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At least 91 records · Page 5

Towards a study protocol: A data-driven workflow to identify error sources in direct ink write mechatronics

Abstract Using Direct Ink Write (DIW) technology in a rapid and large-scale production requires reliable quality control for printed parts. Data streams generated during printing, such as print mechatronics, are massive and diverse which impedes extracting insights. In our study protocol approach, we developed a data-driven workflow to understand the behavior of sensor-measured X- and Y- axes positional errors with process parameters, such as print velocity and velocity control. We uncovered patterns showing that instantaneous changes in the velocity, when the build platform accelerates and decelerates, largely influence the positional errors, especially in the X- axis due to the hardware architecture. Since DIW systems share similar mechatronic inputs and outputs, our study protocol approach is broadly applicable and scalable across multiple systems. Graphical abstract

36 MATERIALS SCIENCE↗

MC Formula Protocol for H35HF Fueling (CRADA Final Report)

The National Renewable Energy Lab (NREL), Frontier Energy, and the industry partners worked together to help SAE J2601-5 develop an H35 high-flow (HF) medium-duty (MD) and heavy-duty (HD) fueling protocol. The team upgraded NREL's hydrogen filling simulations (H2FillS) model to accommodate an MC Formula fueling (t-final) table generation capability by leveraging NREL's high-performance computing system. Based on protocol boundary conditions (e.g., allowable maximum flow rate, range of storage system size) set by SAE J2601-5, the team generated the fueling tables and then validated the reliability of those tables by installing them on NREL's HD dispenser and ZBT's H35HF dispenser and then performing H35HF fueling experiments. Through the validation process, this team certified that the fueling tables generated were reliable to install in commercial H35HF dispensers and then performed H35HF fueling of commercial MD/HD vehicles.

08 HYDROGEN↗

Protocol-dependent frictional granular jamming simulations: cyclical, compression, and expansion

Granular matter takes many paths to pack in natural and industrial processes. The path influences the packing microstructure, particularly for frictional grains. We perform discrete element modeling simulations of different paths to construct packings of frictional spheres. Specifically, we explore four stress-controlled protocols implementing packing expansions and compressions in various combinations thereof. We characterize the eventual packed states through their dependence of the packing fraction and coordination number on packing pressure, identifying non-monotonicities with pressure that correlate with the fraction of frictional contacts. These stress-controlled, bulk-like particle simulations access very low-pressure packings, namely, the marginally stable limit, and demonstrate the strong protocol dependence of frictional granular matter.

36 MATERIALS SCIENCE↗

How Advanced Hydrogen Fueling Protocols Can Improve Fueling Performance and H2 Station Design

This presentation introduces concepts to lower the cost of hydrogen fueling by making improvements to the existing SAE J2601 protocols and by utilizing completely new protocol approaches that can facilitate customer acceptable fueling at warmer hydrogen pre-cooling temperatures. These methods would reduce the cost of chillers at the station, reduce energy consumption, and increase station reliability without sacrificing fueling performance. These approaches are especially applicable to high flow fueling at 70 MPa, a key aspect of H2@Scale, wherein station energy consumption and customer sensitivity to fuel costs is even more prominent than it is for light-duty fueling.

ADVANCED PROPULSION SYSTEMS↗

High-yield recombinant bacterial expression of 13 C-, 15 N-labeled, serine-16 phosphorylated, murine amelogenin using a modified third generation genetic code expansion protocol

Amelogenin constitutes ~ 90% of the enamel matrix in the secretory stage of amelogenesis, a still poorly understood process that results in the formation of the hardest and most mineralized tissue in vertebrates – enamel. Most biophysical research with amelogenin uses recombinant protein expressed in Escherichia coli. In addition to providing copious amounts of protein, recombinant expression allows 13 C- and 15 N-labelling for detailed structural studies using NMR spectroscopy. However, native amelogenin is phosphorylated at one position, Ser-16 in murine amelogenin, and a lingering question overshadowing decades of enamel research with recombinant amelogenin is the effect of phosphorylation on its biophysical properties. Using a modified genetic code expansion protocol we have expressed and purified uniformly 13 C-, 15 N-labeled murine amelogenin (pS16M179) with ~95% of the protein being correctly phosphorylated. Homogeneous phosphorylation was achieved using commercially available, enriched, 13 C-, 15 N-labeled media and protein expression was induced with isopropyl β-D-1-thiogalactopyranoside at 310 K. Phosphoserine incorporation was verified from one-dimensional 31P NMR spectra, comparison of 1 H- 15 N HSQC spectra, Phos-tag SDS PAGE, and mass spectrometry. Phosphorus-31 NMR spectra for pS16M179 under conditions known to trigger amelogenin self-assembly into nanospheres confirm nanosphere models with buried N-termini. Lambda phosphatase treatment of these nanospheres results in the dephosphorylation of pS16M179, confirming that smaller oligomers and monomers with exposed N-termini are in equilibrium with nanospheres. Such 13 C-, 15 N-labeling of amelogenin with accurately encoded phosphoserine incorporation will accelerate biomineralization research to understand amelogenesis and stimulate the expanded use of genetic code expansion protocols to introduce phosphorylated amino acids into proteins.

31P-NMR↗

Installation protocol for charge transfer dissociation mass spectrometry on ion trapping mass spectrometers

Abstract Rationale Charge transfer dissociation (CTD) is a novel fragmentation technique that demonstrates enhanced structural characterization for a wide variety of molecules compared to standard fragmentation techniques like collision‐induced dissociation (CID). Alternative fragmentation techniques, such as electron transfer dissociation, electron capture dissociation, and ultraviolet photodissociation, also overcome many of the shortfalls of CID, but none of them are a silver bullet that can adequately characterize a wide variety of structures and charge states of target compounds. Given the diversity of structural classes and their occasional obstinance towards certain activation techniques, alternative fragmentation techniques are required that rely on novel or alternative modes of activation. Methods Herein, we present a step‐by‐step protocol for the installation of CTD on a quadrupole ion trap mass spectrometer and best practices for optimizing the signal‐to‐noise ratio and acquisition times for CTD mass spectra. Results In addition to two CTD installations in the Jackson laboratory, CTD has also been installed, and is currently in operation, on two 3D ion trap mass spectrometers in France: one in the laboratory of Dr. David Ropartz and Dr. Hélène Rogneaux at INRAE in Nantes, and the other in the laboratory of Dr. Jean‐Yves Salpin at Université d'Évry Val‐d'Essonne, part of the Paris‐Saclay University system. Conclusions Here, we provide a visual protocol to help others accomplish the instrument modification.

47 OTHER INSTRUMENTATION↗

A traversable wormhole teleportation protocol in the SYK model

In this paper, we propose a concrete teleportation protocol in the SYK model based on a particle traversing a wormhole. The required operations for the communication, and insertion and extraction of the qubit, are all simple operators in terms of the basic qubits. We determine the effectiveness of this protocol, and find a version achieves almost perfect fidelity. Many features of semiclassical traversable wormholes are manifested in this setup.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Protocol for assembling and operating bipolar membrane water electrolyzers

Renewable energy-driven bipolar membrane water electrolyzers (BPMWEs) are a promising technology for sustainable production of hydrogen from seawater and other impure water sources. Here, we present a protocol for assembling BPMWEs and operating them in a range of water feedstocks, including ultra-pure deionized water and seawater. We describe steps for membrane electrode assembly preparation, electrolyzer assembly, and electrochemical evaluation. For complete details on the use and execution of this protocol, please refer to Marin et al. (2023).

Rios Amador, Isabela↗

X-ray Photoelectron Spectroscopy Analysis of Nafion-Containing Samples: Pitfalls, Protocols, and Perceptions of Physicochemical Properties

X-ray photoelectron spectroscopy (XPS) is one of the most common techniques used to analyze the surface composition of catalysts and support materials used in polymer electrolyte membrane (PEM) fuel cells and electrolyzers, providing important insights for further improvement of their properties. Characterization of catalyst layers (CLs) is more challenging, which can be at least partially attributed to the instability of ionomer materials such as Nafion during measurements. This work explores the stability of Nafion during XPS measurements, illuminating and addressing Nafion degradation concerns. The extent of Nafion damage as a function of XPS instrumentation, measurement conditions, and sample properties was evaluated across multiple instruments. Results revealed that significant Nafion damage to the ion-conducting sulfonic acid species (>50% loss in sulfur signal) may occur in a relatively short time frame (tens of minutes) depending on the exact nature of the sample and XPS instrument. This motivated the development and validation of a multipoint XPS data acquisition protocol that minimizes Nafion damage, resulting in reliable data acquisition by avoiding significant artifacts from Nafion instability. The developed protocol was then used to analyze both thin film ionomer samples and Pt/C-based CLs. Comparison of PEM fuel cell CLs to Nafion thin films revealed several changes in Nafion spectral features attributed to charge transfer due to interaction with conductive catalyst and support species. This study provides a method to reliably characterize ionomer-containing samples, facilitating fundamental studies of the catalyst-ionomer interface and more applied investigations of structure-processing-performance correlations in PEM fuel cell and electrolyzer CLs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Designing the Protocols for Programmable Ammonia Catalysis

Programmable catalysis can provide a more energy-efficient and cost-effective route to enhancing commercial ammonia production, a key process in the advancement of renewable energy technologies and the manufacture of fertilizers and basic chemicals. This work explores the computational discovery of optimal forcing protocols to drive such dynamic catalysis models. By employing matrix-free time-stepper methods, coupled with an optimization approach, that integrates Bayesian optimization with a Bayesian continuation strategy to efficiently discover the periodic steady states of such periodically forced systems, we enable the discovery of complex optimal catalyst strain waveforms, while ensuring robust solver convergence. We demonstrate the flexibility of our approach to discover optimized forcing protocols under varying physical constraints on strain modulation or other catalyst operating parameters. We show that these can have a temporal structure more complex than simple step functions. In order to detect undesirable catalytic loops that may correlate with overall reduced performance, we perform a study using graph-theoretical analysis to investigate the dynamics of catalytic kinetic networks formed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental Protocols for Studying Organic Non-aqueous Redox Flow Batteries

We report that Redox flow batteries (RFBs) are promising devices for grid-scale energy storage due to the decoupling of power and energy, which can be independently scaled by the electrode area and storage tank size, respectively. To date, only aqueous RFBs, such as the vanadium RFB, have been implemented commercially. Nevertheless, the limited energy densities and high-cost materials may preclude their wider market penetration. Organic non-aqueous redox-flow batteries (O-NRFBs), which utilize redox-active organic molecules (ROMs), have been offered as an attractive alternative. Many possible advantages include the use of earth-abundant elements (C, H, N, O, S, F), wherein the ROMs can be prepared from low-cost and sustainable materials. Additionally, a large variety of electroactive moieties are accessible as building blocks, providing a synthetic platform to tune the properties of ROMs through rational design. As a consequence, the development of novel ROMs has attracted researchers with diverse backgrounds, prompting remarkable innovations in the past decade. However, consistency in experimental protocols (e.g., electrochemical methods, cycling stability, experimental conditions) has not coincided with this uptick in research, leading to sometimes ambiguous and incomparable results. This is further convoluted by the complexity innate to battery development, such as cell design, detection, and characterization of reactions and active components. The O-NRFB application imposes stringent requirements on the physical or/and chemical processes involved in electrochemical cycling. Yet such considerations are often overlooked. Further, while quantum mechanical calculations provide a convenient tool for evaluating and selecting ROM candidates, this simulation is not always performed. Thus, in this Energy Focus, we detail a means to standardize experimental protocols for studies of O-NRFBs and suggest practices to facilitate fundamental understanding and development of ROMs.

25 ENERGY STORAGE↗

A bending test protocol for characterizing the mechanical performance of flexible photovoltaics

Flexible photovoltaics (PV) represents a promising research field with great potential for wearable, portable, and indoor applications. Significant progress has been made in recent years, with flexible emerging PV reporting power conversion efficiency (PCE) over 24%. Yet, there is a need for a unifying protocol to assess PV performance, compare research results, and evaluate the state- of-the-art achievements in flexible PV. In this paper, a consensus protocol is presented for measuring PCE over 1,000 bending cycles under 1% strain. Moreover, several good practice guidelines are proposed including bending procedures, flexibility testing with and without encapsulation, and ambient conditions during testing (e.g., temperature, humidity, illumination). Notably, the importance of uniform application of bending radius and the testing of parallel and perpendicular orientations of bending axis with respect to the direction of the electric current are emphasized. These recommendations aim to promote consistency in device comparison and allow for better reproducibility.

Fukuda, Kenjiro↗

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The influence of electrochemical cycling protocols on capacity loss in nickel-rich lithium-ion batteries

The transition towards electric vehicles and more sustainable transportation is dependent on lithium-ion battery (LIB) performance. Ni-rich layered transition metal oxides, such as NMC811 (LiNi 0.8 Mn 0.1 Co 0.1 O 2 ), are promising cathode candidates for LIBs due to their higher specific capacity and lower cost compared with lower Ni content materials. However, complex degradation mechanisms inhibit their use. In this work, tailored aging protocols are employed to decouple the effect of electrochemical stimuli on the degradation mechanisms in graphite/NMC811 full cells. Using these protocols, impedance measurements, and differential voltage analysis, the primary drivers for capacity fade and impedance rise are shown to be large state of charge changes combined with high upper cut-off voltage. Focused ion beam-scanning electron microscopy highlights that extensive microscale NMC particle cracking, caused by electrode manufacturing and calendering, is present prior to aging and not immediately detrimental to the gravimetric capacity and impedance. Scanning transmission electron microscopy electron energy loss spectroscopy reveals a correlation between impedance rise and the level of transition metal reduction at the surfaces of aged NMC811. The present study provides insight into the leading causes for LIB performance fading, and highlights the defining role played by the evolving properties of the cathode particle surface layer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TeraChem protocol buffers ( TCPB ): Accelerating QM and QM/MM simulations with a client–server model

The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. Here, we describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior file-based implementation for a QM region with ~250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI - )—a model chromophore in green fluorescent proteins—on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the non-commercial freely-available version of TeraChem, which is sufficient for many QM region sizes in common use.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Unified Protocol for CRISPR/Cas9-Mediated Gene Knockout in Tephritid Fruit Flies Led to the Recreation of White Eye and White Puparium Phenotypes in the Melon Fly

Abstract Tephritid fruit flies are among the most invasive and destructive agricultural pests worldwide. Over recent years, many studies have implemented the CRISPR/Cas9 genome-editing technology to dissect gene functions in tephritids and create new strains to facilitate their genetics, management, and control. This growing literature allows us to compare diverse strategies for delivering CRISPR/Cas9 components into tephritid embryos, optimize procedures, and advance the technology to systems outside the most thoroughly studied species within the family. Here, we revisit five years of CRISPR research in Tephritidae and propose a unified protocol for candidate gene knockout in fruit flies using CRISPR/Cas9. We demonstrated the efficiency of our protocol by disrupting the eye pigmentation gene white eye (we) in the melon fly, Zeugodacus cucurbitae (Coquillett) (Diptera: Tephritidae). High rates of somatic and germline mutagenesis were induced by microinjecting pre-assembled Cas9-sgRNA complexes through the chorion of embryos at early embryogenesis, leading to the rapid development of new mutant lines. We achieved comparable results when targeting the we orthologue in the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), illustrating the reliability of our methods when transferred to other related species. Finally, we functionally validated the recently discovered white pupae (wp) loci in the melon fly, successfully recreating the white puparium phenotype used in suppression programs of this and other major economically important tephritids. This is the first demonstration of CRISPR-based genome-editing in the genus Zeugodacus, and we anticipate that the procedures described here will contribute to advancing genome-editing in other non-model tephritid fruit flies.

Entomology↗

End-to-end protocol for high-quality quantum approximate optimization algorithm parameters with few shots

The quantum approximate optimization algorithm (QAOA) is a quantum heuristic for combinatorial optimization that has been demonstrated to scale better than state-of-the-art classical solvers for some problems. For a given problem instance, QAOA performance depends crucially on the choice of the parameters. While average-case optimal parameters are available in many cases, meaningful performance gains can be obtained by fine-tuning these parameters for a given instance. This task is especially challenging, however, when the number of circuit executions (shots) is limited. In this work, we develop an end-to-end protocol that combines multiple parameter settings and fine-tuning techniques. We use large-scale numerical experiments to optimize the protocol for the shot-limited setting and observe that optimizers with the simplest internal model (linear) perform best. We implement the optimized pipeline on a trapped-ion processor using up to 32 qubits and 5 QAOA layers, and we demonstrate that the pipeline is robust to small amounts of hardware noise. To the best of our knowledge, these are the largest demonstrations of QAOA parameter fine-tuning on a trapped-ion processor in terms of two-qubit gate count.

quantum algorithms & computation↗

Advancing quantum simulations of the nuclear shell model with Gray-code–based resource-efficient protocols

Background: Some of the computational limitations in solving the nuclear many-body problem could be overcome by utilizing quantum computers. The nuclear shell-model calculations providing deeper insights into the properties of atomic nuclei are one such case with high demand for resources, as the size of the Hilbert space grows exponentially with the number of particles involved. Quantum algorithms are being developed to overcome these challenges and advance such calculations. Purpose: To develop quantum circuits for the nuclear shell-model, leveraging the capabilities of noisy intermediate-scale quantum (NISQ) devices. Here, we aim to minimize resource requirements (specifically in terms of qubits and gates) and strive to reduce the impact of noise by employing relevant mitigation techniques. Methods: We achieve noise resilience by designing an optimized Ansatz for the variational quantum eigensolver (VQE) based on Givens rotations and incorporating qubit-ADAPT-VQE in combination with variational quantum deflation (VQD) to compute ground and excited states, incorporating the zero-noise extrapolation mitigation technique. Furthermore, the qubit requirements are significantly reduced by mapping the basis states to qubits using Gray-code encoding and generalizing transformations of fermionic operators to efficiently represent many-body states. Results: By employing the resource-efficient protocols, we achieve the ground and excited state energy levels of 38 Ar and 6 Li with better accuracy. These energy levels are presented for noiseless simulations, noisy conditions, and after applying noise mitigation techniques. Results are compared for Jordan-Wigner and Gray-code encoding using VQE, qubit-ADAPT-VQE, and VQD. Conclusions: Our work highlights the potential of resource-efficient protocols to leverage the full potential of NISQ devices in scaling the nuclear shell model calculations, offering a pathway toward more complex quantum simulations in nuclear physics. This approach establishes a framework for studying other nuclear systems with improved quantum resource efficiency, marking a significant advancement in applying quantum computing to realistic nuclear physics applications.

Physics - Nuclear physics and radiation physics↗