Designing heterogeneous hierarchical material systems: a holistic approach to structural and materials design

Ryan, Emily M.; Pollard, Zoe A.; Ha, Quang-Thinh; Roshandelpoor, Athar; Vakili, Pirooz; Goldfarb, Jillian L.

doi:10.1557/mrc.2019.60

Cited by 12 publications

(11 citation statements)

References 35 publications

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“…We collected data for a specific protein-protein interaction from the literature and predicted the effect on the whole group of proteins for which minimal experimental data was available. Integrating computational insights to characterize or design complex system increases our understanding and optimizes experimental resources ( Montero-Oleas et al., 2018 ; Ryan et al., 2019 ). By doing so, we can escalate the study of protein-protein interactions to specific families of proteins, as we did with the Arabidopsis TIFY class II family.…”

Section: Discussionmentioning

confidence: 99%

The Molecular Basis of JAZ-MYC Coupling, a Protein-Protein Interface Essential for Plant Response to Stressors

et al. 2020

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The jasmonic acid (JA) signaling pathway is one of the primary mechanisms that allow plants to respond to a variety of biotic and abiotic stressors. Within this pathway, the JAZ repressor proteins and the basic helix-loop-helix (bHLH) transcription factor MYC3 play a critical role. JA is a volatile organic compound with an essential role in plant immunity. The increase in the concentration of JA leads to the decoupling of the JAZ repressor proteins and the bHLH transcription factor MYC3 causing the induction of genes of interest. The primary goal of this study was to identify the molecular basis of JAZ-MYC coupling. For this purpose, we modeled and validated 12 JAZ-MYC3 3D in silico structures and developed a molecular dynamics/machine learning pipeline to obtain two outcomes. First, we calculated the average free binding energy of JAZ-MYC3 complexes, which was predicted to be-10.94 +/-2.67 kJ/mol. Second, we predicted which ones should be the interface residues that make the predominant contribution to the free energy of binding (molecular hotspots). The predicted protein hotspots matched a conserved linear motif SL••FL•••R, which may have a crucial role during MYC3 recognition of JAZ proteins. As a proof of concept, we tested, both in silico and in vitro, the importance of this motif on PEAPOD (PPD) proteins, which also belong to the TIFY protein family, like the JAZ proteins, but cannot bind to MYC3. By mutating these proteins to match the SL••FL•••R motif, we could force PPDs to bind the MYC3 transcription factor. Taken together, modeling protein-protein interactions and using machine learning will help to find essential motifs and molecular mechanisms in the JA pathway.

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Section: Discussionmentioning

confidence: 99%

The Molecular Basis of JAZ-MYC Coupling, a Protein-Protein Interface Essential for Plant Response to Stressors

et al. 2020

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“…Adsorption capacity, uptake rate, breakthrough time, and saturation time of toluene through the packed bed was measured for the three AC size ranges. The experimental setup was validated previously for the adsorption of toluene onto bulk AC 30 . Briefly, each AC was packed between glass wool in a borosilicate tube 3.3 mm in diameter with a 7.6‐mm bed height.…”

Section: Methodsmentioning

confidence: 99%

“…A 2D computational model of the system was developed using the smoothed particle hydrodynamics (SPH) method implemented in the LAMMPS code base 32 . A previously developed SPH model to simulate a uniform particle size 30 was used as the basis for the model. Nitrogen and toluene gas flow is governed by the continuity, species, and momentum conservation equations, and a Langmuir adsorption equation is used to model toluene adsorption at the AC surface.…”

Section: Methodsmentioning

confidence: 99%

“…The experimental setup was validated previously for the adsorption of toluene onto bulk AC. 30 Briefly, each AC was packed between glass wool in a borosilicate tube 3.3 mm in diameter with a 7.6-mm bed height. The experimental packing density (0.38-0.42 g/mL) was measured as a ratio of the mass of AC to the volume of the fixed bed system.…”

Section: Experimental Adsorption Studiesmentioning

confidence: 99%

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Capturing the effects of particle heterogeneity on adsorption in a fixed bed

et al. 2022

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To efficiently design new adsorption systems, industrial scale fixed beds are often scaled down to bench‐top experiments and/or modeled using computational fluid dynamics (CFD). While there has been considerable work exploring adsorption of volatile organics onto activated carbon fixed beds in the literature, this article attempts to reckon with the high variability of adsorption capacities observed at small scales and improve small‐scale experiments for industrial scale reactor design. This study integrates experimental results with CFD simulations, which can explicitly model system heterogeneities and their influence on adsorption by resolving local packing densities and flow paths. Activated carbon physical properties were determined through surface area analysis, proximate analysis, and toluene adsorption (measured via mass spectroscopy). Variability in the small‐scale systems was not attributed to surface area or carbon content, as is often stated, but instead was due to local packing density variations and the heterogeneity of particle size distributions.

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“…Reactive transport in porous media is a multiscale problem relevant to a broad range of applications, including: water filtration systems, carbon sequestration, and pollutant transport [36,17,18,27]. A description of the bulk behavior requires resolution of transport through pores at the submicron level to capture the tortuous transport leading to anomalous diffusion [22].…”

Section: Introductionmentioning

confidence: 99%

Parallel implementation of a compatible high-order meshless method for the Stokes' equations

Ha,

Kuberry,

Trask

et al. 2021

Preprint

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A parallel implementation of a compatible discretization scheme for steady-state Stokes problems is presented in this work. The scheme uses generalized moving least squares to generate differential operators and apply boundary conditions. This meshless scheme allows a high-order convergence for both the velocity and pressure, while also incorporates finite-difference-like sparse discretization. Additionally, the method is inherently scalable: the stencil generation process requires local inversion of matrices amenable to GPU acceleration, and the divergence-free treatment of velocity replaces the traditional saddle point structure of the global system with elliptic diagonal blocks amenable to algebraic multigrid. The implementation in this work uses a variety of Trilinos packages to exploit this local and global parallelism, and benchmarks demonstrating high-order convergence and weak scalability are provided.

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Designing heterogeneous hierarchical material systems: a holistic approach to structural and materials design

Abstract: Abstract

Cited by 12 publications

References 35 publications

The Molecular Basis of JAZ-MYC Coupling, a Protein-Protein Interface Essential for Plant Response to Stressors

The Molecular Basis of JAZ-MYC Coupling, a Protein-Protein Interface Essential for Plant Response to Stressors

Capturing the effects of particle heterogeneity on adsorption in a fixed bed

Parallel implementation of a compatible high-order meshless method for the Stokes' equations

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