Scalable adaptive PDE solvers in arbitrary domains

Saurabh, Kumar; Ishii, Masado; Fernando, Milinda; Gao, Boshun; Tan, Kendrick; Hsu, Ming‐Chen; Krishnamurthy, Adarsh; Sundar, Hari; Ganapathysubramanian, Baskar

doi:10.1145/3458817.3476220

Cited by 10 publications

(6 citation statements)

References 55 publications

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“…In addition, we utilized an incomplete octree-based adaptive mesh generation technique that enables massive parallelization along with the ability to carve out complex objects. 39 Zeta potential, denoted by ζ, describes the potential difference between the bulk, electroneutral solution, and the potential at the wall. Since the bulk potential is not known a priori but is a time-dependent variation, the imposition of the ζ potential needs careful attention.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

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Electrokinetic Enrichment and Label-Free Electrochemical Detection of Nucleic Acids by Conduction of Ions along the Surface of Bioconjugated Beads

et al. 2023

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In this paper, we report a method to integrate the electrokinetic pre-enrichment of nucleic acids within a bed of probe-modified microbeads with their label-free electrochemical detection. In this detection scheme, hybridization of locally enriched target nucleic acids to the beads modulates the conduction of ions along the bead surfaces. This is a fundamental advancement in that this mechanism is similar to that observed in nanopore sensors, yet occurs in a bed of microbeads with microscale interstices. In application, this approach has several distinct advantages. First, electrokinetic enrichment requires only a simple DC power supply, and in combination with nonoptical detection, it makes this method amenable to point-of-care applications. Second, the sensor is easy to fabricate and comprises a packed bed of commercially available microbeads, which can be readily modified with a wide range of probe types, thereby making this a versatile platform. Finally, the sensor is highly sensitive (picomolar) despite the modest 100-fold pre-enrichment we employ here by faradaic ion concentration polarization (fICP). Further gains are anticipated under conditions for fICP focusing that are known to yield higher enrichment factors (up to 100,000-fold enrichment). Here, we demonstrate the detection of 3.7 pM single-stranded DNA complementary to the bead-bound oligoprobe, following a 30 min single step of enrichment and hybridization. Our results indicate that a shift in the slope of a current–voltage curve occurs upon hybridization and that this shift is proportional to the logarithm of the concentration of target DNA. Finally, we investigate the proposed mechanism of sensing by developing a numerical simulation that shows an increase in ion flux through the bed of insulating beads, given the changes in surface charge and zeta potential, consistent with our experimental conditions.

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Section: ■ Results and Discussionmentioning

confidence: 99%

“…For the PNP equation, a streamline upwind Petrov–Galerkin (SUPG)-style stabilizer was adopted for the convection and electromigration terms. In addition, we utilized an incomplete octree-based adaptive mesh generation technique that enables massive parallelization along with the ability to carve out complex objects …”

Section: Resultsmentioning

confidence: 99%

Electrokinetic Enrichment and Label-Free Electrochemical Detection of Nucleic Acids by Conduction of Ions along the Surface of Bioconjugated Beads

et al. 2023

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“…Tree-based adaptive mesh generation would be a suitable approach for the creation of the meshes in a parameter study [ 19 , 20 ]. This mesh generation approach involves immersing the geometries into a background mesh before carving out the mesh that resides within the geometries.…”

Section: Computational Frameworkmentioning

confidence: 99%

“…In this study, several geometrically different computational domains with different mesh requirements are required due to the presence of varying objects (such as additional computers or mannequins) placed within the computational domain. Hence, we use an incomplete octree-based adaptive discretization approach for the mesh generation in the computational domains used in this study [ 19 , 20 ]. The generation of the incomplete octree-based mesh begins with creating a cuboid background mesh composed of cubic elements.…”

Section: Computational Frameworkmentioning

confidence: 99%

“…Here, we deploy a framework that can democratize the execution of such risk assessment studies. This framework consists of (a) immersogeometric carved-out analysis that allows automated consideration of geometrically complex objects in a principled analysis platform [ 18 ], (b) a massively parallel octree-based mesh generator that rapidly constructs high-quality meshes [ 19 ], (c) a detailed flow physics simulation (LES) to produce accurate flow features [ 20 ], (d) a coupled thermal solver to account for the thermal plumes produced by humans and electronics [ 21 ], and (e) a passive scalar transport model that accounts for the distribution of virion-laden aerosols. We illustrate this framework by assessing the risk of transmission across various seating plans, operating conditions, and aerosol source locations in a canonical classroom setting, specifically a room where several of us teach (Fig.…”

Section: Introductionmentioning

confidence: 99%

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A computational framework for transmission risk assessment of aerosolized particles in classrooms

Tan

Gao

Yang

et al. 2023

Engineering with Computers

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Infectious airborne diseases like the recent COVID-19 pandemic render confined spaces high-risk areas. However, in-person activities like teaching in classroom settings and government services are often expected to continue or restart quickly. It becomes important to evaluate the risk of airborne disease transmission while accounting for the physical presence of humans, furniture, and electronic equipment, as well as ventilation. Here, we present a computational framework and study based on detailed flow physics simulations that allow straightforward evaluation of various seating and operating scenarios to identify risk factors and assess the effectiveness of various mitigation strategies. These scenarios include seating arrangement changes, presence/absence of computer screens, ventilation rate changes, and presence/absence of mask-wearing. This approach democratizes risk assessment by automating a key bottleneck in simulation-based analysis—creating an adequately refined mesh around multiple complex geometries. Not surprisingly, we find that wearing masks (with at least 74% inward protection efficiency) significantly reduced transmission risk against unmasked and infected individuals. While the use of face masks is known to reduce the risk of transmission, we perform a systematic computational study of the transmission risk due to variations in room occupancy, seating layout and air change rates. In addition, our findings on the efficacy of face masks further support use of face masks. The availability of such an analysis approach will allow education administrators, government officials (courthouses, police stations), and hospital administrators to make informed decisions on seating arrangements and operating procedures. Supplementary Information The online version contains supplementary material available at 10.1007/s00366-022-01773-9.

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Efficient Application of Hanging-Node Constraints for Matrix-Free High-Order FEM Computations on CPU and GPU

Münch

Ljungkvist

Kronbichler

2022

Lecture Notes in Computer Science

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Scalable adaptive PDE solvers in arbitrary domains

Cited by 10 publications

References 55 publications

Electrokinetic Enrichment and Label-Free Electrochemical Detection of Nucleic Acids by Conduction of Ions along the Surface of Bioconjugated Beads

Electrokinetic Enrichment and Label-Free Electrochemical Detection of Nucleic Acids by Conduction of Ions along the Surface of Bioconjugated Beads

A computational framework for transmission risk assessment of aerosolized particles in classrooms

Efficient Application of Hanging-Node Constraints for Matrix-Free High-Order FEM Computations on CPU and GPU

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