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Demonstration of Acoustically Driven Ferromagnetic Resonance Using Leaky Surface Acoustic Waves in Lithium Tantalate
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MassIVE MSV000100641 - Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli: Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclease translation and activity can occur despite the use of inducible promoters to control expression, leading to extensive cell death. This background killing caused by promoter leakiness severely limits the application of Cas9 for generating mutant libraries because of the potential for population skew. We demonstrate the utility of temperature sensitive RNA elements as a layer of post-transcriptional regulation to reduce the impact of promoter leak. We observe significant temperature-dependent increases in cell survival when certain RNA thermometers (RNATs) are placed upstream of the cas9 coding sequence. We also show that the most highly repressing RNAT, hsp17rep, significantly reduces population skew with a library of characterized guide RNAs in Escherichia coli. This strategy should be applicable to all bacterial Cas9-based methods and technologies.
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Leaky Buddies: Cross-Component Covert Channels on Integrated CPU-GPU Systems
Graphics Processing Units (GPUs) are ubiquitous components used across the range of today’s computing plat- forms, from phones and tablets, through personal computers, to high-end server class platforms. With the increasing importance of graphics and video workloads, recent processors are shipped with GPU devices that are integrated on the same chip. Integrated GPUs share some resources with the CPU and as a result, there is a potential for microarchitectural attacks from the GPU to the CPU or vice versa. We consider the potential for covert channel attacks that arise either from shared microarchitectural components (such as caches) or through shared contention domains (e.g., shared buses). We illustrate these two types of channels by developing two reliable covert channel attacks. The first covert channel uses the shared LLC cache in Intel’s integrated GPU architectures. The second is a contention based channel targeting the ring bus connecting the CPU and GPU to the LLC. This is the first demonstrated microarchitectural attack crossing the component boundary (GPU to CPU or vice versa). Cross-component channels introduce a number of new challenges that we had to overcome since they occur across heterogeneous components that use different computation models and are interconnected using asymmetric memory hierarchies. We also exploit GPU parallelism to increase the bandwidth of the communication, even without relying on a common clock. The LLC based channel achieves a bandwidth of 120 kbps with a low error rate of 2%, while the contention based channel delivers up to 400 kbps with a 0.8% error rate. We also demonstrate a proof- of-concept prime-and-probe side channel attack that probes the full LLC from the GPU.
Leakage From Coexisting Geologic Forcing and Injection‐Induced Pressurization: A Semi‐Analytical Solution for Multilayered Aquifers With Multiple Wells
Abstract Abnormal fluid pressures (above or below hydrostatic pressure) can develop and persist in sedimentary basins. The common occurrence of abnormal pressures may cause challenges for project permitting of geological carbon sequestration (GCS), particularly in reservoirs with pre‐injection overpressure. The leaky wells that may exist in some sedimentary basins can provide flow paths between deep brine aquifers and shallower freshwater aquifers. Pre‐injection relative overpressures can cause brine leakage through leaky wells even before any injection occurs. The tendency for flow through leaky wells is coupled with the process of pressure dissipation that occurs through aquitards. Specifically, with non‐zero permeability, aquitards can dissipate pressure over large areal extents and thereby reduce leakage rates through leaky wells. This study presents development of a semi‐analytical solution for hydraulic head and brine leakage in multilayered aquifer–aquitard systems with geologic pressure forcing. The geologic forcing that causes abnormal pressures in the multilayered system can coexist with any number of injection, extraction, and leaky wells that also affect fluid pressure. The semi‐analytical model is applied to explore how leakage through leaky wells varies as functions of pressurization rate, along with aquitard and leaky well properties in an overpressured multilayered system. The results show that although injection‐induced pressures can dissipate rapidly through suitably permeable aquitards, coexisting geologic forcing may create sustained rates of brine leakage into freshwater aquifers through leaky wells. In GCS, a very low‐permeability aquitard with high capillary entry pressure to free‐phase CO 2 is desired to serve as the caprock to prevent leakage of CO 2 from the storage reservoir. Nevertheless, the results from this study show that the brine leakage impact to shallow freshwater aquifers through leaky wells might substantially decrease with increasing aquitard permeability values, as long as small aquitard permeability and high capillary entry pressure serve to prevent CO 2 leakage.
Electromechanical memcapacitor model offering biologically plausible spiking.
In this article, we introduce a new nanoscale electromechanical device - a leaky memcapacitor - and show that it may be useful for the hardware implementation of spiking neurons. The leaky memcapacitor is a movableplate capacitor that becomes quite conductive when the plates come close to each other. The equivalent circuit of the leaky memcapacitor involves a memcapacitive and memristive system connected in parallel. In the leaky memcapacitor, resistance and capacitance depend on the same internal state variable, which is the displacement of the movable plate. We have performed a comprehensive analysis showing that several types of spiking observed in biological neurons can be implemented with the leaky memcapacitor. Significant attention is paid to the dynamic properties of the model. As in leaky memcapacitors the capacitive, leaking resistive, and reset functionalities are implemented naturally within the same device structure, their use will simplify the creation of spiking neural networks.
Risk-based area of review estimation in overpressured reservoirs to support injection well storage facility permit requirements for CO 2 storage projects
This paper by the Energy & Environmental Research Center presents a workflow and modeling approach for delineating a risk-based area of review (AOR) to support a U.S. Environmental Protection Agency (EPA) Class VI permit for a carbon dioxide (CO 2 ) storage project. The approach combines semianalytical solutions for estimating formation fluid leakage through a hypothetical leaky wellbore with the results of numerical reservoir simulations to define the AOR. The modeling utilizes 1) semianalytical solutions from the peer-reviewed literature for formation fluid leakage through abandoned wellbores by Raven (1990) and Avci (1994), 2) a FORTRAN model compiled and described in Cihan et al. (2011, 2012) called ASLMA (Analytical Solution for Leakage in Multilayered Aquifers), and 3) a computational framework for estimating a risk-based AOR first proposed by Oldenburg et al. (2014, 2016). Therefore, the approach builds upon well-established research and underlying hydrogeological principles that have been upheld for nearly three decades. Moreover, the ASLMA model has been broadly applied to an array of storage projects. The work presented herein extends these earlier works using a custom wrapper written in the software environment, R (R Core Team, 2020), which was developed to perform multiple runs of the ASLMA model using given ranges for one or more input parameters. In addition, the current work simulates the pressure buildup within the storage reservoir in response to CO 2 injection using a compositional simulator to better accommodate the temporospatial evolution of pressure buildup within the storage reservoir that is more accurately modeled using a heterogeneous geologic model and a compositional simulator that accounts for the multiphase interactions. The workflow is demonstrated using a case study for a 180,000-metric-ton-per-year storage project located in the PCOR (Plains CO 2 Reduction) Partnership region. For the storage project evaluated here, under the scenario where the leaky wellbore is open to a saline aquifer (thief zone) between the overlying seal (cap rock) and the underground sources of drinking water (USDW), the risk-based AOR essentially collapses to the areal extent of the CO 2 plume in the storage reservoir because the pressure buildup in the storage reservoir beyond the CO 2 plume is insufficient to drive formation fluids up a hypothetical leaky wellbore into the USDW. However, even under the conservative assumption that the leaky wellbore is not open to a thief zone, beyond the areal extent of the CO 2 plume, the incremental leakage is less than 400 m 3 over 20 years, which represents ~0.0001% or less of the total volume of water contained within the USDW rock volume. As discussed in the text, the threshold criterion for defining the risk-based AOR is site-specific and should be informed by the results of the sensitivity analysis and available site characterization data. The approach outlined in this paper is designed to be protective of USDWs and, therefore, comply with the Safe Drinking Water Act requirements and provisions for the U.S. EPA Class VI Underground Injection Control (UIC) Program (Class VI Rule) and North Dakota Administrative Code Chapter 43-05-01.
A modular chromosomally integrated toolkit for ectopic gene expression in Vibrio cholerae
The ability to express genes ectopically in bacteria is essential for diverse academic and industrial applications. Two major considerations when utilizing regulated promoter systems for ectopic gene expression are (1) the ability to titrate gene expression by addition of an exogenous inducer and (2) the leakiness of the promoter element in the absence of the inducer. Here, we describe a modular chromosomally integrated platform for ectopic gene expression in Vibrio cholerae . We compare the broadly used promoter elements P tac and P BAD to versions that have an additional theophylline-responsive riboswitch (P tac -riboswitch and P BAD -riboswitch). These constructs all exhibited unimodal titratable induction of gene expression, however, max induction varied with P tac > P BAD > P BAD -riboswitch > P tac -riboswitch. We also developed a sensitive reporter system to quantify promoter leakiness and show that leakiness for P tac > P tac -riboswitch > P BAD ; while the newly developed P BAD -riboswitch exhibited no detectable leakiness. We demonstrate the utility of the tightly inducible P BAD -riboswitch construct using the dynamic activity of type IV competence pili in V. cholerae as a model system. The modular chromosomally integrated toolkit for ectopic gene expression described here should be valuable for the genetic study of V. cholerae and could be adapted for use in other species.
Semi-Analytical Leakage Solutions for Aquifers (SALSA) v1
SALSA is a semi-analytical modeling tool that can provide assessments of pressure perturbations and brine leakage because of fluid injection and extraction activities in sedimentary basins. Sedimentary basins typically contain vertical sequences of near-horizontal aquifers separated by less-permeable aquitards. In the context of geologic carbon sequestration (GCS), while aquitards are relied upon to contain injected buoyant free-phase CO2 and limit inter-aquifer brine flow, the large number of leaky wells (e.g., unused/unsuccessful exploration wells, or improperly plugged water or oil/gas wells) that are present in sedimentary basins creates concerns for potential leakage and groundwater contamination. The mathematical theory and solution method included in SALSA is presented in our recent manuscript under review. SALSA is the first to account for the coupled leakage through aquitards and leaky wells, with geologic pressurization sources. SALSA based on semi-analytical solutions can be computationally very efficient for problems containing many injection and leaky wells in multilayered sedimentary systems, compared to any numerical simulation software requiring local mesh refinement around each well to obtain accurate results. Therefore, stakeholders (e.g., regulators, operators) for site screening, injection and post-injection pressure behavior and assessing leakage risks can use SALSA as a fast-predictive tool in GCS applications in multilayered aquifer systems.
ReLU, Sparseness, and the Encoding of Optic Flow in Neural Networks
Accurate self-motion estimation is critical for various navigational tasks in mobile robotics. Optic flow provides a means to estimate self-motion using a camera sensor and is particularly valuable in GPS- and radio-denied environments. The present study investigates the influence of different activation functions—ReLU, leaky ReLU, GELU, and Mish—on the accuracy, robustness, and encoding properties of convolutional neural networks (CNNs) and multi-layer perceptrons (MLPs) trained to estimate self-motion from optic flow. Our results demonstrate that networks with ReLU and leaky ReLU activation functions not only achieved superior accuracy in self-motion estimation from novel optic flow patterns but also exhibited greater robustness under challenging conditions. The advantages offered by ReLU and leaky ReLU may stem from their ability to induce sparser representations than GELU and Mish do. Our work characterizes the encoding of optic flow in neural networks and highlights how the sparseness induced by ReLU may enhance robust and accurate self-motion estimation from optic flow.
Evaluating Probability of Containment Effectiveness at a GCS Sites using integrated assessment modeling approach with Bayesian decision Networks
Improved scientific and engineering understanding of the behavior of geologic CO2 storage together with established regulatory framework and incentive structures raise the prospects for accelerated, large-scale deployment of this greenhouse gas emissions reduction approach. Incentive structures call for the establishment of appropriate verification and accounting approaches to support claims of the integrity of a geologic storage complex and to justify taking credit for long-term storage. In this study, we present a framework for assessing the probability of containment effectiveness over the lifetime of a geologic carbon storage site (e.g., after 70 years of injection and post-injection site performance) using forward stochastic model realizations based on site characterization data and using a monitoring-informed Bayesian network based on hypothetical detectability from surface seismic surveys over the site injection and post-injection phases. The National Risk Assessment Partnership’s open-source Integrated Assessment Model (NRAP-Open-IAM) was utilized to develop an ensemble of 10,000 a priori stochastic forecasts of CO2 containment. Those simulations were used to train the Bayesian network model to estimate the prior probabilities of the CO2 leakage mass into overlying, monitorable aquifers considering the uncertainties in the reservoir properties, permeability of potentially leaky wells and the overlying aquifers. The conditional probabilities in the Bayesian network were either learned from the NRAP-Open-IAM simulations or derived from the predefined detection thresholds for the monitoring method. Observations obtained from monitoring, over time during the site operation phases were then used to generate updated posterior probabilities of containment (and any loss from containment) in the Bayesian network by propagating the prior probabilities through the conditional probabilities. We demonstrate how to construct and use the Bayesian network for verifying the long-term storage complex effectiveness informed by monitoring based on the NRAP-Open-IAM simulations previously developed for the FutureGen 2.0 site. This approach may have relevance for stake holders to demonstrate secure geologic storage, provide a defensible, probabilistic approach to claim credit for geologic storage, and to estimate the likelihood that any fraction of the claimed credit may need to be refunded to the creditor based on available monitoring information.
Time-Lapse Gravity Monitoring of CO2 Migration Based on Numerical Modeling of a Faulted Storage Complex
In this study, the performance of both surface and borehole time-lapse gravity monitoring to detect CO2 leakage from a carbon storage site is evaluated. Several hypothetical scenarios of CO2 migration in a leaky fault, and thief zones at different depths at the Kimberlina site (California, USA) constitute the basis of the approach. The CO2 displacement is simulated using the TOUGH2 simulator applied to a detailed geological model of the site. The gravity responses to these CO2 plumes are simulated using forward modeling with sensors at ground surface and in vertical boreholes. Results of inversion on one scenario are also presented. The surface-based gravity responses obtained for the different leakage scenarios demonstrate that leakage can be detected at the surface in all the scenarios but the time to detection is highly variable (10 to 40 years) and dependent on the detection threshold considered. Borehole measurements of the vertical component of gravity provide excellent constrains in depth when they are located in proximity of the density anomaly associated with the presence of CO2, thus discriminating multiple leaks in different thief zones. Joint inversion of surface and borehole data can bring valuable information of the occurrence of leakages and their importance by providing a reasonable estimate of mass of displaced fluids. This study demonstrates the importance of combining multiphase flow simulations with gravity modeling in order to define if and when gravity monitoring would be applicable at a given storage site.
Uncertainty propagation in feed-forward neural network models
We develop new uncertainty propagation methods for feed-forward neural network architectures with leaky ReLU activation functions subject to random perturbations in the input vectors. In particular, we derive analytical expressions for the probability density function (PDF) of the neural network output and its statistical moments as a function of the input uncertainty and the parameters of the network, i.e., weights and biases. A key finding is that an appropriate linearization of the leaky ReLU activation function yields accurate statistical results even for large perturbations in the input vectors. This can be attributed to the way information propagates through the network. We also propose new analytically tractable Gaussian copula surrogate models to approximate the full joint PDF of the neural network output. To validate our theoretical results, we conduct Monte Carlo simulations and a thorough error analysis on a multi-layer neural network representing a nonlinear integro-differential operator between two polynomial function spaces. Our findings demonstrate excellent agreement between the theoretical predictions and Monte Carlo simulations.
Dictionary Learning with Accumulator Neurons
The Locally Competitive Algorithm (LCA) uses local competition between non-spiking leaky integrator neurons to infer sparse representations, allowing for potentially real-time execution on massively parallel neuromorphic architectures such as Intel's Loihi processor. Here, we focus on the problem of inferring sparse representations from streaming video using dictionaries of spatiotemporal features optimized in an unsupervised manner for sparse reconstruction. Non-spiking LCA has previously been used to achieve unsupervised learning of spatiotemporal dictionaries composed of convolutional kernels from raw, unlabeled video. We demonstrate how unsupervised dictionary learning with spiking LCA (\hbox{S-LCA}) can be efficiently implemented using accumulator neurons, which combine a conventional leaky-integrate-and-fire (\hbox{LIF}) spike generator with an additional state variable that is used to minimize the difference between the integrated input and the spiking output. We demonstrate dictionary learning across a wide range of dynamical regimes, from graded to intermittent spiking, for inferring sparse representations of both static images drawn from the CIFAR database as well as video frames captured from a DVS camera. On a classification task that requires identification of the suite from a deck of cards being rapidly flipped through as viewed by a DVS camera, we find essentially no degradation in performance as the LCA model used to infer sparse spatiotemporal representations migrates from graded to spiking. We conclude that accumulator neurons are likely to provide a powerful enabling component of future neuromorphic hardware for implementing online unsupervised learning of spatiotemporal dictionaries optimized for sparse reconstruction of streaming video from event based DVS cameras.
Relative permeabilities for two-phase flow through wellbore cement fractures
Multiple fluids are likely to exist in fractures and flow paths associated with leaky wellbores, including liquids (e.g., crude oil) and gases (e.g., gas exsolved from liquid). These fluids occupy and move through different portions of the pore spaces within the fractures depending on many factors, including fluid properties, fracture size, and the amount of the different fluids. Upward leakage of any phase, through the fracture, can contaminate water-bearing formations, create hazardous surface conditions, and compromise the functionality of the wellbore. Early signs of wellbore leaks may be expressed by anomalous pressure behavior at surface monitoring points on cavern storage wells. These pressure anomalies are difficult to interpret, necessitating knowledge of the factors that affect the multiphase flow in fractures and porous media. These parameters are critical to modeling multiphase flow in fractures. This insight can guide further diagnosis and maximize leak remediation. Here, our study focuses on the relationship of the liquid–gas relative permeabilities for representative variable-aperture wellbore cement fracture. To obtain the relative permeability of each phase, two-phase flow tests were conducted where both fluids were flowing simultaneously through a fractured wellbore cement specimen under a range of factors, namely (1) aperture size, (2) capillary numbers, and (3) viscosity ratio. The flow experiments were conducted under a range of confining stresses and flow velocities, using nitrogen gas and silicone oils (of different viscosities) in a specially designed pressure vessel. The sum of gas and oil relative permeabilities were found to be less than one under all conditions, which indicates that the presence of one phase affects the permeability of the other phase, and vice versa. Since the gas phase flow conditions include a significant inertial flow component in addition to viscous flow, the inertial flow coefficients at different saturation states are presented. The factors affecting the relationship between the relative permeabilities are discussed in detail. A new mathematical model for estimating the relative permeability of wellbore cement fracture is presented and experimentally validated.