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At least 217 records · Page 12

Genome-wide fetalization of enhancer architecture in heart disease

Heart disease is associated with re-expression of key transcription factors normally active only during prenatal development of the heart. However, the impact of this reactivation on the regulatory landscape in heart disease is unclear. Here, we use RNA-seq and ChIP-seq targeting a histone modification associated with active transcriptional enhancers to generate genome-wide enhancer maps from left ventricle tissue from up to 26 healthy controls, 18 individuals with idiopathic dilated cardiomyopathy (DCM), and five fetal hearts. Healthy individuals have a highly reproducible epigenomic landscape, consisting of more than 33,000 predicted heart enhancers. In contrast, we observe reproducible disease-associated changes in activity at 6,850 predicted heart enhancers. Combined analysis of adult and fetal samples reveals that the heart disease epigenome and transcriptome both acquire fetal-like characteristics, with 3,400 individual enhancers sharing fetal regulatory properties. We also provide a comprehensive data resource (http://heart.lbl.gov) for the mechanistic exploration of DCM etiology.

60 APPLIED LIFE SCIENCES↗

An asymptotically compatible treatment of traction loading in linearly elastic peridynamic fracture

Meshfree discretizations of state-based peridynamic models are attractive due to their ability to naturally describe fracture of general materials. However, two factors conspire to prevent meshfree discretizations of state-based peridynamics from converging to corresponding local solutions as resolution is increased: quadrature error prevents an accurate prediction of bulk mechanics, and the lack of an explicit boundary representation presents challenges when applying traction loads. Herein, we develop a reformulation of the linear peridynamic solid (LPS) model to address these shortcomings, using improved meshfree quadrature, a reformulation of the nonlocal dilatation, and a consistent handling of the nonlocal traction condition to construct a model with rigorous accuracy guarantees. In particular, these improvements are designed to enforce discrete consistency in the presence of evolving fractures, whose a priori unknown location render consistent treatment difficult. In the absence of fracture, when a corresponding classical continuum mechanics model exists, our improvements provide asymptotically compatible convergence to corresponding local solutions, eliminating surface effects and issues with traction loading which have historically plagued peridynamic discretizations. When fracture occurs, our formulation automatically provides a sharp representation of the fracture surface by breaking bonds, avoiding the loss of mass. We provide rigorous error analysis and demonstrate convergence for a number of benchmarks, including manufactured solutions, free-surface, nonhomogeneous traction loading, and composite material problems. Finally, we validate simulations of brittle fracture against a recent experiment of dynamic crack branching in soda-lime glass, providing evidence that the scheme yields accurate predictions for practical engineering problems.

42 ENGINEERING↗

Effect of the numerical discretization scheme in Shock-Driven turbulent mixing simulations

In this work, we evaluate the effects of distinct numerical strategies in simulations of shock-driven turbulent mixing. An air-SF 6 -air gas curtain subjected to Mach 1.2 shock-waves is computed with Implicit Large-Eddy Simulation based on three numerical schemes: directional-split with Harten-Lax-van Leer (HLL) solver; directional-unsplit using HLL-Contact (HLLC) solver; and directional-unsplit with HLLC solver and a Low Mach number Correction (LMC). The results illustrate the importance of the numerical strategy to the accuracy of the predictions. Whereas both split and unsplit schemes result in a similar spatial development of the initial shock-driven instability, only the unsplit schemes can predict the turbulent mixing transition after reshock observed by the laboratory experiments. Such feature increases the mixing rate of the two fluids, this being particularly pronounced when the LMC is active due to i) the reduced flow Mach number, and ii) the larger effective Reynolds number. Since the selected mixing problem is driven by the deposition of vorticity at the fluids’ interface, the resultant flow physics is analyzed by investigating the contribution of distinct inviscid mechanisms to the production of vorticity: baroclinicity, stretching, and dilatation. As expected, it is observed that the production of vorticity is initially dominated by the baroclinicity mechanism. Yet, the relevance of the remainder mechanisms is enhanced after the reshock and may even surpass the baroclinicity term.

42 ENGINEERING↗

A better understanding of the mechanics of borehole breakout utilizing a finite strain gradient-enhanced micropolar continuum model

Borehole breakout denotes the failure in rock mass subjected to drilling, caused by stress concentrations exceeding the material strength. Depending on the material properties, the preexisting in situ stress state, and the borehole dimensions, different types of borehole breakout, such as spiral-shaped breakout or v-shaped breakout, are distinguished in the literature. In the present work, we address the influence of the material properties on the predicted borehole breakout mode in a comprehensive finite element study. To this end, herein we employ a gradient-enhanced micropolar damage-plasticity model based on the Mohr–Coulomb strength criterion, formulated in the finite strain regime, which is calibrated based on experimental results from plane strain compression tests on Red Wildmoor sandstone. In the numerical study, the influence of the in situ stress state, the material friction angle, plastic dilation, post peak residual strength, and the inherent material length scale parameters are investigated. Thereby, we demonstrate that depending on the material parameters, substantially different failure modes, characterized by strongly localized shear bands or diffuse failure zones, are predicted. It is shown that in particular the brittleness of the material in the post peak regime has a major influence on the predicted breakout type. Moreover, a statistical validation of the results is obtained by considering different random field distributions of the initial material strength.

58 GEOSCIENCES↗

Hyperelastic nature of the Hoek–Brown criterion

In this article, we propose a nonlinear elasto-plastic model, for which a specific class of hyperbolic elasticity arises as a straight consequence of the yield criterion invariance on the plasticity level. We superimpose this nonlinear elastic (or hyperelastic) behavior with plasticity obeying the associated flow rule. Interestingly, we find that a linear yield criterion on the thermodynamical force associated with plasticity results in a quadratic yield criterion in the stress space. This suggests a specific hyperelastic connection between Mohr–Coulomb and Hoek–Brown (or alternatively between Drucker–Prager and Pan–Hudson) yield criteria. We compare the elasto-plastic responses of standard tests for the Drucker–Prager yield criterion using either linear or the suggested hyperbolic elasticity. Notably, the nonlinear case stands out due to dilatancy saturation observed during cyclic loading in the triaxial compression test. We conclude this study with structural finite element simulations that clearly demonstrate the numerical applicability of the proposed model.

97 MATHEMATICS AND COMPUTING↗

High pressure/high temperature multiphase simulations of dodecane injection to nitrogen: Application on ECN Spray-A

The present work investigates the complex phenomena associated with pressure/high temperature dodecane injection for the Engine Combustion Network (ECN) Spray-A case, employing more elaborate thermodynamic closures, to avoid well known deficiencies concerning density and speed of sound prediction using traditional cubic models. A tabulated thermodynamic approach is proposed here, based on log 10 (p)-T tables, providing very high accuracy across a large range of pressures, spanning from 0 to 2500 bar, with only a small number of interpolation points. The tabulation approach is directly extensible to any thermodynamic model, existing or to be developed in the future. Here NIST REFPROP properties are used, combined with PC-SAFT Vapor-Liquid-Equilibrium to identify the liquid in mixtures penetration, hence avoiding the use of an arbitrary threshold for mass fraction. Identified liquid and vapour penetration are compared against experimental data from the ECN database showing a good agreement, within approximately 3–8% for axial penetration of liquid, 2% for vapor axial penetration and within experimental uncertainty for radial distribution of mass fraction. Analysis of the vortex evolution indicates that driving mechanisms behind the jet break-up are vortex tilting/stretching, then baroclinic torque, leading to Rayleigh-Taylor instabilities, closely followed by vortex dilation and finally viscous effects.

42 ENGINEERING↗

Dynamic stability of a crude oil/brine interface: Effect of anion type

The chemical composition of the aqueous phase plays an essential role in water-based enhanced-oil recovery processes. The aqueous phase ionic profile affects the snap-off response of a crude oil-brine system by linking it to the brine-crude oil interfacial rheology. In this work, we focus on the effect of the anion on the snap-off response. To this end, a sample of crude oil from the Minnelusa Sandstone formation in Wyoming was selected, and several aqueous solutions were prepared with salts containing sodium cation and different anions (chlorides, sulfates, and phosphates) at two ionic strength values, 0.6 M and 6 mM, as cases of high- and low-salinity water. Interfacial tension, interfacial viscoelasticity and interface stability were analyzed as functions of aging time using pendant drop, dilatational rheology, and liquid bridge techniques, respectively. Here the results show that solutions with higher ionic strength led to the formation of more rigid interfaces, i.e. higher elastic modulus, and faster formation kinetics. In the low-salinity regime, solutions with polyvalent anions produce more viscoelastic interfaces at faster rates than solutions with monovalent anions. Finally, an excellent correlation (R 2 greater than 0.97) between the relative stability of the interfacial film, predicted in liquid bridge tests, and the ratio of interfacial tension and interfacial elastic modulus was found.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Soft interface instability and gas flow channeling in low-permeability deformable media

Understanding gas percolation through a clay layer or a shale formation is of great importance for the development of a geologic repository for nuclear waste disposal, a subsurface system for gas storage, and an engineering approach for hydrocarbon extraction from unconventional reservoirs. Gas injection experiments have revealed complex dynamic behaviours of gas percolation through water saturated compacted bentonite, characterized by a high breakthrough pressure, rapid breakthrough, a pressure/stress decay after the breakthrough, a relatively high migration rate, high-frequency periodic/nonperiodic variations in flow rate, stepwise rate reductions during relaxation, and low gas saturation over the whole process, all indicating channelling nature of the processes. Using linear stability analyses, we show that this channelling can autonomously emerge from the instability of the deformable interface between the injected gas and the compacted bentonite matrix driven by local stress concentration, pore dilation, and hydrologic gradient. Channel patterns formed would possess a fractal geometry. We further show that, once a percolating channel is established, the gas injected would percolate through the channel in a chain of gas bubbles, also due to the interface instability, resulting in periodic/chaotic variations in gas flow rate. Our work provides a unified explanation for key features observed for gas percolation in low-permeability deformable media. The work also suggests a possibility of designing an engineered barrier system for a nuclear waste repository that can have controllable gas release while limit water transport.

Bentonite↗

Field-scale fault reactivation experiments by fluid injection highlight aseismic leakage in caprock analogs: Implications for CO 2 sequestration

Observations on tens-of-meter scale experiments of fault activation by fluid injection conducted in shales allow exploring how aseismic and seismic events may jeopardize the integrity of a sealing caprock overlying a CO 2 sequestration reservoir. We contrast the behavior of shale faults with another set of experiments conducted in carbonates. Significant fluid leakage occurs along the initially low-permeability shale faults when rupture is activated. Most of the leakage pathway closes when fluid injection ceases and fluid pressure drops. Dilatant slip on the fault plane alone does not explain the observed leakage behavior, which is also caused by fault opening favored by the softness of the shale, and by the structure of the fault zone that prevents fluids from diffusing into the adjacent damage zone. Experiments show a large amount of aseismic deformation. Small-magnitude seismicity (M w < -2.5) is observed outside the pressurized leakage patch. Stress transferred from this aseismic deformation patch can build up to stress-criticality and favor seismicity. Thus, in terms of fault activation in caprocks, aseismic fault slip leading to increased permeability and a loss of seal integrity is of great concern.

58 GEOSCIENCES↗

Cyclic loading–unloading impacts on geomechanical stability of multiple salt caverns for underground hydrogen storage

Underground caverns in a salt dome are promising geologic features to store hydrogen because of salt’s extremely low permeability and self-healing behavior. The salt cavern storage community, however, has not fully understood the geomechanical behaviors of salt rock driven by quick operation cycles of injection–production, which may significantly impact the cost-effective storage-recovery performance of multiple caverns. Our field-scale generic model captures the impact of cyclic loading–unloading on the salt creep behavior and deformation under different cycle frequencies, operating pressure, and spatial order of operating cavern(s). This systematic simulation study indicates that the initial operation cycle and arrangement of multiple caverns play a significant role in the creep-driven loss of cavern volumes and cavern deformation. Finally, our future study will develop a new salt constitutive model based on geomechanical tests of site-specific salt rock to probe the cyclic behaviors of salt precisely both beneath and above the dilatancy boundary, including reverse (inverse transient) creep, the Bauschinger effect, and damage-healing mechanism.

08 HYDROGEN↗

A micromechanical hydro-mechanical-damage coupled model for layered rocks considering multi-scale structures

An anisotropic Hydro-Mechanical-Damage coupled model was established in the framework of thermodynamics for saturated layered rocks, which contain arbitrarily-distributed cracks of smaller scales and orientated bedding planes of much larger scales. Here, the proposed model considers the anisotropic damage growth and frictional sliding of cracks and shear sliding and dilatancy of bedding planes, as well as the interaction between cracks and bedding planes. Numerical implementation of the nonlinear coupled model was developed based on TOUGHREACT, which is a well-established simulator for multiphase fluid flow and reactive transport analysis. The proposed model was first validated with laboratory water injection test results on rock blocks, and then used to study the effects of injection rates, in situ stresses and bedding planes on fluid injection processes at the field scale, demonstrating the importance to consider the variation of multi-scale structures for better understanding the coupled Hydro-Mechanical responses in layered rocks.

58 GEOSCIENCES↗

3D Simulations of gas injection on callovo-oxfordian claystone assuming spatial heterogeneity and anisotropy

A series of gas injection tests on Callovo-Oxfordian (COx) claystone from the Bure underground research laboratory (URL) in France were carried out at the British Geological Survey (BGS). The tests were performed using a triaxial apparatus specifically designed to capture small volumetric strains induced by the injected gas flow and consequent material dilatancy. The long-duration experiments were monitored throughout. Measurements also included pressure, stresses (axial and radial stresses prescribed for each test stage), rate of gas inflow, gas outflow volume as well as pore-pressures observed at various points of the sample. A coupled hydro-gas-mechanical 3D numerical model has been developed to simulate the tests. Initial permeability is assumed heterogeneous throughout the specimen and embedded fractures are incorporated in the formulation. Gas pressure-induced deformations during the test lead to variations of permeability due to changes in matrix porosity and, especially, fracture aperture as well as fracture orientation due to material anisotropy. A programme of sensitivity analyses involving the variation of different aspects and parameters of the model contributes to a better understanding of the phenomena and highlights its complexity. The model is able to reproduce the observed behaviour of the tests.

58 GEOSCIENCES↗

Structural Insights into the Mechanisms and Pharmacology of K 2P Potassium Channels

Leak currents, defined as voltage and time independent flows of ions across cell membranes, are central to cellular electrical excitability control. The K 2P (KCNK) potassium channel class comprises an ion channel family that produces potassium leak currents that oppose excitation and stabilize the resting membrane potential in cells in the brain, cardiovascular system, immune system, and sensory organs. Due to their widespread tissue distribution, K 2P s contribute to many physiological and pathophysiological processes including anesthesia, pain, arrythmias, ischemia, hypertension, migraine, intraocular pressure regulation, and lung injury responses. Structural studies of six homomeric K 2P s have established the basic architecture of this channel family, revealed key moving parts involved in K 2P function, uncovered the importance of asymmetric pinching and dilation motions in the K 2P selectivity filter (SF) C-type gate, and defined two K 2P structural classes based on the absence or presence of an intracellular gate. Further, a series of structures characterizing K 2P :modulator interactions have revealed a striking polysite pharmacology housed within a relatively modestly sized (~70 kDa) channel. Binding sites for small molecules or lipids that control channel function are found at every layer of the channel structure, starting from its extracellular side through the portion that interacts with the membrane bilayer inner leaflet. This framework provides the basis for understanding how gating cues sensed by different channel parts control function and how small molecules and lipids modulate K 2P activity. Such knowledge should catalyze development of new K 2P modulators to probe function and treat a wide range of disorders.

59 BASIC BIOLOGICAL SCIENCES↗

Hydrocarbon production reduces natural methane seeps in the Santa Barbara channel

Abundant natural hydrocarbon seepage in the Santa Barbara Channel includes large amounts of gas, mainly methane. Numerous seeps are focused along a faulted anticlinal axis where in 1982 ARCO placed two large (900 m 2 each) steel gas capture tents on the seabed adjacent to Platform Holly. The seep rate into the tent at high tide is about 5 percent less compared with low tide (2m tidal range). An earthquake in 2013 (M = 4.8) did not affect seepage rates into the steel tents, indicating that gas was not released by fault dilation. The CO 2 and H 2 S content of the captured gas are anomalously low compared to typical Holly gas due to bacterial and sea water-gas interaction at the seep tent. Platform Holly production had an overall effect of reducing gas seepage into the tents over time. Wells beneath the tents at 1-km depth had a much greater influence on the seepage rate than more distal wells. The nearby wells had a direct effect on seepage rate when they were put on production (seepage decreased) versus shut in (seepage increased). The response time was within hours, indicating a direct hydraulic connection between the reservoir at 1 km subsea and the seabed. Permeability of the approximate 1-km fault pathway between the reservoir and the seep tent is calculated to be about 3 × 10 -14 m 2 (30 millidarcys). Gradually, the seep rate declined from peak flow in 1990 (4.5×10 4 m 3 dy-1) to less than 7.1×10 3 m 3 dy -1 in 2013. In June of 2013, a horizontal well was completed high on the structural anticline between Platform Holly and directly beneath the seep tents. Within three weeks of turning on this new well, seepage into the tents completely ceased, ending more than 30 years of natural methane seepage captured by the tents.

58 GEOSCIENCES↗

Impact of humidity on gas transport in polybenzimidazole membranes

Polybenzimidazoles (PBIs) are promising materials for high temperature H 2 /CO 2 separation in applications such as steam reforming and pre-combustion carbon capture where significant amounts of water are often present. However, PBIs are hydrophilic, and the impact of humidity on PBI gas separation properties is relatively unexplored. Furthermore, opportunity exists to elucidate the interplay between plasticization, free volume, and gas transport in glassy polymer membranes such as PBIs. Here, this study investigates the effect of humidity on H 2 , O 2 , and CO 2 permeabilities at 35 °C in a commercial PBI and two sulfone-containing PBIs. Water uptake significantly reduces PBI gas permeabilities at low humidities due to competitive sorption and antiplasticization. At high humidities, plasticization increases the permeabilities of larger gases in more hydrophilic PBIs. Effective fractional free volumes evaluated from gas permeation data and previously reported water sorption and dilation data suggest water plasticizes PBIs by increasing accessible free volume via enhanced molecular dynamics rather than by creating new free volume cavities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Local stress within a granular molecular solvent matrix, a mechanism for individual ion hydration

The activity of water is important in many natural systems and directed processes. To better understand water activity, the hydration of individual ions is approximated for a recently developed speciation-based solution model. Here a matrix of values for hydration of complete salts (anion and cation) was used as source data to calculate individual ion hydration values. Some electrolytes were excluded from calculations of individual ion hydration due to the prevalence of ion pairing and resulting liberation of water upon ion pairing. Evaluation of the periodic trends emerging from individual ion hydration values suggests that ionic volume, relative to the volume of molecular water, dictates both modeled hydration requirements (related to vapor-liquid-equilibrium-derived activity) as well as properties historically described by hydrodynamic radius (ion diffusion and solution viscosity). When water is conceptualized as a granular three-dimensional matrix, solutes may function as substitutional defects (dilation or constriction) inducing local compressive or tensile stress. These results have implications on the mechanism of the Hofmeister series and series reversals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Susceptibility weighted MRI pinpoints spontaneous intracerebral hemorrhage in stroke-prone spontaneously hypertensive rats

Purpose: To find magnetic resonance imaging (MRI) precursors of spontaneous intracerebral hemorrhage in stroke-prone spontaneously hypertensive rats (SHRSP). Method: SHRSP rats were used with both a low/high salt (n = 18 or 11) Japanese diet and salty drinking water to generate spontaneous intracerebral hemorrhage (ICH). Various MRI sequences, and in particular, susceptibility weighted imaging (SWI), were used and combined with a gadolinium (Gd) contrast agent or oxygen gas to identify the rupture of the blood brain barrier (BBB) and the temporal ICH. Results: Most rats developed hypertensive ICH stroke in the high salt group during the 10–13 week period compared to only one third of rats in the low salt group during the 14–18 week period. The location of stroke for both the low/high-salt groups was highest in the striatum (58%/43%), followed by the cortex (21%/30%). The edematous enhancement on T2 weighted (T2W) imaging or Gd based T1 weighted (Gd-T1W) imaging due to the ruptured BBB preceded the striatal hemorrhages seen on SWI. The most recent bleeds were observed on temporal SWI or on oxygen-enhanced SWI. The mode of the volume of bleeds was 0.4 mm 3 . A positive correlation between susceptibility x volume and R2* x volume of the bleeds was observed. Conclusions: SHRSP rats with the high salt diet effectively generated a hypertensive hemorrhagic stroke which could be monitored by various MRI sequences. The venous dilation on SWI may precede any abnormality on T2W or Gd-T1W imaging. The edematous enhancement on T2W or Gd-T1W indicated a BBB breakdown that may precede striatal ICH by several days. This suggests the need for immediate treatment to improve outcome if this finding is observed. Here, the use of oxygen with SWI was able to help differentiate old bleeds from very recent bleeds.

60 APPLIED LIFE SCIENCES↗

Interplay of strain and phase evolution of laser powder bed fusion Ti–6Al–4V

While additive manufacturing (AM) provides a method of producing geometrically complex and highly detailed structures, the generation of residual strain in AM processes like laser powder bed fusion (L-PBF) can negatively impact performance-enabling properties. In applications such as orthopedic implants, specific performance windows require optimized microstructures in order to obtain desirable properties from multi-phase alloys like Ti–6Al–4V. This research aims to quantify the microscale origins of strain in L-PBF manufactured Ti–6Al–4V by understanding how strain is distributed at the grain and sub-grain scale, the interplay between phase evolution and strain, and examining post-processing strain relief strategies to control these features. Model spinal cage implants were manufactured from Ti–6Al–4V powder via L-PBF and then subjected to strain relieving heat treatment cycles above and below the Ti–6Al–4V β transus as a function of time and cooling rate. Residual strain was then studied via high resolution electron backscatter diffraction (HR-EBSD), and 2D strain maps with sub-micron resolution were generated for each post-processing state. It was found that macroscale thermal strains decreased with heat treatment time, but additional contributions from phase stabilizing residual strains retained primarily in the α' grains as lattice distortive strain remained. Additionally, the retention of β phase significantly changed the strain and dislocation distribution while reducing overall residual strain. In conclusion, these results were validated and reinforced with 3D mesoscopic micromechanical modeling of strain behavior across simulated microstructures, confirming that the local lattice dilation of α’ martensite is a primary contributor of microscale strain generation and retention in L-PBF Ti–6Al–4V.

36 MATERIALS SCIENCE↗