    ABSTRACT: A neutron imaging diagnostic has recently been commissioned at the National Ignition Facility (NIF). This new system is an important diagnostic tool for inertial fusion studies at the NIF for measuring the size and shape of the burning DT plasma during the ignition stage of Inertial Confinement Fusion (ICF) implosions. The imaging technique utilizes a pinhole neutron aperture, placed between the neutron source and a neutron detector. The detection system measures the two dimensional distribution of neutrons passing through the pinhole. This diagnostic has been designed to collect two images at two times. The long flight path for this diagnostic, 28 m, results in a chromatic separation of the neutrons, allowing the independently timed images to measure the source distribution for two neutron energies. Typically the first image measures the distribution of the 14 MeV neutrons and the second image of the 6-12 MeV neutrons. The combination of these two images has provided data on the size and shape of the burning plasma within the compressed capsule, as well as a measure of the quantity and spatial distribution of the cold fuel surrounding this core.
    The Review of scientific instruments 10/2012; 83(10):10D317. DOI:10.1063/1.4739242 · 1.58 Impact Factor
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    ABSTRACT: The National Ignition Facility has been used to compress deuterium-tritium to an average areal density of ~1.0plusmn0.1 g cm -2, which is 67% of the ignition requirement. These conditions were obtained using 192 laser beams with total energy of 1-1.6 MJ and peak power up to 420 TW to create a hohlraum drive with a shaped power profile, peaking at a soft x-ray radiation temperature of 275-300 eV. This pulse delivered a series of shocks that compressed a capsule containing cryogenic deuterium-tritium to a radius of 25-35 mum. Neutron images of the implosion were used to estimate a fuel density of 500-800 g cm -3.
    Physical Review Letters 05/2012; 108(21):215005 (5 pp.). DOI:10.1103/PhysRevLett.108.215005 · 7.51 Impact Factor
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    ABSTRACT: The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.
    PLoS ONE 08/2011; 6(8):e22522. DOI:10.1371/journal.pone.0022522 · 3.23 Impact Factor
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    ABSTRACT: We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs. LAVA identifies combinations of six primer regions for basic LAMP signatures, or combinations of eight primer regions for LAMP signatures with loop primers, which can be used as LAMP signatures. The identified primers are conserved among target organism sequences. Primer combinations are optimized based on lengths, melting temperatures, and spacing among primer sites. We compare LAMP signature candidates for Staphylococcus aureus created both by LAVA and by PrimerExplorer. We also include signatures from a sample run targeting all strains of Mycobacterium tuberculosis. We have designed and demonstrated new software for identifying signature candidates appropriate for LAMP assays. The software is available for download at http://lava-dna.googlecode.com/.
    BMC Bioinformatics 06/2011; 12(1):240. DOI:10.1186/1471-2105-12-240 · 2.67 Impact Factor
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    ABSTRACT: form only given. The neutron imaging diagnostic has recently been commissioned at the National Ignition Facility. We will present the diagnostic performance characteristics, which have been measured with the collection of these first neutron images. The goal for this diagnostic is to collect two pinhole images at two different times. The long flight path results in a chromatic separation of the neutrons, the first image will be of the 14 MeV neutrons and the second image of the 10-12 MeV neutrons. The combination of these two images will provide data on the size and shape of the compressed capsule as well as a measure of the quantity and spatial distribution of the cold fuel surrounding this core. The imager uses an array of 20 pinholes and three mini-penumbra machined in 20 cm of layered gold and tungsten, with an apex at 32.5 cm from the source to produce images in a scintillator array at 2800 cm. This geometry provides a magnification factor of 85 at the scintillator. The scintillator is a coherent array of scintillating fibers, which is viewed from the two ends by two fast-gated image collection systems. The first neutron images, collected in February, 2011, have provided the first measure of system performance at NIF. These results will be presented along with an interpretation of future system performance.
    Plasma Science (ICOPS), 2011 Abstracts IEEE International Conference on; 01/2011
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    ABSTRACT: form only given. We have installed the National Ignition Facility Neutron Imaging System. The imaging system provides information about the areal density of fuel in the various regions of the capsule implosion. A long line of sight enables imaging both the primary 14 MeV neutrons as well as the down-scattered neutrons with energies in the range of 9-12 MeV. The imager is a pinhole camera where the pinhole is located 325 mm from the target and the imaging plane is located 28 m from the target. The long absorption length of neutrons requires precise alignment of these extended imager components in order to have high detection efficiency and strong background rejection. The imaging plane is a 150 mm square scintillating fiber bundle 50 mm thick. The bundle consists of 250 μm square fibers. The fiber bundle is aligned such that the fibers point at the target. The pointing is accomplished using a retro reflection of a laser alignment device aligned to the imager line of sight. The 200 mm long pinhole is aligned to the imager line of sight using the Opposed Port Alignment System. The imager line of sight was registered to the alignment system to calculate the precise position of the pinhole. The ability of the positioning manipulator to both place and maintain the precise location of the pinhole, were monitored using the positioning imaging system as well as laser alignment device. Here we describe the various aspects of the imaging system alignment to enable the acquisition of neutron images as well as the estimated pointing errors of the first shot imaged.
    Plasma Science (ICOPS), 2011 Abstracts IEEE International Conference on; 01/2011
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    ABSTRACT: DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.
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    ABSTRACT: A team headed by LANL and including many members from LLNL and NSTec LO and NSTec LAO fielded a neutron imaging system (NIS) at the National Ignition Facility at the start of 2011. The NIS consists of a pinhole array that is located 32.5 cm from the source and that creates an image of the source in a segmented scintillator 28 m from the source. The scintillator is viewed by two gated, optical imaging systems: one that is fiber coupled, and one that is lens coupled. While there are a number of other pieces to the system related to pinhole alignment, collimation, shielding and data acquisition, those pieces are discussed elsewhere and are not relevant here. The system is operational and has successfully obtained data on more that ten imaging shots. This remainder of this whitepaper is divided in five main sections. In Section II, we identify three critical areas of improvement that we believe should be pursued to improve the performance of the system for future experiments: spatial resolution, temporal response and signal-to-noise ratio. In Section III, we discuss technologies that could be used to improve these critical performance areas. In Section IV, we describe a path to evolve the current system to achieve improved performance with minimal impact on the ability of the system to operate on shots. In Section V, we discuss the abilities, scope and timescales of the current teams and the Commissariat energie atomique (CEA). In Section VI, we summarize and make specific recommendations for collaboration on improvements to the NIS.
  • J M Dzenitis · A J Makarewicz
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    ABSTRACT: We developed, tested, and now operate a civilian biological defense capability that continuously monitors the air for biological threat agents. The Autonomous Pathogen Detection System (APDS) collects, prepares, reads, analyzes, and reports results of multiplexed immunoassays and multiplexed PCR assays using Luminex{copyright} xMAP technology and flow cytometer. The mission we conduct is particularly demanding: continuous monitoring, multiple threat agents, high sensitivity, challenging environments, and ultimately extremely low false positive rates. Here, we introduce the mission requirements and metrics, show the system engineering and analysis framework, and describe the progress to date including early development and current status.
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    ABSTRACT: We have developed and field-tested a now operational civilian biodefense capability that continuously monitors the air in high-risk locations for biological threat agents. This stand-alone instrument, called the Autonomous Pathogen Detection System (APDS), collects and selectively concentrates particles from the air into liquid samples and analyzes the samples using multiplexed PCR amplification coupled with microsphere array detection. During laboratory testing, we evaluated the APDS instrument's response to Bacillus anthracis and Yersinia pestis by spiking the liquid sample stream with viable spores and cells, bead-beaten lysates, and purified DNA extracts. APDS results were also compared to a manual real-time PCR method. Field data acquired during 74 days of continuous operation at a mass-transit subway station are presented to demonstrate the specificity and reliability of the APDS. The U.S. Department of Homeland Security recently selected the APDS reported herein as the first autonomous detector component of their BioWatch antiterrorism program. This sophisticated field-deployed surveillance capability now generates actionable data in one-tenth the time of manual filter collection and analysis.
    Analytical Chemistry 10/2008; 80(19):7422-9. DOI:10.1021/ac801125x · 5.83 Impact Factor
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    ABSTRACT: We present a fully automated DNA purification module comprised of a micro-fabricated chip and sequential injection analysis system that is designed for use within autonomous instruments that continuously monitor the environment for the presence of biological threat agents. The chip has an elliptical flow channel containing a bed (3.5 x 3.5 mm) of silica-coated pillars with height, width and center-to-center spacing of 200, 15, and 30 microm, respectively, which provides a relatively large surface area (ca. 3 cm(2)) for DNA capture in the presence of chaotropic agents. We have characterized the effect of various fluidic parameters on extraction performance, including sample input volume, capture flow rate, and elution volume. The flow-through design made the pillar chip completely reusable; carryover was eliminated by flushing lines with sodium hypochlorite and deionized water between assays. A mass balance was conducted to determine the fate of input DNA not recovered in the eluent. The device was capable of purifying and recovering Bacillus anthracis genomic DNA (input masses from 0.32 to 320 pg) from spiked environmental aerosol samples, for subsequent analysis using polymerase chain reaction-based assays.
    The Analyst 03/2008; 133(2):248-55. DOI:10.1039/b713332d · 4.11 Impact Factor
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    ABSTRACT: We developed an automated point-of-care diagnostic instrument that is capable of analyzing nasal swab samples for the presence of respiratory diseases. This robust instrument, called FluIDx, performs autonomous multiplexed RT-PCR reactions that are analyzed by microsphere xMAP technology. We evaluated the performance of FluIDx, in comparison rapid tests specific for influenza and respiratory syncytial virus, in a clinical study performed at the UC Davis Medical Center. The clinical study included samples positive for RSV (n = 71), influenza A (n = 16), influenza B (n = 4), adenovirus (n = 5), parainfluenza virus (n = 2), and 44 negative samples, according to a composite reference method. FluIDx and the rapid tests detected 85.9% and 62.0% of the RSV positive samples, respectively. Similar sensitivities were recorded for the influenza B samples; whereas the influenza A samples were poorly detected, likely due to the utilization of an influenza A signature that did not accurately match currently circulating influenza A strains. Data for all pathogens were compiled and indicate that FluIDx is more sensitive than the rapid tests, detecting 74.2% (95% C.I. of 64.7-81.9%) of the positive samples in comparison to 53.6% (95% C.I. of 43.7-63.2%) for the rapid tests. The higher sensitivity of FluIDx was partially offset by a lower specificity, 77.3% versus 100.0%. Overall, these data suggest automated flow-through PCR-based instruments that perform multiplexed assays can successfully screen clinical samples for infectious diseases.

Publication Stats

245 Citations
55.65 Total Impact Points

Institutions

  • 1970–2013
    • Lawrence Livermore National Laboratory
      • • Physical & Life Sciences Directorate
      • • Physics Division
      Livermore, California, United States