Tomographic Reservoir Imaging with DNA-Labeled Silica Nanotracers: The First Field Validation

Temperature stability and enhanced transport properties by surface modifications of silica nanoparticle tracers for geo-reservoir exploration

Tracer tests are an important tool for characterizing and monitoring subsurface reservoir properties. However, they are limited both because of the tracer molecules constraining factors such as irreversible adsorption, retention, and degradations, i.e. interaction processes of fluorophore molecule with surrounding media resulting in a large variation in transport properties. Elaborate tests utilizing more than one tracer to distinguish time or location of injection are complex and interpretation is ambiguous because each tracer interacts differently. In this study, we present an approach to increase tracer stability and enhance the transport uniformity of different tracers, thus making tests utilizing multiple tracers simpler and more feasible. We present this concept of tracer multiplicity by encapsulating an anionic, cationic or amphoteric fluorophore inside mesoporous silica nanoparticle carriers coated with a protective titania layer. Upon encapsulation, increased thermal resistance and drastically lowered sorption affinity towards quartz sand was detected in batch and flow-through experiments. An additional advantage of the presented nanoparticle tracers over molecular tracers is their modularity, which is demonstrated by surface modifications and application of additives that greatly reduce sorption and increase recovery rates in the flow experiments. With the here presented concept of tracer multiplicity, we introduce a new approach for colloidal tracer design that has the potential to expand and enhance measurable parameters, measurement accuracy and simplicity of analysis.

A strategy to build a library of oil tracers by oleophilic silica-encapsulated DNA nanoparticles

Artificially synthesized DNA is involved in the construction of a library of oil tracers due to their unlimited number and no-biological toxicity. The strategy of the construction is proposed by oleophilic Silica-encapsulated DNA nanoparticles, which offers fresh thinking in developing novel tracers, sensors, and molecular machines in engineering & applied sciences based on artificially synthesized DNA blocks.

Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications

Synthetic DNA barcodes are double-stranded DNA molecules designed to carry recoverable information, information that can be used to represent and track objects and organisms. DNA barcodes offer robust, sensitive detection using standard amplification and sequencing techniques. While numerous research groups have promoted DNA as an information storage medium, less attention has been devoted to the design of economical, scalable DNA barcode libraries. Here, we present an alternative modular approach to sequence design. Barcode sequences were constructed from smaller, interchangeable blocks, allowing for the combinatorial assembly of numerous distinct tags. We demonstrated the design and construction of first-generation (N = 256) and second-generation (N = 512) modular barcode libraries, from fewer than 50 total single-stranded oligonucleotides for each library. To avoid contamination during experimental validation, a liquid-handling robot was employed for oligonucleotide mixing. Generating barcode sequences in-house reduces dependency upon external entities for unique tag generation, increasing flexibility in barcode generation and deployment. Next generation sequencing (NGS) detection of 256 different samples in parallel highlights the multiplexing afforded by the modular barcode design coupled with high-throughput sequencing. Deletion variant analysis of the first-generation library informed sequence design for enhancing barcode assembly specificity in the second-generation library.

Degradation and adsorption of synthetic DNA water tracers in environmental matrices

Synthetic DNA tracers are gaining interest as tools for tracking contamination pathways and hydraulic connections in surface water and groundwater systems. However, few quantitative data exist that describe DNA tracer degradation and adsorption in environmental matrices. We undertook laboratory experiments to quantify the degradation of multiple double-stranded DNA tracers in stream water, groundwater, and domestic and dairy-shed effluent, and adsorption to stream sediments, soils, coastal sand aquifer media and alluvial sandy gravel aquifer media. Faster DNA tracer degradation seemed to be associated with high bacterial concentrations in the liquid phase. Overall, the degradation of the 352 base pair (bp) DNA tracers in the aqueous phase was significantly (P = 0.018) slower than that of the 302 bp DNA tracers. Although the tracers' internal amplicon lengths were similar, the longer non-amplified flanking regions of the 352 bp tracers may better protect them from environmental degradation. Thermodynamic analysis suggests that longer flanking regions contribute to greater tracer stability. This finding may explain our previous field observations that 352 bp tracer mass reductions were often lower than 302 bp tracer mass reductions. The 2 sets of DNA tracers did not differ significantly regarding their adsorption to stream sediment-stream water or aquifer media-groundwater mixtures (P > 0.067), but the 352 bp tracers showed significantly less adsorption to soil-effluent mixtures than the 302 bp tracers (P = 0.005). The DNA tracers' adsorption to soil-effluent mixtures was comparatively less than their adsorption to the aquifer media-groundwater and stream sediment-stream water mixtures, suggesting that DNA tracers may compete with like-charged organic matter for adsorption sites. These findings provide insights into the fate of DNA tracers in the environment. The DNA tracers' degradation rate constants determined in this study for a range of environmental conditions could assist the design of future field investigations.

Mosquito tagging using DNA-barcoded nanoporous protein microcrystals

Conventional mosquito marking technology for mark-release-recapture (MRR) is quite limited in terms of information capacity and efficacy. To overcome both challenges, we have engineered, lab-tested, and field-evaluated a new class of marker particles, in which synthetic, short DNA oligonucleotides (DNA barcodes) are adsorbed and protected within tough, crosslinked porous protein microcrystals. Mosquitoes self-mark through ingestion of microcrystals in their larval habitat. Barcoded microcrystals persist trans-stadially through mosquito development if ingested by larvae, do not significantly affect adult mosquito survivorship, and individual barcoded mosquitoes are detectable in pools of up to at least 20 mosquitoes. We have also demonstrated crystal persistence following adult mosquito ingestion. Barcode sequences can be recovered by qPCR and next-generation sequencing (NGS) without detectable amplification of native mosquito DNA. These DNA-laden protein microcrystals have the potential to radically increase the amount of information obtained from future MRR studies compared to previous studies employing conventional mosquito marking materials.

The Role of High-Permeability Inclusion on Solute Transport in a 3D-Printed Fractured Porous Medium: An LIF–PIV Integrated Study

It is well-known that the presence of geometry heterogeneity in porous media enhances solute mass mixing due to fluid velocity heterogeneity. However, laboratory measurements are still sparse on characterization of the role of high-permeability inclusions on solute transport, in particularly concerning fractured porous media. In this study, the transport of solutes is quantified after a pulse-like injection of soluble fluorescent dye into a 3D-printed fractured porous medium with distinct high-permeability (H-k) inclusions. The solute concentration and the pore-scale fluid velocity are determined using laser-induced fluorescence and particle image velocimetry techniques. The migration of solute is delineated with its breakthrough curve (BC), temporal and spatial moments, and mixing metrics (including the scalar dissipation rate, the volumetric dilution index, and the flux-related dilution index) in different regions of the medium. With the same H-k inclusions, compared to a H-k matrix, the low-permeability (L-k) matrix displays a higher peak in its BC, less solute mass retention, a higher peak solute velocity, a smaller peak dispersion coefficient, a lower mixing rate, and a smaller pore volume being occupied by the solute. The flux-related dilution index clearly captures the striated solute plume tails following the streamlines along dead-end fractures and along the interface between the H-k and L-k matrices. We propose a normalization of the scalar dissipation rate and the volumetric dilution index with respect to the maximum regional total solute mass, which offers a generalized examination of solute mixing for an open region with a varying total solute mass. Our study presents insights into the interplay between the geometric features of the fractured porous medium and the solute transport behaviors at the pore scale.

Transport characteristics of DNA-tagged silica colloids as a colloidal tracer in saturated sand columns; role of solution chemistry, flow velocity, and sand grain size

In recent years, DNA-tagged silica colloids have been used as an environmental tracer. A major advantage of this technique is that the DNA-coding provides an unlimited number of unique tracers without a background concentration. However, little is known about the effects of physio-chemical subsurface properties on the transport behavior of DNA-tagged silica tracers. We are the first to explore the deposition kinetics of this new DNA-tagged silica tracer for different pore water chemistries, flow rates, and sand grain size distributions in a series of saturated sand column experiments in order to predict environmental conditions for which the DNA-tagged silica tracer can best be employed. Our results indicated that the transport of DNA-tagged silica tracer can be well described by first order kinetic attachment and detachment. Because of massive re-entrainment under transient chemistry conditions, we inferred that attachment was primarily in the secondary energy minimum. Based on calculated sticking efficiencies of the DNA-tagged silica tracer to the sand grains, we concluded that a large fraction of the DNA-tagged silica tracer colliding with the sand grain surface did also stick to that surface, when the ionic strength of the system was higher. The experimental results revealed the sensitivity of DNA-tagged silica tracer to both physical and chemical factors. This reduces its applicability as a conservative hydrological tracer for studying subsurface flow paths. Based on our experiments, the DNA-tagged silica tracer is best applicable for studying flow routes and travel times in coarse grained aquifers, with a relatively high flow rate. DNA-tagged silica tracers may also be applied for simulating the transport of engineered or biological colloidal pollution, such as microplastics and pathogens.

Computing Localized Breakthrough Curves and Velocities of Saline Tracer from Ground Penetrating Radar Monitoring Experiments in Fractured Rock

Solute tracer tests are an established method for the characterization of flow and transport processes in fractured rock. Such tests are often monitored with borehole sensors which offer high temporal sampling and signal to noise ratio, but only limited spatial deployment possibilities. Ground penetrating radar (GPR) is sensitive to electromagnetic properties, and can thus be used to monitor the transport behavior of electrically conductive tracers. Since GPR waves can sample large volumes that are practically inaccessible by traditional borehole sensors, they are expected to increase the spatial resolution of tracer experiments. In this manuscript, we describe two approaches to infer quantitative hydrological data from time-lapse borehole reflection GPR experiments with saline tracers in fractured rock. An important prerequisite of our method includes the generation of GPR data difference images. We show how the calculation of difference radar breakthrough curves (DRBTC) allows to retrieve relative electrical conductivity breakthrough curves for theoretically arbitrary locations in the subsurface. For sufficiently small fracture apertures we found the relation between the DRBTC values and the electrical conductivity in the fracture to be quasi-linear. Additionally, we describe a flow path reconstruction procedure that allows computing approximate flow path distances using reflection GPR data from at least two boreholes. From the temporal information during the time-lapse GPR surveys, we are finally able to calculate flow-path averaged tracer velocities. Our new methods were applied to a field data set that was acquired at the Grimsel Test Site in Switzerland. DRBTCs were successfully calculated for previously inaccessible locations in the experimental rock volume and the flow path averaged velocity field was found to be in good accordance with previous studies at the Grimsel Test Site.

Rapid Visual Authentication Based on DNA Strand Displacement

Novel ways to track and verify items of a high value or security is an ever-present need. Taggants made from deoxyribonucleic acid (DNA) have several advantageous properties, such as high information density and robust synthesis; however, existing methods require laboratory techniques to verify, limiting applications. Here, we leverage DNA nanotechnology to create DNA taggants that can be validated in the field in seconds to minutes with a simple equipment. The system is driven by toehold-mediated strand-displacement reactions where matching oligonucleotide sequences drive the generation of a fluorescent signal through the potential energy of base pairing. By pooling different "input" oligonucleotide sequences in a taggant and spatially separating "reporter" oligonucleotide sequences on a paper ticket, unique, sequence-driven patterns emerge for different taggant formulations. Algorithmically generated oligonucleotide sequences show no crosstalk and ink-embedded taggants maintain activity for at least 99 days at 60 °C (equivalent to nearly 2 years at room temperature). The resulting fluorescent signals can be analyzed by the eye or a smartphone when paired with a UV flashlight and filtered glasses.

Development of thermo-reporting nanoparticles for accurate sensing of geothermal reservoir conditions

The inaccessibility of geological reservoirs, both for oil and gas production or geothermal usage, makes detection of reservoir properties and conditions a key problem in the field of reservoir engineering, including for the development of geothermal power plants. Herein, an approach is presented for the development of messenger nanoparticles for the determination of reservoir conditions, with a proof of concept example of temperature detection under controlled laboratory conditions. Silica particles are synthesized with a two-layer architecture, an inner enclosed core and an outer porous shell, each doped with a different fluorescent dye to create a dual emission system. Temperature detection happens by a threshold temperature-triggered irreversible release of the outer dye, thus changing the fluorescence signal of the particles. The reported particle system consequently enables a direct, reliable and fast way to determine reservoir temperature. It also displays a sharp threshold for accurate sensing and allows detection at concentration ranges as low as few nanograms of nanoparticles per milliliter.