Physics Project 2: Commissioning and Characterization of LUX-ZEPLIN (LZ) Detector

Dark matter constitutes about 85% of the mass in the universe [7,8], but its composition is still unknown. A leading theory postulates that dark matter are Weakly Interacting Massive Particles (WIMPs). The LZ collaboration is a merging of the LUX and ZEPLIN experiments and will be searching for the elusive WIMP signal. LZ is one of the two Generation-2 direct detection experiments supported by the US Department of Energy and the NSF. The LZ detector will consist of a 7 tonne liquid xenon target, scaling up from LUX’s 380 kg. The detector will be located in SURF’s Davis cavern where the LUX experiment operated previously, inside of the existing water shield. Detector commissioning will begin soon. LZ will be a world-leading instrument in our hunt for Dark Matter. In order to achieve this sensitivity, the collaboration is measuring and controlling radioactivity and contamination of all detector components. All detector materials are assayed for radioactive contamination, usually U-, Th- chains, K, Cs and other radioactive species.

Example Student Project:. The student will become familiar with underground clean rooms (including becoming proficient with clean room protocols); assisting with routine maintenance of the clean rooms, creating and filing electronic log entries; and assisting with physical assembly tasks. Later student projects could involve the characterization of the detector and data and systems monitoring and evaluating.

Physics/Chemistry Project 3: Inductively Coupled Plasma Mass Spectrometry for Radiopurity Measurements

Inductively Coupled Plasma Mass Spectrometry (ICP-MS) is a complementary technique to the HPGe detectors that are ubiquitously used in underground labs (as described in Project 1). In the standard ICP-MS technique, liquid samples are pumped into a nebulizer where it is mixed with argon gas to form a fine aerosol and sent into the plasma torch. The molecules of the aerosol are broken into ions by the plasma and sent through the mass spectrometry interface consisting of sampling and skimmer cones and into an ion focusing system which directs the ions into the mass separation device and finally onto the detector. One advantage of ICP-MS over HPGe is in the measurement speed. Once the sample is prepared, ICP-MS takes less than five minutes to analyze one sample, whereas the HPGe detector may take up to a month. Additionally, smaller sample sizes are required with ICP-MS and if laser ablation is utilized, ICP-MS can become a location-specific technique. A disadvantage of ICP-MS is in the preparation of the sample (if laser ablation is not used). A solid sample must be dissolved to a concentration of less than 1%. Preconcentration methods may be used prior to introduction into the ICP-MS.

Example Student Project: Perhaps more important than the ICP-MS itself is the sample preparation required to achieve ultra-trace sensitivities required for low background experiments. The preparation of a sample for ICP-MS analysis requires great care. The sample must be tracked from its origin, through preparation and to the ICP-MS itself. Any step taken along the way could cause contamination of the sample and must be examined carefully. Sample preparation techniques for ICP-MS radiopurity measurements are constantly being researched and refined. The student would work to develop new sample preparation methods with applications to low background physics experiments.

Biology Project 4: Eukaryotic Extremophile Diversity in Aquatic Microbial Ecosystems of the Deep Subsurface

Eukaryotic microbes in subsurface aquatic and terrestrial ecosystems remain underexplored. While it had been assumed that the likelihood of finding nematodes, flatworms, protozoa and fungi in the pristine rock strata at any significant depth would diminish due to spatial and nutrient constraints, such organisms have been found to inhabit fissure and fracture water in South African gold mines [15]. Our lab has isolated similar organisms from the soils and fracture waters emanating from a drill hole at the 1480 m level of SURF (unpublished). In both the South African gold mines, and in our SURF findings, the habitat is not considered overly extreme, but nutrient deficient. While the origin of most of the organisms identified in these subsurface environments is most likely due to recharge of surface waters into the subsurface ecosystems, whether these organisms have adapted to life in deeper aquatic ecosystems remains underexplored. SURF offers a unique opportunity to sample an aquatic ecosystem approximately 2438.4 m below the surface, as well as to obtain terrestrial samples from biofilms along the walls of the boreholes and drill holes in the areas surrounding the access point to the water source. This would allow us to explore both the prokaryotic and eukaryotic microbial diversity in this water source and adjacent terrestrial ecosystems where the environment is more extreme with respect to temperature, oxygen saturation, and nutrient availability.

Example Student Project: Next Generation sequencing technologies vastly improves the ability to capture the entire diversity present at SURF. Analysis of rDNA and ITS sequences from earlier student projects conducted at SURF (unpublished) were supported by the isolation and SEM observation of some of the same taxa (nematodes, platyhelminthes and fungi). Students involved in this REU project would use Next Generation sequencing technology, light microscopy and SEM to explore the prokaryotic and eukaryotic diversity of this deep subsurface aquatic ecosystem, and the biofilms found in the surrounding terrestrial areas. Comparison of the deep open water source, water from deep drill holes, water emanating from drill holes and biofilms would provide us with a much more thorough view of the prokaryotic and eukaryotic microbial diversity in this isolated ecosystem and lead to hypotheses about colonization of water and biofilms, and the organismal relationships occurring in the systems. Culture independent DNA analyses will be employed to explore both the prokaryotic and the eukaryotic microbial diversity. Students will PCR amplify the intergenic spacer region of the rDNA, ITS1-5.8S-ITS2, and construct amplicon libraries for NextGen sequencing and will use bioinformatics data analysis tools to estimate the eukaryotic diversity throughout several sampling areas. By collaborating with students working in other related projects such as water chemistry in these areas, a deeper understanding of the possible roles of microbes will allow us to further our understanding of their roles in biogeochemical processes as well as the syntrophic relationships in a complex ecosystem.

Biology Project 5: New Techniques to Isolate Novel Microbial Groups from Deep Underground Sediments

Microbes are abundant in nearly all terrestrial and subsurface habitats on earth, often with over 103-104 species of microbes and over 108 microbial cells per gram of soil [16]. Nonetheless, detailed characterization of the microbes in most habitats has proved challenging, because it is estimated that only about 0.1-15% of most microbes can be isolated from the environment using standard bacteriological techniques [17]. Recent advances in analysis of environmental DNA (eDNA) has greatly expanded our knowledge of the composition and functioning of microbial communities. In many cases, the 16S rRNA gene is amplified from eDNA by PCR and sequenced to describe the taxonomic composition of microbial communities [17]. In other cases, direct shotgun sequencing of eDNA is performed to make inferences into community metabolism [17]. However, to compile a detailed picture of the phenotypic characteristics of individual microbial species and their interactions with other species in the community requires that these species be isolated and cultured in the laboratory under controlled conditions. During the past 20 years, techniques have been developed to improve the diversity of microbes which can be isolated from environmental samples; some involve in situ culturing of diluted environmental samples in low-nutrient media. These techniques have enabled the isolation of many microbes which cannot otherwise be cultured [18,19].

SURF presents a wide variety of habitats for microbes, including pools and seeps of fracture water, sediments, decomposing wood, and rock surfaces wetted by condensation. Differences in temperature, oxygen levels, and water chemistry among different sites within SURF result in a diverse assemblage of microbial communities in SURF, many of which contain phyla with few or no cultured members [20]. From 16s rDNA analysis, sediments in portions of SURF are predicted to have a diverse microbial community, which includes both chemoautotrophic and chemoheterotrophic Bacteria and Archaea [21].

Example Student Project: Past REU projects have focused on examining the diversity of microbes on rock surfaces and sediments, especially, the “cave silver” biofilms found on several levels of SURF, by sequencing 16S rRNA libraries. In the future, we would like to complement this work on the microbes of sediments and rock surfaces in SURF by isolating bacteria from these habitats using a variety of techniques. These bacteria could be characterized in the lab and screened for antibiotic activity against various target bacteria. It is hoped that some new antibiotics may be found, which could potentially be used in antibiotic drug therapy in the future.

In particular, we would like to attempt in-situ culturing of microbes using small diffusion chambers. Diluted samples of SURF sediment would be placed in these diffusion chambers. The chambers are about 100 microliters in size, bounded by 0.05 micrometer pore membranes, and allow exchange of molecules with the surrounding sediment. After a period of incubation in situ in SURF sediment, the diffusion chambers are opened and the microbes within are transferred to suitable media in the laboratory. This technique has been shown to enhance the isolation of novel groups bacteria from aquatic habitats and soils [22,23]. The microbes from diffusion chambers will then be tested for antibiotic effects on several target bacteria, such as Escherichia coli B, Pseudomonas putida, Enterococcus raffinosus, and Bacillus subtilis.

Chemistry Project 6: Analysis of Organic Compounds Present in Microbial Habitats Deep Underground

Microbes produce and consume a diverse array of organic compounds and investigation of the organic content in microbial habitats increases the understanding of the diversity of microbes present in various environments deep underground, as well as the requirements necessary to culture species in the laboratory. In particular, we are interested in detecting one-carbon compounds, such as methanol, and methylamine, used by methylotrophs, as well as more complex organic compounds, such as siderophores, which are produced by microbes to chelate iron(III), and homoserine lactones, which are signaling compounds used by microbes for quorum sensing.

Example Student Project: A student will collect water samples underground and develop assays for the detection of organic compounds. Methanol and methylamine can be detected via derivatization with fluorescent compounds followed by analysis by high-performance liquid chromatography (HPLC)[24]. Siderophore presence can be detected using the chrome azurol sulfonate assay [25]. The chrome azurol iron complex serves as an indicator in this assay, turning from blue to orange in the presence of siderophores, which have a high affinity for Fe3+ and will remove iron from the indicator. Following a positive test for siderophores, individual siderophore compounds shall be analyzed via HPLC. Homoserine lactones will be tested for via extraction with an organic solvent, such as dichloromethane, concentration, and evaluation of the extracts with gas chromatography mass spectrometry [26]. A student working on this project with have the unique opportunity to go underground to collect samples, gain experience developing new analytical chemistry techniques, and collaborate with biologists to improve conditions for culturing diverse forms of microbial life.

Geology Project 7: Use of LA-ICP-MS and Petrographic Microscopy to understand underground geology and geochemistry

SURF occupies the former Homestake Gold Mine, which at its full 8000 foot depth was the deepest gold mine in North America. Due to the former activity as a gold mine, numerous rock samples and core samples already exist that can be utilized for geological and geochemical research. The structure of the mine provides unparalleled access to geologic formations at a range of depths and allows for better understanding of the 3D structure of local geology. Laser ablation tools and inductively-coupled plasma mass spectrometers (LA-ICP-MS), like the Agilent 7900 at BHSU, are commonly used to get detailed information on geologic materials. Using an ICP-MS we can determine major, minor, and trace geochemistry of rocks, or of the groundwater passing through these rocks. These geochemical data sets help us better understand the petrogeneses of these rock units and of the source and history of local groundwater.

Example Student Project: Thin bodies of rhyolite magma intruded into the local metamorphic rock in the region of SURF roughly 45-55 million years ago. These hardened magma bodies, called dikes, are visible in the open cut mine in Lead and in other areas in the Lead-Deadwood region. How dikes emplace is an area of active research in the volcanological community. The depth and exposure of these dikes at SURF give us an opportunity to analyze these intrusions at depth and all the way up to the surface. A student will research if there are any variations in geochemistry, mineralogy, or mineral orientation that give us information as to how the magma moved as it approached the surface. A student will use LA-ICP-MS to get geochemical data on specific dikes: geochemistry can help us determine the viscosity of the magma involved. A petrographic microscope looks at thin sections of rhyolite from these dikes. Alignment of micro-crystals in thin section reflects the velocity and shear profile across the dike. A student working on this project gets the unique opportunity to access and sample geology at depth in SURF, and the experience of learning how to run an ICP-MS for geochemistry data. This student will also gain skills in identifying minerals in thin-section and using physical equations to understand magma flow through a dike.

Project 8: Exploring the correspondence between the algebra of observables in Classical system and Quantum System by the mechanism of Gelfand-Naimark theorem and canonical quantization

In classical system the phase space is a smooth symplectic manifold of even dimension. Then the set of real valued infinitely differentiable functions form the set of classical observables. Then the set of classical observables can be characterized as C* algebra. It can be shown the set of classical observables are the self-adjoint elements of a separable commutative unital C*-algebra. Moreover, the classical observables also has the structure of a Lie algebra with the Lie-Poisson bracket. On the other hand, the quantum system is characterized by a separable Hilbert space over the field of complex numbers. The quantum observables are self-adjoint operators on the Hilbert space. It is well known via Gelfand-Neumark Theorem that an arbitrary C* algebra is isometrically *-isomorphic to a C* algebra of bounded linear operators on the Hilbert space. Then, the self-adjoint elements of that C* algebra forms the quantum observables. This correspondence between these two C* algebras can be established via the famous Gelfand-Naimark theorem and the Gelfand-Naimark-Segal construction. Moreover, the quantum observables is a Lie algebra with a scaling parameter which is a function of the Plank’s constant. There is also a correspondence between the two Lie algebras via the quantization process.

Example Student Project: The student will study the mathematical tools necessary to understand the Hamiltonian formulation of classical mechanics and the concepts associated with formulating the classical observables as self-adjoint elements of a separable commutative C* algebra. The student will also study the Lie algebraic properties of the classical observables via the Lie-Poisson bracket formulation. Then, the important result that the student need to study along with the necessary pre-requisites the Gelfand-Neumark theorem and the Gelfand-Neumark-Segal construction. Using this knowledge one would the try to understand the correspondence between the C* algebra of classical observables and (non-commutative) C* algebra of quantum observables. Finally the student will study the correspondence between the Lie algebra of the classical observables and quantum observables by the quantization process. This work is primarily to develop an insight into the foundations of Quantum Mechanics.