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Exploring New Science Domains with Atom Probe Tomography Enabled by an Environmental Transfer Hub
The liquid/solid and gas/solid interface represents a rich scientific and technological frontier for discovery and innovation in many areas of science. However, the direct nano- to atomic-scale characterization of these interfaces is technically challenging within broad range of analytical tools that require high to ultrahigh vacuum conditions. This challenge has been largely addressed within the electron microscopy (EM) community through the development of unique specimen holders and differentially-pumped vacuum systems that allow researchers to probe, in situ, liquid/solid and gas/solid interfaces using electron probes [1]. However, the direct application of APT to liquid/solid and gas/solid interfaces is not possible and requires the development of unique specimen preparation and handling of cryogenically-frozen specimens and/or work with specimens under environmentally-protected conditions. At PNNL, we have developed unique suite of hardware and experimental protocols for the preparation and handling of environmentally-sensitive materials centered around the combination of a unique environmental transfer hub, specimen suitcase device, and modified cryo FIB/SEM capabilities (Fig. 1a) [2-3]. The ability to prepare, manipulate, and transfer specimens under either cryogenic or vacuum conditions thus provides a means to uniquely apply APT analysis to a wide variety of material systems that would not be possible otherwise. Here we describe some specific examples, shown in Figure 1b, of APT analysis applied to temperature sensitive material systems requiring cryo specimen preparation and transfer, as well as air sensitive materials systems requiring vacuum or inert vacuum transfer.
Targeted Single-Site MOF Node Modification: Trivalent Metal Loading via Atomic Layer Deposition
Postsynthetic functionalization of metal organic frameworks (MOFs) enables the controlled, high-density incorporation of new atoms on a crystallographically precise framework. Leveraging the broad palette of known atomic layer deposition (ALD) chemistries, ALD in MOFs (AIM) is one such targeted approach to construct diverse, highly functional, few-atom clusters. We here demonstrate the saturating reaction of trimethylindium (InMe3) with the node hydroxyls and ligated water of NU-1000, which takes place without significant loss of MOF crystallinity or internal surface area. We computationally identify the elementary steps by which trimethylated trivalent metal compounds (ALD precursors) react with this Zr-based MOF node to generate a uniform and well characterized new surface layer on the node itself, and we predict a final structure that is fully consistent with experimental X-ray pair distribution function (PDF) analysis. We further demonstrate tunable metal loading through controlled number density of the reactive handles (-OH and -OH2) achieved through node dehydration at elevated temperatures.
A Semi-Empirical Density Law for Ternary, Homogeneous PuCl 3 /HCl/H 2 O Solutions
Nuclear material operations pose unique hazards that are not encountered in other chemical, energy, or manufacturing industries. One of these hazards is the potential for a nuclear criticality accident when handling fissile isotopes such as 235 U and 239 Pu. These hazards are particularly high when fissile material is dissolved in solution as the neutron behaviors of the system can change rapidly with the physical and chemical changes accessible in solution. Current estimates of solution density used for criticality safety are outdated and hinder fissile material handling. Developing new estimates for these safety calculations requires experimental characterization and the derivation of empirical density models. We have derived a density law describing PuCl 3 /HCl/H 2 O solutions from experimental data characterizing solution density. Density data was treated using a Pitzer-derived eight-parameter equation, defining density as a function of analyte concentrations, temperature, and interactions between these variables. The model is predictive across the concentration and temperature ranges from which it was derived. The potential effects of varying oxidation states of plutonium, which are easily accessible in aqueous media, on the bulk solution density of the ternary system were also investigated. The resulting Pitzer-derived density law was applied to a nuclear criticality safety model, and the impact of the experimental characterization of solution density relative to previous estimates was demonstrated to be significant and suggest that the current approach to estimating density in nuclear criticality safety calculations may lead to overly conservative controls.
Direct Air Capture Using Aqueous Amino Acid Solvents in a Crossflow Absorber
Carbon dioxide (CO 2 ) is the most abundant of all greenhouse gases (GHGs). CO 2 levels in the atmosphere are 50% higher than in the preindustrial era, trapping heat. CO 2 removal from the atmosphere by direct air capture (DAC) is needed to achieve the internationally agreed global temperature goals. The most common CO 2 capture technology is absorption by aminebased solvents in packed columns. Amino acid solutions have recently gained attention due to their advantages over traditional amine solvents. To be implemented effectively, DAC industrial processes need to handle large airflow rates in separation absorbers. The large air and solvent flow rates preclude the use of countercurrent columns due to high-pressure drops and the occurrence of flooding. Crossflow air−liquid absorbers are used to handle large air and liquid volumes due to their lower-pressure drop. The objective of this work is to study the influence of crossflow absorber geometric parameters and operating conditions on product formation and process efficiency. An already derived theoretical model for countercurrent absorbers has been modified to simulate the operation of a crossflow DAC absorber. The predictive model was implemented into a computer code that was used to study the efficiency of the processes as geometric equipment dimensions and operating parameters vary. Practical suggestions are made to design more efficient DAC processes.
ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data
Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit.
Influence of Surface Oxidation on Ion Dynamics and Capacitance in Porous and Nonporous Carbon Electrodes
We investigate the influence of surface chemistry and ion confinement on capacitance and electrosorption dynamics of room-temperature ionic liquids (RTILs) in supercapacitors. Using air oxidation and vacuum annealing, we produced defunctionalized and oxygen-rich surfaces of carbide-derived carbons (CDCs) and graphene nanoplatelets (GNPs). While oxidized surfaces of porous CDCs improve capacitance and rate handling abilities of ions, defunctionalized nonporous GNPs improve charge storage densities on planar electrodes. Quasi-elastic neutron scattering (QENS) and inelastic neutron scattering (INS) probed the structure, dynamics, and orientation of RTIL ions confined in divergently functionalized pores. Oxidized, ionophilic surfaces draw ions closer to pore surfaces and enhance potential-driven ion transport during electrosorption. Molecular dynamics (MD) simulations corroborated experimental data and demonstrated the significance of surface functional groups on ion orientations, accumulation densities, and capacitance.
Understanding Trigger Linkage Dynamics in Energetic Materials Using Mixed Picramide Nitrate Ester Explosives
The ability to predict the handling sensitivity of new organic energetic materials has been a longstanding goal. We report the synthesis and characterization of six new nitropicramide energetic materials with mixed functional groups that mimic known explosives such as nitroglycerin, erythritol tetranitrate (ETN), and pentaerythritol tetranitrate (PETN). The molecules have been studied theoretically using quantum molecular dynamics (QMD) simulations and density functional theory (DFT) calculations to identify the weakest bond in the reactants - the trigger-linkages - which control handling sensitivity, and to quantify their specific enthalpies of explosion. In good accord with the drop weight impact sensitivity data, our calculations predict that the sensitivities of the molecules are very similar owing to the small variations of the energy output and rates of trigger linkage rupture. In addition, both the QMD and DFT calculations point to the nitropicramide N–NO 2 bonds as the trigger linkages rather than the more typical O–NO 2 bonds. We propose that the switch of the trigger linkage from the nitrate esters to the nitramine groups arises from the strongly electron withdrawing character of the adjacent trinitrobenzene groups.
OmicsMLMentor: A Web Application for Guided Machine Learning Analysis of Omics Data
Expression-based omics technologies (e.g. proteomics, metabolomics, transcriptomics, etc.) increasingly rely on supervised and unsupervised machine learning (ML) models to find key biomolecules distinguishing conditions, identify natural groupings in biological data, or generate predictions for outcomes of interest. Fitting ML models to omics data presents several challenges, including handling missing data, selecting a normalization method, choosing a valid model, and optimizing hyperparameters, all requiring statistical programming skills to address these challenges. Thus, the open-source web application SLOPE was designed to lower the barrier to ML modeling for omics data. SLOPE supports the fitting of 15 ML models (10 supervised and 5 unsupervised) tailored to omics datasets, such as proteomics, metabolomics, lipidomics, and transcriptomics. SLOPE offers several omics-specific features, including methods for handling missingness (imputation, conversion, removal), normalization tests, ranking of models based on the structure of a user’s data and user input, and optimal hyperparameter selections using cross-validation splits. By streamlining ML workflows for omics analysis, SLOPE address critical gaps in existing online web tools, facilitating a broader adoption of these models for omics research. Here, SLOPE is applied to data from a lignin exposure study to highlight the workflow for fitting both supervised and unsupervised models to data.
Tuning the Double Gyroid Phase Window in Block Copolymers via Polymer Chain Conformation Near the Interface
Block copolymer network morphologies have been proven interesting for applications ranging from mechanical to transport and optical properties. The shape of the polymer chain and its ability to stretch across an interface can be used as handles to target these network morphologies. Here, we show that the double gyroid phase window is broadened when there is a flexible segment near the interface and narrowed when a more constrained segment is placed there by using a series of poly(styrene-b-peptoid) block copolymers in which the polypeptoid block chain conformation can be tuned to adopt either a helical or a coil conformation (NRpe 6 vs Npe 6 ). The double gyroid phase is accessed in both block copolymer series, while the phase boundaries are shifted toward larger polypeptoid volume fractions in the helix-forming PS–(NRpe 6 Nmey) series, due to the more compact helix segment (i.e., the helix segment has the same chain volume as its random coil counterpart but occupies less space). The space-filling difference between the helix and coil segment is further confirmed by the smaller domain spacing of PS–(NRpe 6 Nme 39 ) compared to PS–(Npe 6 Nme 36 ) (13.9 nm vs 14.3 nm) despite the former having a longer polypeptoid block. Furthermore, a broadened double gyroid phase window is accessed in the PS–(Npe 6 Nme y ) series that has a flexible coil segment near the interface. These results demonstrate the possibility of tuning the double gyroid phase in linear block copolymers by chain conformation near the interface alone, highlighting chain conformation as a versatile handle in block copolymer design.
A Review of Computational Models for the Flow of Milled Biomass Part I: Discrete-Particle Models
Biomass is a renewable and sustainable energy resource. Current design of biomass handling and feeding equipment leverage both experiments and numerical modeling. This paper reviews the state-of-the-art discrete element methods (DEM) for the flow of milled biomass (Part I), accompanied by a comprehensive review on continuum-based computational models (Part II). The present review on DEM is primarily focused on the features and suitability of various particle shape models for different types of milled biomass because particle shape is the predominant attribute controlling the flow behavior of complex-shaped granular material. The general strengths and weaknesses in the applicability of those models for the milled biomass modeling are summarized. In particular, comments are provided to balance the numerical model capabilities and the computational cost for the development of DEM models. To our best knowledge, this is the first-of-its-kind review on DEM specifically for biomass. Our study indicates that the current DEM models require further development, calibration, and validation based on a deep understanding of biomass particle contact mechanics and experimental data support before they can be reliably used for predictive simulations in handling and feeding systems.
A Review of Computational Models for the Flow of Milled Biomass Part II: Continuum-Mechanics Models
The design of efficient material-handling systems for milled lignocellulosic biomass is challenging due to their complex particle morphologies and frictional interactions. Computational modeling, including the discrete element method (DEM) and continuum-based finite-element/volume methods, may offer scientific insight and predictive capabilities for the flow of milled biomass in hoppers and feeders. Herein, this article (Part II) presents a review of current state-of-the-art continuum models for the flow of milled biomass, whereas DEM models are reviewed in a companion article (Part I). Advances of numerical methods to solve the global governing equations are discussed first, followed by a comprehensive review of constitutive models for granular materials, including Drucker–Prager, hypoplastic, Cambridge-type, inertial-rheology, and nonlocal granular fluidity models. Specifically, we provide in-depth discussion on the suitability of those models for milled lignocellulosic biomass materials in terms of nonlinear elasticity, dependence of flow strength on pressure, density and shear rate, and compaction (dilation) associated with hardening (softening). Furthermore, our study shows that, despite the recent advances in continuum granular flow modeling, the most suitable constitutive models still need further development to account for material parametrization, multiflow regimes, and multiscale behavior before they can be reliably used to optimize the design and operation of biomass handling systems.
Surface Fluorination of Reactive Battery Anode Materials for Enhanced Stability
Significant increases in the energy density of batteries must be achieved by exploring new materials and cell configurations. Lithium metal and lithiated silicon are two promising high-capacity anode materials. Unfortunately, both of these anodes require a reliable passivating layer to survive the serious environmental corrosion during handling and cycling. Here we developed a surface fluorination process to form a homogeneous and dense LiF coating on reactive anode materials, with in situ generated fluorine gas, by using a fluoropolymer, CYTOP, as the precursor. The process is effectively a “reaction in the beaker”, avoiding direct handling of highly toxic fluorine gas. For lithium metal, this LiF coating serves as a chemically stable and mechanically strong interphase, which minimizes the corrosion reaction with carbonate electrolytes and suppresses dendrite formation, enabling dendrite-free and stable cycling over 300 cycles with current densities up to 5 mA/cm 2 . Lithiated silicon can serve as either a pre-lithiation additive for existing lithium-ion batteries or a replacement for lithium metal in Li–O 2 and Li–S batteries. However, lithiated silicon reacts vigorously with the standard slurry solvent N -methyl-2-pyrrolidinone (NMP), indicating it is not compatible with the real battery fabrication process. With the protection of crystalline and dense LiF coating, Li x Si can be processed in anhydrous NMP with a high capacity of 2504 mAh/g. With low solubility of LiF in water, this protection layer also allows Li x Si to be stable in humid air (~40% relative humidity). Furthermore, this facile surface fluorination process brings huge benefit to both the existing lithium-ion batteries and next-generation lithium metal batteries.
PR-PR: Cross-Platform Laboratory Automation System
To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.
Gigahertz-frequency acousto-optic phase modulation of visible light in a CMOS-fabricated photonic circuit
Optical phase modulators operating at visible wavelengths are essential components for photonic technologies such as those for quantum control, communications, and laser ranging. However, they remain challenging to implement in scalable, integrated platforms capable of handling high optical powers. Here we present a visible-light, gigahertz-frequency acousto-optic phase modulator, fabricated on a 200-mm wafer in a volume CMOS foundry, that supports greater than 500 mW of optical power at 730 nm. The device combines a piezoelectric transducer and a photonic waveguide within a single, wavelength-scale structure that confines both a propagating optical mode and an electrically excitable breathing-mode mechanical resonance. By tuning the device’s geometry to optimize the optomechanical interaction, we achieve modulation depths up to 4.85 rad with 80 mW of applied microwave power at 2.31 GHz in a 2-mm-long device. This corresponds to resonant modulation figures of merit of V π = 1.32V and V π ⋅ L = 0.26V cm. To our knowledge, this is the lowest V π ever demonstrated in any acousto-optic phase modulator and represents a 15-fold reduction in V π and a 100-fold reduction in required microwave power relative to state-of-the-art modulators with high visible-wavelength power handling commonly employed in quantum control systems.
Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data
Abstract While the advances in synchrotron light sources, together with the development of focusing optics and detectors, allow nanoscale ptychographic imaging of materials and biological specimens, the corresponding experiments can yield terabyte-scale volumes of data that can impose a heavy burden on the computing platform. Although graphics processing units (GPUs) provide high performance for such large-scale ptychography datasets, a single GPU is typically insufficient for analysis and reconstruction. Several works have considered leveraging multiple GPUs to accelerate the ptychographic reconstruction. However, most of these works utilize only the Message Passing Interface to handle the communications between GPUs. This approach poses inefficiency for a hardware configuration that has multiple GPUs in a single node, especially while reconstructing a single large projection, since it provides no optimizations to handle the heterogeneous GPU interconnections containing both low-speed (e.g., PCIe) and high-speed links (e.g., NVLink). In this paper, we provide an optimized intranode multi-GPU implementation that can efficiently solve large-scale ptychographic reconstruction problems. We focus on the maximum likelihood reconstruction problem using a conjugate gradient (CG) method for the solution and propose a novel hybrid parallelization model to address the performance bottlenecks in the CG solver. Accordingly, we have developed a tool, called PtyGer ( Pty chographic G PU(multipl e )-based r econstruction), implementing our hybrid parallelization model design. A comprehensive evaluation verifies that PtyGer can fully preserve the original algorithm’s accuracy while achieving outstanding intranode GPU scalability.
An open-source data storage and visualization platform for collaborative qubit control
Developing collaborative research platforms for quantum bit control is crucial for driving innovation in the field, as they enable the exchange of ideas, data, and implementation to achieve more impactful outcomes. Furthermore, considering the high costs associated with quantum experimental setups, collaborative environments are vital for maximizing resource utilization efficiently. However, the lack of dedicated data management platforms presents a significant obstacle to progress, highlighting the necessity for essential assistive tools tailored for this purpose. Current qubit control systems are unable to handle complicated management of extensive calibration data and do not support effectively visualizing intricate quantum experiment outcomes. In this paper, we introduce Qubit Control Storage and Visualization ( QubiCSV ), a platform specifically designed to meet the demands of quantum computing research, focusing on the storage and analysis of calibration and characterization data in qubit control systems. As an open-source tool, QubiCSV facilitates efficient data management of quantum computing, providing data versioning capabilities for data storage and allowing researchers and programmers to interact with qubits in real time. The insightful visualization are developed to interpret complex quantum experiments and optimize qubit performance. QubiCSV not only streamlines the handling of qubit control system data but also improves the user experience with intuitive visualization features, making it a valuable asset for researchers in the quantum computing domain.
A Hybrid Pathway to Biojet Fuel via 2,3-Butanediol
Production of biomass-derived sustainable alternative jet fuels (SAJF) has been considered as an important approach to decarbonize the aviation industry but still possesses various challenges in technology advancement, particularly in achieving high carbon efficiency. Here we report a hybrid pathway to SAJF from 2,3-butanediol (2,3-BDO), integrating biologically converting biomass to 2,3-BDO with catalytically upgrading of 2,3-BDO to jet-range hydrocarbons. This pathway is demonstrated to have a high carbon recovery to liquid hydrocarbons from corn stover (25–28%) (74–82% of the theoretical maximum efficiency). The catalytic conversion steps involve 2,3-BDO to C3+ olefins, oligomerization, and hydrogenation where the first two steps are the focus of this study. Under optimum reaction conditions (523 K, 115 kPa, 1.0 h-1 weight hourly space velocity), 2,3-BDO conversion and C3+ olefin selectivity are >97% and 94–98% during 40 h time on stream, respectively. To demonstrate the adaptability of this technology with bio-derived 2,3-BDO, we also investigated the impact of water and other organic coproducts (acetoin and acetic acid) inherited from the fermentation broth on the catalyst performance and product selectivities. We have shown that the catalyst can handle a significant amount of water in the liquid feed (40 wt% water/60 wt% 2,3-BDO) and maintain catalyst stability for ~40 h. Acetoin can be converted to similar C3+ olefins as 2,3-BDO with complete conversion of acetoin. Co-feeding 10 wt% acetoin with 2,3-BDO is found to have no impact on 2,3-BDO conversion, C3+ olefin selectivity, and catalyst stability. The utilization of organic coproduct like acetoin can help to improve overall carbon conversion efficiency when using real biomass-derived 2,3-BDO. On the other hand, the presence of 10 wt% acetic acid is shown to drastically inhibit methyl ethyl ketone (MEK) hydrogenation and butene oligomerization as revealed by the increased MEK and butene selectivities, implying the importance of separating organic acids when feeding bio-derived 2,3-BDO. The formed C3–C6 olefins from 2,3-BDO are further oligomerized over Amberlyst-36 catalyst to longer-chain hydrocarbons with >70 wt% jet-range hydrocarbons including predominantly iso-olefins/iso-paraffins. The overall carbon efficiency for the jet-range hydrocarbons is 19–22%, exceeding most of the reported biojet pathways, which makes it a promising approach for SAJF production.