Depletion Front Research Articles

An integrated ion-exchange membrane-based microfluidic device for irreversible dissociation and quantification of miRNA from ribonucleoproteins.

Ribonucleoproteins (RNPs), particularly microRNA-induced silencing complex (miRISC), have been associated with cancer-related gene regulation. Specific RNA-protein associations in miRISC complexes or those found in let-7 lin28A complexes can downregulate tumor-suppressing genes and can be directly linked to cancer. The high protein-RNA electrostatic binding affinity is a particular challenge for the quantification of the associated microRNAs (miRNAs). We report here the first microfluidic point-of-care assay that allows direct quantification of RNP-associated RNAs, which has the potential to greatly advance RNP profiling for liquid biopsy. Key to the technology is an integrated cation-anion exchange membrane (CEM/AEM) platform for rapid and irreversible dissociation (k = 0.0025 s-1) of the RNP (Cas9-miR-21) complex and quantification of its associated miR-21 in 40 minutes. The CEM-induced depletion front is used to concentrate the RNP at the depletion front such that the high electric field (>100 V cm-1) within the concentration boundary layer induces irreversible dissociation of the low KD (∼0.5 nM) complex, with ∼100% dissociation even though the association rate (kon = 6.1 s-1) is 1000 times higher. The high field also electrophoretically drives the dissociated RNA out of the concentrated zone without reassociation. A detection limit of 1.1 nM is achieved for Cy3 labelled miR-21.

Aerobic respiration controls on shale weathering

The weathering of shale exerts an important control on the hydrochemical fluxes to river systems, thus influencing the global carbon, nutrient, and geochemical cycles. However, the quantitative understanding of shale weathering and its impact on global biogeochemical cycles remains inadequate due to the complex interplay between hydrological, biogeochemical, and physical processes. In this study, we develop a novel modeling approach to quantitatively interpret the long-term chemical weathering of shale occurring since the last glaciation period (15,000 years) leading to the present geochemical conditions. The model explicitly considers processes occurring across multiple phases and involved in the weathering, including: (i) the infiltration of meteoric water, (ii) the interactions between the water and the mineral assemblage via dissolution/precipitation reactions, (iii) the microbially-mediated oxidation of organic matter, (iv) the evolution of porosity induced by mineral reactions, and (v) the exchange of gases between the subsurface and the atmosphere. To implement and test our model, we conduct this study at a well-instrumented hillslope underlain by Mancos Shale and located at the East River study site, Western Colorado. Consistent with field observations, the model successfully reproduces the stratified weathering front, the complex spatial distribution of organic carbon, and the gaseous emissions of carbon dioxide from the subsurface. Model simulations show that aerobic respiration exerts a fundamental control on the weathering of shale. While previous studies have highlighted the diffusion of oxygen from the atmosphere as the primary mechanism for shale weathering, our model simulations demonstrate that aerobic respiration limits the propagation of oxygen in the shallow subsurface, and thereby inhibits the dissolution of pyrite at depth. Aerobic respiration is particularly favored in the top soil horizon due to the constant flux of oxygen from the atmosphere, the replenishment of fresh litter/plant-derived organic matter, and to a lesser extent the presence of fossil shale-associated organic matter. The acidic pore water generated through aerobic respiration within the shallow subsurface is transported to greater depths, where it sustains the dissolution of carbonate (dolomite in this example). Overall, our results demonstrate that the evolution of pyrite and carbonate depletion fronts are significantly different, and primarily depend on the ability of microorganisms to carry out microbial respiration and the various transport pathways of reactants controlling the mineral reactions under partially saturated conditions.

Drying-induced stresses in poroelastic drops on rigid substrates.

We develop a theory for drying-induced stresses in sessile, poroelastic drops undergoing evaporation on rigid surfaces. Using a lubrication-like approximation, the governing equationsof three-dimensional nonlinear poroelasticity are reduced to a single thin-film equationfor the drop thickness. We find that thin drops experience compressive elastic stresses but the total in-plane stresses are tensile. The mechanical response of the drop is dictated by the initial profile of the solid skeleton, which controls the in-plane deformation, the dominant components of elastic stress, and sets a limit on the depth of delamination that can potentially occur. Our theory suggests that the alignment of desiccation fractures in colloidal drops is selected by the shape of the drop at the point of gelation. We propose that the emergence of three distinct fracture patterns in dried blood drops is a consequence of a nonmonotonic drop profile at gelation. We also show that depletion fronts, which separate wet and dry solid, can invade the drop from the contact line and localize the generation of mechanical stress during drying. Finally, the finite element method is used to explore the stress profiles in drops with large contact angles.

Comparison of pressure front with tracer front advance and principal flow regimes in hydraulically fractured wells in unconventional reservoirs

Pressure depletion patterns near hydraulically fractured wells in ultra-low permeability reservoirs occupy a much larger region than outlined by fluid withdrawal contours. When used for reservoirs with moderate or high permeability (say k > 1 mD), industry never needed to caution using pressure depletion plots as a proxy for fluid removal or drained rock volume (DRV). For such conventional reservoirs, pressure depletion plots are good proxies for fluid removal or drained rock volume (DRV). The fluid that moves from the margins of a pressure front, indicative of the so-called diffusive depth of investigation (DOI), will reach the well on the time-scale of economic life of the well. However, a whole new way of thinking is required when studying ultra-low permeability shales (nanoDarcy range), where the distinction between pressure depletion zones and the DRV regions (where fluid is recovered from) becomes crucial to understand which factors control the hydrocarbon recovery process. Our detailed analysis compares the diffusive DOI, of the leading edge of the pressure depletion front, and that of the convective DRV given by a tracer front. Results show that the pressure depletion front between the fractures quickly approaches the adjoining fracture pressure, and most of the production originates from the fracture tips after 12 months. The pressure depletion pattern vastly overestimates the DRV, whereas the tracer front shows the actual produced rock volume. A final section evaluates the specific flow regimes that correspond to certain diffusive DOI and convective DRV growth stages in the life of the well. The discussion section explains how production diagnostic plots can be used to identify the moment in the well life when enhanced oil recovery methods should be applied. This study can facilitate a better understanding of the fluid flow in fractured porous media and can be used to optimize fracture and well spacing to maximize the DRV.

<inline-formula> <tex-math notation="LaTeX">${C}_{\textsf{OSS}}$ </tex-math> </inline-formula> Measurements for Superjunction MOSFETs: Limitations and Opportunities

Small-signal measurements of output capacitance ( ${C_{\textsf {OSS}}}$ ) are ubiquitous in power semiconductor datasheets and determine critical features of power converters. For silicon superjunction power MOSFETs (SJs), we report ${C_{\textsf {OSS}}}$ measurements with two key anomalies: variation with ac perturbation frequency and hysteresis with dc sweep direction. Using mixed-mode simulations, we attribute the frequency shift to the fundamental SJ structure and find that dc hysteresis is caused by charge trapping from uneven depletion fronts. We show that ${C_{\textsf {OSS}}}$ measurements on SJs do not accurately characterize large-signal operation, underestimating stored energy by up to four times and giving no indication of ${C_{\textsf {OSS}}}$ losses.

Flame propagation through three-phase methane-hydrate particles

A new mathematical solution for the laminar combustion of a spray containing three-phase particles is derived. The three-phase particles are represented by methane hydrate (MH) particles. These particles melt and evaporate following a spherical symmetric model that demonstrates the unique nature of that process. The methane-hydrate particles are uniformly distributed, yet the gaseous methane is not initially premixed, until they reach the particle depletion front. A one-dimensional, laminar flame then propagates into a homogeneous mixture of oxidizer, inert gases and small methane-hydrate particles. Characteristics of the laminar methane-hydrate spray combustion are examined at different methane-to-water mass ratio values within the particles. The methane-hydrate evaporation model serves as a building block for the evaluation of these characteristics. Previous constraints on the evaporation front are relaxed. Instead, the unique profiles of the evaporation process of the methane-hydrate particles are integrated over the entire evaporation period. Thus, an energy balance is employed to evaluate the flame location, velocity and temperature at which all liquid is evaporated. Using this approach it is shown that modeling the initial transient evaporation stage is crucial in MH and leads to non-linear evaporation characteristics. This in turn alters the dynamics of the supported flame temperature, location and velocity. Particle loading is shown to have significant impact on the evaporation and flame as well.

Selectivity enhancements in gel-based DNA-nanoparticle assays by membrane-induced isotachophoresis: thermodynamics versus kinetics.

Selectivity against mutant nontargets with a few mismatches remains challenging in nucleic acid sensing. Sensitivity enhancement by analyte concentration does not improve selectivity because it affects targets and nontargets equally. Hydrodynamic or electrical shear enhanced selectivity is often accompanied by substantial losses in target signals, thereby leading to poor limits of detection. We introduce a platform based on depletion isotachophoresis in agarose gel generated by an ion-selective membrane that allows both selectivity and sensitivity enhancement with a two-step assay involving concentration polarization at an ion-selective membrane. By concentrating both the targets and probe-functionalized nanoparticles by ion enrichment at the membrane, the effective thermodynamic dissociation constant is lowered from 40nM to below 500pM, and the detection limit is 10pM as reported previously. A dynamically optimized ion depletion front is then generated from the membrane with a high electrical shear force to selectively and irreversibly dehybridize nontargets. The optimized selectivity against a two-mismatch nontarget (in a 35-base pairing sequence) is shown to be better than the thermodynamic equilibrium selectivity by more than a hundred-fold, such that there is no detectable signal from the two-mismatch nontarget. We offer empirical evidence that irreversible cooperative dehybridization plays an important role in this kinetic selectivity enhancement and that mismatch location controls the optimum selectivity even when there is little change in the corresponding thermodynamic dissociation constant.

Concentration-Gradient Stabilization with Segregated Counter- and Co-Ion Paths: A Quasistationary Depletion Front for Robust Molecular Isolation or Concentration.

We study the spatiotemporal dynamics of a microfluidic system with a nonselective microfluidic channel gated by an ion-selective membrane which separates the ion flux paths of cations and anions. To preserve electroneutrality, the ionic concentration in the system is shown to converge to a specific inhomogeneous distribution with robust constant current fluxes. A circuit scaling theory that collapses measured asymptotic currents verifies that this is a generic and robust mechanism insensitive to channel geometry, ion selectivity, and electrolyte ionic strength. This first temporally stationary but spatially inhomogeneous depletion front can be used for modulating ionic current and for isotachophoretic isolation of low-mobility molecules and exosomes on small diagnostic chips for various medical applications that require robust high-throughput and integrated platforms.

Enhancement of the spin Hall voltage in a reverse-biased planarp−njunction

We report an experimental demonstration of a local amplification of the spin Hall voltage using an expanding depletion zone at a pn-junction in GaAs/AlGaAs Hall-bar microdevices. It is demonstrated that the depletion zone can be spatially expanded by applying reverse bias by at least 10~$\mu$m at low temperature. In the depleted regime, the spin Hall signals reached more than one order of magnitude higher values than in the normal regime at the same electrical current flowing through the micro-device. It is shown that the pn-bias has two distinct effects on the detected spin Hall signal. It controls the local drift field at the Hall cross which is highly non-linear in the pn-bias due to the shift of the depletion front. Simultaneously, it produces a change in the spin-transport parameters due to the non-linear change in the carrier density at the Hall cross with the pn-bias.

Induced nanoparticle aggregation for short nucleic acid quantification by depletion isotachophoresis

A rapid (<20min) gel-membrane biochip platform for the detection and quantification of short nucleic acids is presented based on a sandwich assay with probe-functionalized gold nanoparticles and their separation into concentrated bands by depletion-generated gel isotachophoresis. The platform sequentially exploits the enrichment and depletion phenomena of an ion-selective cation-exchange membrane created under an applied electric field. Enrichment is used to concentrate the nanoparticles and targets at a localized position at the gel-membrane interface for rapid hybridization. The depletion generates an isotachophoretic zone without the need for different conductivity buffers, and is used to separate linked nanoparticles from isolated ones in the gel medium and then by field-enhanced aggregation of only the linked particles at the depletion front. The selective field-induced aggregation of the linked nanoparticles during the subsequent depletion step produces two lateral-flow like bands within 1cm for easy visualization and quantification as the aggregates have negligible electrophoretic mobility in the gel and the isolated nanoparticles are isotachophoretically packed against the migrating depletion front. The detection limit for 69-base single-stranded DNA targets is 10 pM (about 10 million copies for our sample volume) with high selectivity against nontargets and a three decade linear range for quantification. The selectivity and signal intensity are maintained in heterogeneous mixtures where the nontargets outnumber the targets 10,000 to 1. The selective field-induced aggregation of DNA-linked nanoparticles at the ion depletion front is attributed to their trailing position at the isotachophoretic front with a large field gradient.

Efficient conversion of light to charge and spin in Hall-bar microdevices

We report an experimental demonstration of a local amplification of the spin Hall voltage using an expanding depletion zone at a pn-junction in GaAs/AlGaAs Hall-bar microdevices. It is demonstrated that the depletion zone can be spatially expanded by applying reverse bias by at least 10~$\mu$m at low temperature. In the depleted regime, the spin Hall signals reached more than one order of magnitude higher values than in the normal regime at the same electrical current flowing through the micro-device. It is shown that the pn-bias has two distinct effects on the detected spin Hall signal. It controls the local drift field at the Hall cross which is highly non-linear in the pn-bias due to the shift of the depletion front. Simultaneously, it produces a change in the spin-transport parameters due to the non-linear change in the carrier density at the Hall cross with the pn-bias.

Assessing the geochemical and tectonic impacts of fluid-rock interaction in mid-crustal shear zones: a case study from the intracontinental Alice Springs Orogen, central Australia

The Reynolds–Anmatjira Ranges, central Australia, form part of a high-grade basement terrane dissected by intensely metasomatized transpressional shear zones active during the Ordovician–Carboniferous Alice Springs Orogeny. Unlike typical retrograde structures associated with discrete fluid flow, the mid-crustal setting and intracontinental nature of these shear systems present significant problems for the source and ingress mechanism of the fluid involved in their rehydration. To address these issues, we describe two detailed traverses across deformed and metasomatized basement rocks in this region, and interrogate their record of fluid–rock interaction from various perspectives. Both traverses combine structural and petrological observations with Zr-in-rutile and Ti-in-quartz thermobarometry, oxygen and hydrogen stable isotope analysis, and major, trace and rare earth element mobility trends. Each technique is critically evaluated for its utility in this study and its more widespread applicability to alternative field areas, providing a strategic framework for the general investigation of fluid-affected shear zones. Ultimately, the integrated data sets specify pressure–temperature conditions of ∼530 °C and 4–5 kbar, implying average apparent thermal gradients of 29–36 °C km−1 and depths of 14–18 km. Other characteristic features to emerge include strongly variable element mobilities and pronounced isotopic depletion fronts consistent with the alteration effects of an externally derived, non-equilibrium fluid. This is confirmed by calculated fluid compositions indicative of contributions from a fluid of meteoric origin, with estimated δ18O and δD values as low as 2.3‰ and −59.8‰, respectively. We propose that these surficial fluid signatures are imposed on the mid-crust by the prograde burial and dehydration of hydrothermally altered fault panels produced during pre-orogenic basin formation. Progressive fluid release with continued subsidence then leads to the accumulation of increasing fluid volumes in the vicinity of the brittle–ductile transition, promoting extensive hydration, metasomatism and reaction softening at the locus of stress transmission from plate-boundary sources. The sustained injection of externally derived fluids into refractory crustal material may thus stimulate a critical reduction in the long-term strength of the lithosphere, providing strong impetus for the initiation and advancement of intracontinental orogenesis.

Electroosmotic pump performance is affected by concentration polarizations of both electrodes and pump

Current methods of optimizing electroosmotic (EO) pump performance include reducing pore diameter and reducing ionic strength of the pumped electrolyte. However, these approaches each increase the fraction of total ionic current carried by diffuse electric double layer (EDL) counterions. When this fraction becomes significant, concentration polarization (CP) effects become important, and traditional EO pump models are no longer valid. We here report on the first simultaneous concentration field measurements, pH visualizations, flow rate, and voltage measurements on such systems. Together, these measurements elucidate key parameters affecting EO pump performance in the CP dominated regime. Concentration field visualizations show propagating CP enrichment and depletion fronts sourced by our pump substrate and traveling at order mm/min velocities through millimeter-scale channels connected serially to our pump. The observed propagation in millimeter-scale channels is not explained by current propagating CP models. Additionally, visualizations show that CP fronts are sourced by and propagate from the electrodes of our system, and then interact with the EO pump-generated CP zones. With pH visualizations, we directly detect that electrolyte properties vary sharply across the anode enrichment front interface. Our observations lead us to hypothesize possible mechanisms for the propagation of both pump- and electrode-sourced CP zones. Lastly, our experiments show the dynamics associated with the interaction of electrode and membrane CP fronts, and we describe the effect of these phenomena on EO pump flow rates and applied voltages under galvanostatic conditions.

Modelling chemical depletion profiles in regolith

Chemical or mineralogical profiles in regolith display reaction fronts that document depletion of leachable elements or minerals. A generalized equation employing lumped parameters was derived to model such ubiquitously observed patterns: C = C 0 C 0 − C x = 0 C x = 0 exp ( Γ ini · k ˆ · x ) + 1 Here C, C x = 0 , and C o are the concentrations of an element at a given depth x, at the top of the reaction front, or in parent respectively. Γ ini is the roughness of the dissolving mineral in the parent and k̂ˆ is a lumped kinetic parameter. This kinetic parameter is an inverse function of the porefluid advective velocity and a direct function of the dissolution rate constant times mineral surface area per unit volume regolith. This model equation fits profiles of concentration versus depth for albite in seven weathering systems and is consistent with the interpretation that the surface area (m 2 mineral m − 3 bulk regolith) varies linearly with the concentration of the dissolving mineral across the front. Dissolution rate constants can be calculated from the lumped fit parameters for these profiles using observed values of weathering advance rate, the proton driving force, the geometric surface area per unit volume regolith and parent concentration of albite. These calculated values of the dissolution rate constant compare favorably to literature values. The model equation, useful for reaction fronts in both steady-state erosional and quasi-stationary non-erosional systems, incorporates the variation of reaction affinity using pH as a master variable. Use of this model equation to fit depletion fronts for soils highlights the importance of buffering of pH in the soil system. Furthermore, the equation should allow better understanding of the effects of important environmental variables on weathering rates.

Control of noise‐induced spatiotemporal patterns in superlattices

AbstractWe investigate a semiconductor superlattice exhibiting complex dynamics of electron accumulation and depletion fronts (travelling field domains) in the presence of noise and control. In the uncontrolled system noise is able to induce electron charge front motion through the device when the system is prepared near a global bifurcation which yields it highly sensitive to fluctuations. The associated current density oscillations exhibit a maximum of coherence at an optimal noise intensity, a phenomenon known as coherence resonance. We show how control in the form of a time‐delayed feedback signal affects the noise‐induced dynamics. We observe that control induces a limit cycle in a wide range of the control parameter space and therefore destroys the effect of coherence resonance. For low noise intensity, time‐delayed feedback control enhances the regularity (coherence) of the noisy oscillations considerably. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Noise-Induced Front Motion: Signature of a Global Bifurcation

We show that front motion can be induced by noise in a spatially extended excitable system with a global constraint. Our model system is a semiconductor superlattice exhibiting complex dynamics of electron accumulation and depletion fronts. The presence of noise induces a global change in the dynamics of the system forcing stationary fronts to move through the entire device. We demonstrate the effect of coherence resonance in our model; i.e., there is an optimal level of noise at which the regularity of front motion is enhanced. Physical insight is provided by relating the space-time dynamics of the fronts with a phase-space analysis.

Bifurcations in a System of Interacting Fronts

We show that the bifurcation scenario in a high-dimensional system with interacting moving fronts can be related to the universal U-sequence which is known from the symbolic analysis of iterated one-dimensional maps. This connection is corroborated for a model of a semiconductor superlattice, which describes the complex dynamics of electron accumulation and depletion fronts. By a suitable Poincare section we reduce the dynamics to a low-dimensional iterated map, for which in the most elementary case the bifurcation points can be determined analytically.

Reaction fronts in a porous medium following injection along a temperature gradient

We consider the displacement of a 'formation fluid' by an 'injection fluid' along a temperature gradient in a reactive porous rock. We assume that the formation fluid is in chemical equilibrium initially and we allow the injection fluid to differ from the formation fluid both in temperature and in chemical composition. Two types of reaction front can form as the injection fluid propagates into the rock: (i) 'depletion fronts' caused by any undersaturation of the injection fluid and (ii) 'thermal reaction fronts' caused by any difference in temperature between the injection fluid and the trailing edge of the formation fluid. As flow proceeds the temperature gradient in the formation fluid is advected at the thermal propagation speed, but the fluid itself moves more quickly at the interstitial fluid speed. This difference in speed causes formation fluid to be carried out of chemical equilibrium and a 'gradient reaction' results. The subsequent dissolution or precipitation alters the amount of reactant present on the rock and this alters the propagation speed of any subsequent depletion front. We derive the six dimensionless parameters controlling the evolution of the system and calculate approximate solution profiles for the limit of fast kinetics and negligible diffusion. These solutions give insight into the physical processes governing the solution and are compared with numerical solutions of the full equations. The behaviour of the system is strongly influenced by three dimensionless parameters in particular. The parameters J C and J T quantify the chemical and thermal difference between the fluids at the point of injection and they control the relative positions of the depletion and thermal fronts at short times. On the other hand, the parameter a quantifies the background thermal gradient and controls the relative positions of the fronts at long times. In the cases where the depletion front moves from one side of the thermal front to the other, we derive approximate expressions for the time at which this 'crossover' occurs.

Hybrid model for chaotic front dynamics: from semiconductors to water tanks.

We present a general method for studying front propagation in nonlinear systems with a global constraint in the language of hybrid tank models. The method is illustrated in the case of semiconductor superlattices, where the dynamics of the electron accumulation and depletion fronts shows complex spatiotemporal patterns, including chaos. We show that this behavior may be elegantly explained by a tank model, for which analytical results on the emergence of chaos are available. In particular, for the case of three tanks the bifurcation scenario is characterized by a modified version of the one-dimensional iterated tent map.

Thermally driven reaction fronts in porous media

We examine the reaction fronts that develop when an undersaturated ‘injection fluid’ displaces a saturated ‘formation fluid’ in a chemically reactive porous medium. We allow the injection and formation fluids to differ both in temperature and in chemical composition. The undersaturation of the incoming fluid drives a dissolution reaction and leads to the formation of a ‘depletion’ front. Under certain circumstances, which we describe, the temperature difference drives a separate thermal reaction front. We develop long-time asymptotic solutions of the governing equations which illustrate the interaction between thermal reaction fronts and depletion fronts. Two distinct regimes arise. If the compositional difference between the injection and formation fluids exceeds a critical value, the depletion front travels faster than the thermal front, leaving the porous medium depleted of reactant from the source to a point downstream of the thermal front and no thermal reaction front develops. Conversely, if the compositional difference is smaller than the critical value, a thermal reaction front advances ahead of the depletion front and so there is a double reaction front structure. We illustrate the evolution of the thermal and compositional fields towards these asymptotic solutions with numerical simulations. We discuss the implications of this work for secondary mineralization in subsurface reservoirs.