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At least 775 records · Page 43

Modular performance prediction for scientific workflows using Machine Learning

Scientific workflows provide an opportunity for declarative computational experiment design in an intuitive and efficient way. A distributed workflow is typically executed on a variety of resources, and it uses a variety of computational algorithms or tools to achieve the desired outcomes. Such a variety imposes additional complexity in scheduling these workflows on large scale computers. As computation becomes more distributed, insights into expected workload that a workflow presents become critical for effective resource allocation. In this paper, we present a modular framework that leverages Machine Learning for creating precise performance predictions of a workflow. The central idea is to partition a workflow in such a way that makes the task of forecasting each atomic unit manageable and gives us a way to combine the individual predictions efficiently. We recognize a combination of an executable and a specific physical resource as a single module. This gives us a handle to characterize workload and machine power as a single unit of prediction. Overall, our modular technique of creating atomic modules and deployment of longest-path approach to estimate workflow performance, allows the framework to adapt to highly complex nested directed acyclic workflows and scale to new scenarios, since it does not make assumptions of underlying workflow structure. We present performance estimation results of independent workflow modules executed on the XSEDE SDSC Comet cluster using various Machine Learning algorithms. The results provide insights into the behavior and effectiveness of different algorithms in the context of scientific workflow performance prediction.

97 MATHEMATICS AND COMPUTING↗

A practical extension of the recursive multi-fidelity model for the emulation of hole closure experiments

We report in regimes of high strain rate, the strength of materials often cannot be measured directly in experiments. Instead, the strength is inferred based on an experimental observable, such as a change in shape, that is matched by simulations supported by a known strength model. In hole closure experiments, the rate and degree to which a central hole in a plate of material closes during a dynamic loading event are used to infer material strength parameters. Due to the complexity of the experiment, many computationally expensive, three-dimensional simulations are necessary to train an emulator for calibration or other analyses. These simulations can be run at multiple grid resolutions, where dense grids are slower but more accurate. In an effort to reduce the computational cost, a combination of simulations with different resolutions can be combined to develop an accurate emulator within a limited training time. We explore the novel design and construction of an appropriate functional recursive multi-fidelity emulator of a strength model for tantalum in hole closure experiments that can be applied to arbitrarily large training data. Hence, by formulating a multi-fidelity model to employ low-fidelity simulations, we were able to reduce the error of our emulator by approximately 81% with only an approximately 1.6% increase in computing resource utilization.

36 MATERIALS SCIENCE↗

Multipoint Aerostructural Optimization of Wind Turbine Rotors Using a Coupled Blade‐Resolved Aerostructural Solver

Physics‐based design optimization workflows thread the needle between computational cost limitations and simulation complexity, often compromising between modeling detail and the range of operating design conditions. Multipoint aerostructural optimization of wind turbine rotors has so far been confined to low‐fidelity analyses or to high‐fidelity studies with simplified structural models, leaving the most complex design trade‐offs unexplored. We close this gap by performing the first tightly coupled gradient‐based multipoint aerostructural rotor optimization using 3D aerodynamic and structural solvers with discrete coupled adjoints. The optimizer simultaneously varies blade planform, airfoil shapes, and structural thickness through more than 270 design variables, minimizing a weighted combination of rotor mass and power across multiple wind speeds. Applied to a modified DTU 10‐MW benchmark under conservative structural and aerodynamic constraints, our multipoint optimization reduces rotor mass by up to 36% and increases power by 12%–15% across the main operating conditions; biasing the objective toward power yields power gains up to 18% and a 17% mass reduction. For a nominal wind distribution, 3‐point rotor designs accounting for low RPM and high thrust conditions capture dominant trade‐offs and outperform single‐point designs. Adding two off‐design points changes individual‐condition power by less than 3% but leaves the weighted average within 0.5%, and the mass‐power bias has a stronger effect on the final design than the operating‐point weighting itself. Our framework extends naturally to richer load cases and site‐specific wind distributions, providing a basis for high‐fidelity multipoint design earlier in industrial workflows.

17 WIND ENERGY↗

Metabolic Pathway Engineering

Modern microbial and enzyme engineering and their advancement are increasingly dependent on the marriage of a wide range of sophisticated technologies. For students entering the field of biotechnology, the outlook is indeed daunting. Expertise at levels beyond that of simple familiarity will be needed to conduct competitive research. It goes without saying that to be competitive, all new researchers in this field will need basic preparation in molecular biology, biochemistry, and genetics. Further, experience working with concepts and experimental tools in enzyme biochemistry and kinetics, gene editing, computational metabolic pathway modeling, experimental pathway flux analysis, and computational clustering tools to process complex data sets will be vital for success. We speculate that most biotechnology researchers in early career at this time will build teams of collaborators to address these disparate science fields rather than attempt to become experts in one lab.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗

Off-shell vertices in heavy particle effective theories and B → Dπℓν

We study the modifications to decay amplitudes in heavy to heavy semileptonic decays with multiple hadrons in the final state due to intermediate heavy hadrons being off-shell or having a finite width. Combining Heavy Hadron Chiral Perturbation Theory (HHχPT) with a BCFW on-shell factorization formula, we show that these effects induce O (1/M) corrections to the standard results computed in the narrow-width approximation and therefore are important in extracting form factors from data. A combination of perturbative unitarity, analyticity, and reparameterization invariance fully determine these corrections in terms of known Isgur-Wise functions without the need to introduce new form factors. In doing so, we develop a novel technique to compute the boundary term at complex infinity in the BCFW formula for theories with derivatively coupled scalars. While we have used the $\overline{B}$ → Dπℓν decay as an example, these techniques can generally be applied to effective field theories with (multiple) distinct reference vectors. Article PDF

Chiral Lagrangian↗

Minimum feature size control in level set topology optimization via density fields

A level set topology optimization approach that uses an auxiliary density field to nucleate holes during the optimization process and achieves minimum feature size control in optimized designs is explored. The level set field determines the solid-void interface and the density field describes the distribution of a fictitious porous material using the solid isotropic material with penalization. These fields are governed by two sets of independent optimization variables which are initially coupled using a penalty for hole nucleation. The strength of the density field penalization and projection is gradually increased during the optimization process to promote a 0-1 density distribution. In addition, a second penalty regulates the evolution of the density field in the void phase. The treatment of the density field combined with the second penalty mitigate the appearance of small design features. The minimum feature size of optimized designs is controlled by the radius of the linear filter applied to the density optimization variables. The structural response is predicted by the extended finite element method, the sensitivities by the adjoint method, and the optimization variables are updated by a gradient-based optimization algorithm. Numerical examples investigate the robustness of this approach with respect to algorithmic parameters and mesh refinement. The results show the applicability of the combined density level set topology optimization approach for both optimal hole nucleation and for minimum feature size control in 2D and 3D. This comes, however, at the cost of a more complex problem formulation and additional computational cost due to an increased number of optimization variables.

42 ENGINEERING↗

A level-of-details framework for representing occupant behavior in agent-based models

We report agent-based modeling is an advanced computational technique capable of representing complex and dynamic processes of human behavior in building performance simulation. Though the agent-based approach supports diverse applications concerning human behavior modeling within the built environment, there is no consensus on the optimal amount of information or level of granularity needed for occupant information representation. This paper attempts to formalize the level of details (LoD) needed for occupant behavior representation in agent-based environments. A novel framework, grounded on the concept of LoD, is proposed to select the required details in representing occupants in agent-based models. Ten attributes related to occupants' presence, movement, behavioral processes, and repertoire are considered to define the LoD. The framework identifies use case parameters as the guiding principle and allows a hybrid approach for selecting varying degrees of occupant attributes to serve the purpose of simulation. A discussion on the pertinence of different occupant behavior LoDs in relation to the desired objective and simulation context is also presented. The study intends to support the occupant behavior research by advancing agent-based occupant modeling in building performance simulation.

42 ENGINEERING↗

Ten questions on building stock modeling to inform energy efficiency and sustainability

To enhance economic competitiveness and ensure energy efficiency, resilience, and security, cities and governments are adopting technologies and strategies to improve their existing building stocks. This approach aims to reduce energy use, improve energy affordability, and ensure a reliable power supply while safeguarding occupants during extreme weather events that may disrupt energy services. The effectiveness of these solutions will depend on building stock characteristics, use patterns, weather conditions, evolving technologies and their markets, and a city’s socio-economic conditions. This paper presents ten questions and answers that highlight the most important issues regarding the use of building stock modeling as a powerful tool to provide insights for informing stakeholders’ actions and decision-making on energy efficiency, costs reduction, and resilience of buildings in cities. Building stock modeling should build upon the fit-for-purpose framework, balancing the use case accuracy requirements, level of complexity, and needed resources (expertise, compute). The advancements in Artificial Intelligence (AI), the increasingly available open dataset of building stock in cities, and the more affordable powerful computing will accelerate the adoption of building stock modeling across scales by researchers and practitioners to inform decision making on sustainability and efficiency.

AI↗

Machine learning magnetism classifiers from atomic coordinates

The determination of magnetic structure poses a long-standing challenge in condensed matter physics and materials science. Experimental techniques such as neutron diffraction are resource-limited and require complex structure refinement protocols, while computational approaches such as first-principles density functional theory (DFT) need additional semi-empirical correction, and reliable prediction is still largely limited to collinear magnetism. Here, we present a machine learning model that aims to classify the magnetic structure by inputting atomic coordinates containing transition metal and rare earth elements. By building a Euclidean equivariant neural network that preserves the crystallographic symmetry, the magnetic structure (ferromagnetic, antiferromagnetic, and nonmagnetic) and magnetic propagation vector (zero or non-zero) can be predicted with an average accuracy of 77.8% and 73.6%. In particular, a 91% accuracy is reached when predicting no magnetic ordering even if the structure contains magneticelement(s). Ourworkrepresents onestepforwardtosolvingthegrand challenge of full magnetic structure determination.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A reduced-order model of concentration polarization in reverse osmosis systems with feed spacers

Feed spacers in reverse osmosis systems generate complex fluid flows that limit computational fluid dynamics (CFD) simulations to small length and time scales. That limits our ability to simulate mineral scaling and other membrane fouling phenomena, which occur over longer length and time scales. Thus motivated, we develop a reduced model that replaces the CFD simulation of the velocity field with an analytical model that mimics spacers. This focuses the remaining numerical effort on simulating the advection–diffusion equation governing solute transport. We motivate and validate the model with CFD simulations and bench-scale experiments of spacer filaments in three different arrangements, including cases of unsteady vortex shedding. We show that the model produces a roughly 10,000-fold speedup compared to CFD, and accurately reproduces CFD predictions of not only the average and maximum concentrations, but also the local concentration distribution along the membrane. Here, we also demonstrate the model for simulating a feed channel with a length-to-height ratio of 200. The model provides a simple testbed for exploratory studies of multispecies transport, precipitation, and membrane fouling phenomena for which simulating spacers is often prohibitive.

Computational fluid dynamics↗

Design, Synthesis, and Biological Activity of Novel Ornithine Decarboxylase (ODC) Inhibitors

We here describe the design, synthesis, and biological activity of novel ornithine decarboxylase (ODC) inhibitors that show significantly higher potency in vitro than α-difluoromethylornithine (DFMO), a U.S. Food and Drug Administration (FDA) approved drug. We report two X-ray structures of ODC complexed with new ODC inhibitors, computational docking, molecular dynamics, and binding free energy calculations to validate the experimental models. The X-ray structures reveal that covalent adducts with pyridoxal phosphate (PLP) are formed in the active site of the human ODC enzyme, as verified by their preparation and enzymatic testing. Finally, we verified that the cellular activity of endogenous ODC was inhibited, and polyamine levels were reduced. Given that ODC is a clinically validated target, combined with the fact that DFMO is currently the only ODC inhibitor in clinical use for several indications, the further development of more potent ODC inhibitors with superior activity and physical properties is warranted.

60 APPLIED LIFE SCIENCES↗

Machine Learning-Accelerated First-Principles Molecular Dynamics Explains Anomalous Lattice Thermal Expansion in BaZr 0.78 Y 0.22 O 3-δ

Fuel cells are a vital clean energy technology that converts chemical energy directly into electricity with high efficiency, making them a cornerstone of a sustainable energy future. Herein we investigate the thermal and chemical lattice expansion behavior of hydrated BaZr 0.78 Y 0.22 O 3-δ using machine learning-accelerated ab initio molecular dynamics simulations. Here, our results reproduce the experimentally observed non-monotonic and anomalous temperature dependence of lattice expansion, which we attribute to the competing effects of thermal expansion and dehydration—two mechanisms that influence the lattice expansion in opposite directions. The importance of this work lies in its detailed demonstration of how advanced computational techniques can accurately capture complex environmental effects, providing a valuable framework for modeling similar phenomena in a variety of material systems and applications.

Proton conducting fuel cell↗

Rapid Polyolefin Plastic Hydrogenolysis Mediated by Single-Site Heterogeneous Electrophilic/Cationic Organo-group IV Catalysts

A homologous series of cationic electrophilic group IV metal hydrides (M = Ti, Zr, Hf) created by chemisorption of the corresponding MNp 4 precursors on highly Brønsted acidic sulfated alumina (AlS) to yield loosely coordinated surface AlS/MNp 2 (Np = neopentyl) species are systematically characterized by ICP, EXAFS/XANES, DRIFTS, and solid-state high-resolution multidimensional NMR spectroscopy (SSNMR), as well as by energy span DFT computation. With effective stirring, these complexes readily undergo reaction with H 2 to yield AlS/M(alkyl)H species, which are highly active for the hydrogenolysis of diverse commercial polyethylenes, α-olefin-ethylene copolymers, isotactic polypropylene, and postconsumer polyolefins including high-density polyethylenes, yielding medium and small linear and branched hydrocarbons at turnover frequencies as high as 36,300 h –1 at 200 °C/17 atm H 2 for M = Zr. For given polyolefin and reaction conditions, turnover frequencies scale approximately as M = Zr > Hf > Ti, whereas catalyst thermal stability scales approximately as M = Hf ≈ Zr > Ti, and these trends are qualitatively understandable from the DFT analysis. These catalytic results reveal that the AlS/Hf(R)H-mediated hydrogenolysis favors wax-like and liquid products, whereas the AlS/Zr(R)H-mediated hydrogenolysis can be tuned between gases and liquids. Finally, DFT analysis identifies β-alkyl elimination as the turnover-limiting C–C scission process, which is particularly facile in these cationic d 0 complexes but not so in the neutrally charged analogues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Circularity in Sequence-Controlled Copolyamides Enabled by Regioselective Enzymatic Hydrolysis

Sequence-controlled polymers enable precise control over macromolecular structures and function, but both their synthesis and end-of-life management remain fundamental challenges. Achieving high sequence fidelity is synthetically demanding, and conventional depolymerization methods lack regioselectivity, leading to irreversible loss of encoded molecular information and limiting polymer circularity. Enzymatic catalysis offers a potential solution by combining substrate specificity with selective bond cleavage. Here, we report the synthesis, characterization, and regioselective enzymatic depolymerization of poly- (X,AMA), a sequence-controlled copolyamide composed of alternating hexamethylenediamine−adipic acid (MA) and pxylylenediamine− adipic acid (XA) repeat units. Poly(X,AMA) was synthesized via solid-state polycondensation (SSP) of sequence-defined oligomers, enabling precise control over repeat-unit order. Polymer microstructure and sequence fidelity were confirmed by 13 C NMR spectroscopy and MALDI−TOF mass spectrometry. Comparison with a statistical copolymer analogue and Nylon-66 demonstrated pronounced differences in crystallinity, morphology, and thermal behavior arising from sequence control. Screening of 96 Nylon hydrolase homologues against poly(X,AMA) revealed strongly enzyme-dependent depolymerization profiles. While tetrad formation was generally favored, enzymes displayed pronounced sequence selectivity, preferentially releasing distinct sequence-defined tetrads XAMA or MAXA. SSP of sequence-defined tetrad MAXA produced a copolyamide with near identical monomer ordering as poly(X,AMA). Computational modeling of enzyme−substrate complexes identified structural features consistent with the observed regioselectivity. Together, these results establish selective enzymatic depolymerization as a viable strategy for the circular recycling of sequence-controlled polymers and provide a foundation for the rational engineering of enzymes for programmable polymer deconstruction.

Amides↗

A neural master equation framework for multiscale modeling of molecular processes: application to atomic-scale plasma processes

Plasma-surface interactions (PSI) play a crucial role in microelectronics fabrication; however, their multiscale nature and array of complex, often unknown interactions make computational modeling of PSIs extremely difficult. To this end, we propose a general neural master equation (NME) framework that uses master equations to describe the dynamics of a molecular process, wherein neural networks learned from atomistic simulations represent unknown transitions between different system states. By leveraging the physics-based structure of master equations and data-driven state transitions, the NME framework promotes generalizability and physics interpretability, and can bridge disparate length and time scales. The framework is demonstrated for multiscale modeling of Si atomic layer etching and reactive ion etching, where the learned NME-based surface kinetic models exhibit good predictive and extrapolative capabilities for predicting experimentally relevant observables as a function of process parameters. The NME-based surface kinetic models obey physical constraints, which are violated in models based on neural ordinary differential equations. The proposed NME framework for multiscale modeling of molecular processes can pave the way for the discovery of new chemistries and materials in atomic-scale plasma processes.

Chemical engineering↗

Allosteric binding properties of a 1,3-alternate thiacalix[4]arene-based receptor having phenylthiourea and 2-pyridylmethyl moieties on opposite faces

The synthesis of three new heteroditopic receptors (5a–c) which are based on thiacalix[4]arenes in the 1,3-alternate conformation is reported herein. These new receptors each have two thiourea moieties linking phenyl groups, two of which are substituted with electron-withdrawing groups at their para-positions, and at the opposite side of the thiacalix[4]arene cavity, with two 2-pyridylmethyl groups. One example (5a) was also characterized by X-ray crystallography. A limited 1 H-NMR and UV-vis anion complexation study was conducted. DFT computational determinations indicated that 5c, which has strongly electron-withdrawing NO 2 groups, had the most effective recognition ability towards the selected anions. The binding of Ag + at the 2-pyridyl moieties, and the binding of the anions at the two thiourea NH groups of the p-substituted phenylthioureido moieties, respectively, was also investigated. The appearance of a positive allosteric effect with receptor 5b was also found using 1 H-NMR titration experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High throughput exploration of the oxidation landscape in high entropy alloys

We report high entropy alloys (HEAs) have gained interest for structural applications in extreme environments. With a potentially vast chemical and phase space, there are significant opportunities to discover superior performing alloys. Crucial for most high-temperature applications is understanding and mitigating the oxidation behavior of these chemically complex alloys. Most experimental and computational HEA studies have focused on a limited set of compositions and only a fraction these compositions have been characterized for oxidation. We present a high-throughput framework that utilizes density-functional theory (DFT) in concert with a combined machine-learning model and grand-canonical linear programming for assessing phase stability, phase-fraction, chemical activity and high-temperature survivability of arbitrary HEAs. This framework considers temperature dependent contributions to the Gibbs energy of the competing phases arising from short-range order and vibrational entropy. We demonstrate the effectiveness of the framework by assessing the thermodynamic stability, oxidation behavior, chemical activity, and phase decomposition of body-centered cubic Mo-W-Ta-Ti-Zr refractory HEAs. A total of 51 compositions were analyzed and ranked in order of their survivability based on the Pareto-front analysis. Oxidation was performed at 1373 K on fours samples in air showing the difference in oxidation behavior determined experimentally through scale thickness and their mass changes. The insights on oxidation behavior presented in this work will enable the fast assessment of technologically useful HEAs needed for future structural application in extreme conditions

36 MATERIALS SCIENCE↗

Dependent scattering and fractal microstructure determine the transparency of aerogel monoliths

This study reveals how dependent scattering and microstructure significantly affect electromagnetic wave propagation through aerogel monoliths, contributing to their transparency. Light scattering by particle ensembles is considered “dependent” when the scattering properties rely not only on particle size and optical constants but also on their spatial distribution, typically occurring when the average interparticle distance is small in comparison with the wavelength of incident radiation. Addressing dependent scattering requires solving Maxwell’s equations for complex heterogeneous structures, which is computationally demanding and usually limited to sample thicknesses on the same scale as the wavelength. This study combines computer-generated ambigel microstructures of fractal aggregates of polydisperse nanoparticles and the radiative transfer with reciprocal transaction method to predict the transmittance of thick ambigel slabs. Transmittance measurements of ambiently dried aerogel monoliths (ambigels) with porosities from about 50% to 90% closely matched the predicted values for their digital twins. However, ignoring dependent scattering or particle aggregation led to inaccurate predictions. This study validated the computational framework, and its findings offer insights for designing photonic metamaterials and analyzing their interactions with electromagnetic waves.

Yalcin, Refet A. (ORCID:0000000339973494)↗