Chaotic-Dynamical Conceptual Model to Describe Fluid Flow and Contaminant Transport in a Fractured Vadose Zone

DOE faces the remediation of numerous contaminated sites, such as those at Hanford, INEEL, LLNL, and LBNL, where organic and/or radioactive wastes were intentionally or accidentally released to the vadose zone from surface spills, underground tanks, cribs, shallow ponds, and deep wells. Migration of these contaminants through the vadose zone has led to the contamination of (or threatens to contaminate) underlying groundwater. A key issue in choosing a corrective action plan to clean up contaminated sites is the determination of the location, total mass, mobility and travel time to receptors for contaminants moving in the vadose zone. These problems are difficult to solve in a technically defensible and accurate manner because contaminants travel downward intermittently, through narrow pathways, driven by variations in environmental conditions. These preferential flow pathways can be difficult to find and predict. The primary objective of this project is to determine if and when dynamical chaos theory can be used to investigate infiltration of fluid and contaminant transport in heterogeneous soils and fractured rocks. The objective of this project is being achieved through the following activities: Development of multi scale conceptual models and mathematical and numerical algorithms for flow and transport, which incorporate both (a) the spatial variability of heterogeneous porous and fractured media and (b) the temporal dynamics of flow and transport; Development of appropriate experimental field and laboratory techniques needed to detect diagnostic parameters for chaotic behavior of flow; Evaluation of chaotic behavior of flow in laboratory and field experiments using methods from non-linear dynamics; Evaluation of the impact these dynamics may have on contaminant transport through heterogeneous fractured rocks and soils and remediation efforts. This approach is based on the consideration of multi scale spatial heterogeneity and flow phenomena that are affected by nonlinear dynamics, and in particular, chaotic processes. The scientific and practical value of this approach is that we can predict the range within, which the parameters of flow and transport change with time, which allows us to design and manage the remediation even when we cannot predict the behavior at any point or time

Development of Extraction Techniques for the Detection of Signature Lipids from Oil

Pure cultures, including Desulfovibrio vulgaris and Methanococcus maripaludus, were combined with model oil samples and oil/diesel mixtures to optimize extraction techniques of signature lipids from oil in support of investigation of microbial communities in oil deposit samples targets for microbial enhanced hydrocarbon recovery. Several techniques were evaluated, including standard phospholipid extraction, ether linked lipid for Archaeal bacterial detection, and high pressure extractiontechniques. Recovery of lipids ranged from 50-80percent as compared to extraction of the pure culture. Extraction efficiency was evaluated by the use of internal standards. Field samples will also be tested for recovery of signature lipids with optimized extraction techniques

High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.

Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms

Revisiting Modes of energy generation in sulfate reducing bacteria

Sulfate reducing bacteria (SRB) play an important role in global sulfur and carbon cycling through their ability to completely mineralize organic matter while respiring sulfate to hydrogen sulfide. They are ubiquitous in anaerobic environments and have the ability to reduce toxic metals like Cr(VI) and U(VI). While SRB have been studied for over three decades, bioenergetic modes of this group of microbes are poorly understood. Desulfovibrio vulgaris strain Hildenborough (DvH) has served as a model SRB over the last decade with the accumulation of transcriptomic, proteomic and metabolic data under a wide variety of stressors. To further investigate the three hypothesized modes of energy generation in this anaerobe we conducted a systematic study involving multiple electron donor and acceptor combinations for growth. DvH was grown at 37oC in a defined medium with (a) lactate + thiosulfate, (b) lactate + sulfite (c) lactate + sulfate, (d) pyruvate + sulfate, (e) H2 + acetate + sulfate, (f) formate + acetate + sulfate, g) formate + sulfate and (h) pyruvate fermentation. Cells were harvested at mid-log phase of growth for all conditions for transcriptomics, when the optical density at 600nm was in the range 0.42-0.5. Initial results indicate that cells grown on lactate do not appear to significantly differentiate their gene expression profiles when presented with different electron acceptors. These profiles however differ significantly from those observed during growth with other electron donors such as H2 and formate, as well as during fermentative growth. Together the gene expression changes in the presence of different electron donors provide insights into the ability of DvH to differentially reduce metals such as Cr(VI). Here we present revised modes of energy generation in DvH in light of this new transcriptomic evidence

Possibilities of technical feasibility for the creation of a digital corpse model

Diese Machbarkeitsstudie beschäftigt sich mit der Prüfung von Möglichkeiten der technischen Umsetzbarkeit für die Erstellung eines digitalen Leichenmodells. Anhand von Informationen der forensischen Bildgebung sowie der Oberfläche des Leichnams, soll die Anfertigung eines digitalen Leichenmodells erfolgen. Dafür wird zunächst der Leichnam durch eine postmortale Computertomografie sowie eine Angiografie basierend auf der Computertomografie dargestellt. Darauffolgend wird die Oberfläche durch Informationen eines handgeführten Laserscanners rekonstruiert. Unter Verwendung verschiedener Methoden lassen sich die erhobenen Daten mit denen der forensischen Bildgebung anreichern und kombinieren. Das Vorgehen sowie Herstellung des digitalen Leichenmodells wird näher betrachtet und eingehend erläutert. Abschließend soll das digitale Leichenmodell animiert in den rekonstruierten Tatort eingefügt werden, um den Tathergang bestmöglich wiederzugeben. Die Erkenntnisse der möglichen Abläufe werden folgend in der Machbarkeitsstudie diskutiert und beurteilt. Letztendlich erfolgt der Vergleich des verwendeten Laserscanners mit einem neueren Modell der gleichen Marke sowie des Laserscanverfahrens mit der Fotogrammmetrie

Large-Scale, Continuous-Flow Production of Stressed Biomass (Desulfovibrio vulgaris Hildenborough)

The Protein Complex Analysis Project (PCAP, http://pcap.lbl.gov/), focuses on high-throughput analysis of microbial protein complexes in the anaerobic, sulfate-reducing organism, DesulfovibriovulgarisHildenborough(DvH).Interest in DvHas a model organism for bioremediation of contaminated groundwater sites arises from its ability to reduce heavy metals. D. vulgarishas been isolated from contaminated groundwater of sites in the DOE complex. To understand the effect of environmental changes on the organism, midlog-phase cultures are exposed to nitrate and salt stresses (at the minimum inhibitory concentration, which reduces growth rates by 50percent), and compared to controls of cultures at midlogand stationary phases. Large volumes of culture of consistent quality (up to 100 liters) are needed because of the relatively low cell density of DvHcultures (one order of magnitude lower than E. coli, for example) and PCAP's challenge to characterize low-abundance membrane proteins. Cultures are grown in continuous flow stirred tank reactors (CFSTRs) to produce consistent cell densities. Stressor is added to the outflow from the CFSTR, and the mixture is pumped through a plug flow reactor (PFR), to provide a stress exposure time of 2 hours. Effluent is chilled and held in large carboys until it is centrifuged. A variety of analyses -- including metabolites, total proteins, cell density and phospholipidfatty-acids -- track culture consistency within a production run, and differences due to stress exposure and growth phase for the different conditions used. With our system we are able to produce the requisite 100 L of culture for a given condition within a week

Experiments and evaluation of chaotic behavior of dripping water in fracture models

Laboratory experiments of water seepage in smooth and rough-walled, inclined fracture models were performed and the monitoring data analyzed for evidence of chaos. One fracture model consisted of smooth, parallel glass plates separated by 0.36 mm. The second model was made with textured glass plates. The fracture model was inclined 60{sup o} from the horizontal. Water was delivered to the fracture model through a capillary tube in contact with the top fracture edge at constant flow rates. Three types of capillary tubes were used: (1) a stainless steel blunt needle of 0.18 mm ID for flow rates of 0.25 to 4 mL/hr, (2) a nylon tube of 0.8 mm ID for flow rates of 0.25 to 10 mL/hr, and (3) a glass tube of 0.75 mm ID for flow rates of 0.5 to 20 mL/hr. Liquid pressure was monitored upstream of the capillary tube. Visual observations showed that water seeped through the fracture models in discrete channels that underwent cycles of snapping and reforming. Observations also showed that liquid segments, or drips, detached at different points along the water channel. The measured liquid pressure responded to the growth and detachment of drips. Separate experiments were carried out to measure pressure time-trends for dripping into open air to compare these data with those obtained in fracture models. Analysis of the pressure time-trends included determination of the time lag from the minimum of the average mutual information function, the local and global embedding dimensions, Lyapunov exponents and the Lyapunov dimension, the Hurst exponent and the entropy as a function of the embedding dimension for each data set. Most of the water pressure data contain oscillations exhibiting chaotic behavior, with local embedding dimensions ranging from 3 to 10, and global embedding dimensions one to two units higher. The higher dimensionality of some of the data sets indicates either the presence of high-dimensional chaos or a significant random component. It was determined that the flow rate, which affects seepage behavior and is reflected in the pressure measurements, is inversely correlated with the Hurst exponent. This supports the hypothesis that at higher flow rates, the random component of seepage behavior (as represented by liquid pressure) increases. However, there was no simple, consistent correlation between the trends for the other diagnostic parameters of chaos and flow rate. Three-dimensional plots of selected data sets in pseudo-phase space exhibit definite structures with some scattering of data points on the attractor. All the analyses confirm that the pressure time trends that describe flow behavior are mostly characterized by low-dimensional, deterministic chaotic dynamics with some random component

Effect of immiscible liquid contaminants on P-wave transmission through natural aquifer samples

We performed core-scale laboratory experiments to examine the effect of non-aqueous phase liquid (NAPL) contaminants on P-wave velocity and attenuation in heterogeneous media. This work is part of a larger project to develop crosswell seismic methods for minimally invasive NAPL detection. The test site is the former DOE Pinellas Plant in Florida, which has known NAPL contamination in the surficial aquifer. Field measurements revealed a zone of anomalously high seismic attenuation, which may be due to lithology and/or contaminants (NAPL or gas phase). Intact core was obtained from the field site, and P-wave transmission was measured by the pulse-transmission technique with a 500 kHz transducer. Two types of samples were tested: a clean fine sand from the upper portion of the surficial aquifer, and clayey-silty sand with shell fragments and phosphate nodules from the lower portion. Either NAPL trichloroethene or toluene was injected into the initially water-saturated sample. Maximum NAPL saturations ranged from 30 to 50% of the pore space. P-wave velocity varied by approximately 4% among the water-saturated samples, while velocities decreased by 5 to 9% in samples at maximum NAPL saturation compared to water-saturated conditions. The clay and silt fraction as well as the larger scatterers in the clayey-silty sands apparently caused greater P-wave attenuation compared to the clean sand. The presence of NAPLs caused a 34 to 54% decrease in amplitudes of the first arrival. The central frequency of the transmitted energy ranged from 85 to 200 kHz, and was sensitive to both grain texture and presence of NAPL. The results are consistent with previous trends observed in homogeneous sand packs. More data will be acquired to interpret P-wave tomograms from crosswell field measurements, determine the cause of high attenuation observed in the field data and evaluate the sensitivity of seismic methods for NAPL detection