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CoSMo is a comprehensive shell model code suite designed for nuclear shell model and configuration interaction calculations. Its highly structured and templated nature allows for flexibility and ease in applications, including those to open quantum systems with non-Hermitian Hamiltonians, clustering, and time-dependent dynamics.
The U.S. Department of Energy (DOE) and Norway’s Royal Ministry of Petroleum and Energy signed an Annex to a previously signed memorandum of understanding (MOU) in February 2020 to collaborate on hydropower research and development (R&D). This MOU Annex has brought together the DOE’s Office of Energy Efficiency and Renewable Energy Water Power Technology Office and the Norwegian Research Center for Hydropower Technology (HydroCen) to plan and coordinate hydropower R&D activities to increase our understanding of hydropower’s role in the future energy grid and how to minimize and mitigate the subsequent environmental impacts. As part of this MOU Annex, hydropower researchers from the U.S. and Norway have come together to conduct collaborative research on hydropower markets and value, hydropower plant capabilities and constraints, monitoring and control technologies, environmental design solutions, environmental impacts and tradeoffs, flexible operation and planning, and technology innovations. This report presents background information on hydropower environmental regulation in the U.S. and Norway and summarizes content and conclusions from this series of two, three-hour workshops on hydropower generation flexibility and environmental outcomes, that included structured discussions used to identify research priorities and collaborative research opportunities.
To cope with legacy greenhouse gas emissions and to achieve net-zero emissions by 2050, the U.S. Department of Energy (DOE) is funding efforts to develop direct air capture (DAC), a method for removing CO2 directly from air. Metal organic frameworks (MOFs) have been well studied as DAC sorbent materials due to their tunable structural and compositional properties. Thermodynamic simulations using force fields are often used to provide predictions of a material’s performance in many separations. However, these force fields often make assumptions about bonds and the physics of the adsorption process. A new class of force fields called machine-learned force fields (MLFFs) use machine learning to form quantitative relationships between a material’s chemical structure and the forces and energies predicted by more accurate quantum mechanical calculations, such as dispersion-corrected density functional theory (DFT). In this work, models were developed to achieve DFT-level accuracy for the forces and energies associated with MOF flexibility and CO2 adsorption using MLFFs. These methods were parametrized based on thousands of DFT calculations of CO2 in flexible MOFs and used to predict MOF structural properties as well as CO2 adsorption in several MOFs.
The opioid crisis in the United States is being fueled primarily by fentanyl and its molecular analogs, which can be anywhere from 50 to 1,000 times more potent than morphine. Fentanyl itself is straightforward to synthesize; furthermore, the structure is such that fentanyl’s flexible, rotatable side chains are easy to modify to create new analogs. Reference-free computational techniques to predict and identify new fentanyls have the potential to provide a desperately needed preemptive advantage to regulatory stakeholders and toxicologists. The computational pipeline Heracles was developed with this preemptive advantage in mind. Heracles has two primary components: 1) the creation of an in silico library of putative fentanyl analogs, and 2) a downselection pipeline to prioritize generated fentanyl analogs predicted to be potent and easy to synthesize. Experimental observables were also predicted for prioritized analogs, with validation of the observables begun. Heracles has demonstrated potential to aid in the advancement of reference-free paradigms while providing new tools to first responders and other stakeholders attempting to mitigate the opioid crisis.
The aerospace, construction/architecture, and transportation manufacturing industries rely heavily on the mass production of near-net shape metallic and composite extrusions. While the production of raw extrusions is a relatively fast process, adding functional features such as holes and slots require additional time, cost, and energy to produce. To compensate for the inherent flexibility of extrusions, conventional machining requires rigid purpose-built fixtures for operations such as trimming, drilling and thinning. This approach requires that the machine tools be as large or larger than the parts themselves. This results in the need for excess shop floor space, energy for auxiliary equipment and motion systems, and significant capital expenditure. Considerable engineering expense and time involved in the designing, building, and proving out of part-specific fixtures for holding the components in specific configurations while machining add to the overall manufacturing cost. The primary objective of the technical collaboration between Oak Ridge National Laboratory and Fairmount Technologies (FT) is to improve the XM-3, a fixtureless CNC milling machine designed by FT. The machine was developed to trim, drill, and thin extrusions without part specific fixturing to make the manufacturing process more efficient and flexible. Dynamic measurements of the existing structure were collected, and modeling efforts were made to evaluate optimal machining parameters for the current system. Areas of improvement to increase the system stiffness, manufacturability, and machining efficiency were evaluated and highlighted for the next generation design. The impact of this effort may enable agile manufacturing across the commercial and defense aerospace industries, and other industries where extrusions are utilized like in the construction, architecture, and transportation industries.
The aerospace, construction/architecture, and transportation manufacturing industries rely heavily on the mass production of near-net shape metallic and composite extrusions. While the production of raw extrusions is a relatively fast process, adding functional features such as holes and slots require additional time, cost, and energy to produce. To compensate for the inherent flexibility of extrusions, conventional machining requires rigid purpose-built fixtures for operations such as trimming, drilling and thinning. This approach requires that the machine tools be as large or larger than the parts themselves. This results in the need for excess shop floor space, energy for auxiliary equipment and motion systems, and significant capital expenditure. Considerable engineering expense and time involved in the designing, building, and proving out of part-specific fixtures for holding the components in specific configurations while machining add to the overall manufacturing cost. The primary objective of the technical collaboration between Oak Ridge National Laboratory and Fairmount Technologies (FT) is to improve the XM-3, a fixtureless CNC milling machine designed by FT. The machine was developed to trim, drill, and thin extrusions without part specific fixturing to make the manufacturing process more efficient and flexible. Dynamic measurements of the existing structure were collected, and modeling efforts were made to evaluate optimal machining parameters for the current system. Areas of improvement to increase the system stiffness, manufacturability, and machining efficiency were evaluated and highlighted for the next generation design. The impact of this effort may enable agile manufacturing across the commercial and defense aerospace industries, and other industries where extrusions are utilized like in the construction, architecture, and transportation industries.
Dataset shift refers to the problem where the input data distribution may change over time (e.g., between training and test stages). Since this can be a critical bottleneck in several safety-critical applications such as healthcare, drug-discovery, etc., dataset shift detection has become an important research issue in machine learning. Though several existing efforts have focused on image/video data, applications with graph-structured data have not received sufficient attention. Therefore, in this paper, we investigate the problem of detecting shifts in graph structured data through the lens of statistical hypothesis testing. Specifically, we propose a practical two-sample test based approach for shift detection in large-scale graph structured data. Our approach is very flexible in that it is suitable for both undirected and directed graphs, and eliminates the need for equal sample sizes. Using empirical studies, we demonstrate the effectiveness of the proposed test in detecting dataset shifts. We also corroborate these findings using real-world datasets, characterized by directed graphs and a large number of nodes.
Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.
Utilizing additive manufacturing (AM) techniques with shape memory alloys (SMAs) like NiTi shows great promise for fabricating highly flexible and functionally superior 3D metallic structures. Compared to methods relying on powder feedstocks, wire-based additive manufacturing processes provide a viable alternative, addressing challenges such as chemical composition instability, material availability, higher feedstock costs, and limitations on part size while simplifying process development. This study presented a novel approach by thoroughly assessing the printability of Ni-rich Ni55.94Ti (Wt. %) SMA using the wire laser-directed energy deposition (WL-DED) technique, addressing the existing knowledge gap regarding the laser wire-feed metal additive manufacturing of NiTi alloys. For the first time, the impact of processing parameters—specifically laser power (400–1000 W) and transverse speed (300–900 mm/min)—on single-track fabrication using NiTi wires in the WL-DED process was examined. An optimal range of process parameters was determined to achieve high-quality prints with minimal defects, such as wire dripping, stubbing, and overfilling. Building upon these findings, we printed five distinct cubes, demonstrating the feasibility of producing nearly porosity-free specimens. Notably, this study investigated the effect of energy density on the printed part density, impurity pick-up, transformation temperature, and hardness of the manufactured NiTi cubes. The results from the cube study demonstrated that varying energy densities (46.66–70 J/mm3) significantly affected the quality of the deposits. Lower to intermediate energy densities achieved high relative densities (>99%) and favorable phase transformation temperatures. In contrast, higher energy densities led to instability in melt pool shape, increased porosity, and discrepancies in phase transformation temperatures. These findings highlighted the critical role of precise parameter control in achieving functional NiTi parts and offer valuable insights for advancing AM techniques in fabricating larger high-quality NiTi components. Additionally, our research highlighted important considerations for civil engineering applications, particularly in the development of seismic dampers for energy dissipation in structures, offering a promising solution for enhancing structural performance and energy management in critical infrastructure.
The goal of the automated mobility platforms (AMPs) initiative is to raise the bar of service regarding equity and sustainability for public mobility systems that are crucial to large facilities, and doing so using electrified, energy efficient technology. Using airports as an example, the rapid growth in air travel demand has led to facility expansions and congested terminals, which directly impacts equity (e.g., increased challenges for Passengers with Reduced Mobility [PRMs]) and sustainability - both of which are important metrics often overlooked during the engineering design process. Therefore, to evaluate systems and inform critical near- and long-term decisions more effectively, a holistic evaluation framework is proposed focused on four key areas: (1) mobility, with emphasis on travel time and accessibility within an airport, (2) environment, focused on energy consumption and greenhouse gas (GHG) emissions associated with intra-airport mobility, (3) equity, specifically to the PRM community, but with an eye to the whole of society, and (4) built environment, or the fundamental changes in building design enabled by different mobility systems for larger and more flexible, functional, and energy-efficient structures. Below, AMPs are defined, and each metric is discussed further, all with a focus on airport mobility.
Automated Mobility Platform (AMP) is a general term for intelligently managed passenger mobility systems that leverage automation and electrification to improve system performance and sustainability through the integration of real-time data streams with advanced decision-making processes tailored for use in large facilities. Using airports as an example, the rapid growth in air travel demand has led to facility expansions and congested terminals, which directly impacts equity (e.g., increased challenges for passengers with reduced mobility [PRMs]) and sustainability - both of which are important metrics often neglected during the engineering design process. Therefore, to evaluate systems and inform critical decisions more effectively, a holistic evaluation framework is proposed that includes equity, sustainability, and infrastructure perspectives - referred to as a multidimensional benefit assessment. More specifically, the following analysis focuses on: (1) mobility, with emphasis on travel time and accessibility within an airport, contrasting existing systems with the proposed AMP system; (2) equity analysis, specifically to the PRM community, but with an eye to the whole of society; (3) energy consumption and greenhouse gas (GHG) emissions associated with intra-airport mobility, comparing and contrasting modes as well as impacts on overall airport operations efficiency; and (4) fundamental changes in building design enabled by AMPs for larger and more flexible, functional, and energy-efficient structures.
Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL . Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.
The plant cell wall is a dynamic and complex extracellular matrix that not only provides structural integrity and determines cell shape but also mediates intercellular communication. Among its major components, pectins play essential roles in cell adhesion, wall porosity, hydration, and flexibility. Rhamnogalacturonan-I (RG-I), a structurally diverse pectic polysaccharide, remains one of the least understood components of the plant cell wall. Its backbone is substituted with arabinan, galactan, and arabinogalactan side chains that vary in length, branching, and composition across tissues, species, and developmental stages. In addition, RG-I can undergo modifications such as backbone acetylation, further contributing to its structural complexity and functional diversity. To advance understanding of RG-I, we present a detailed method for isolating RG-I from the model plant Arabidopsis thaliana . Leveraging Arabidopsis as a model system provides major advantages owing to its well-characterized genome and powerful molecular toolkit, enabling deeper investigation into the roles of RG-I in plant development and responses to environmental stress. Our method consists of two major steps: an initial chemical extraction using oxalate, followed by endo-polygalacturonase (EPG) digestion to fragment the pectic domains. An advantage of this approach is that it produces a dry material that can be stored at room temperature without special handling and does not introduce chemicals that may interfere with downstream analyses. The purified RG-I can be used for detailed compositional and structural analyses, as well as for functional studies of enzymes involved in pectin biosynthesis, modification, and degradation. Although this protocol was developed for isolating RG-I from Arabidopsis rosette leaves, it is also applicable to other Arabidopsis organs and other plant species.
The separation and purification of xylene isomers is an industrially important but challenging process. Developing highly efficient adsorbents is crucial for the implementation of simulated moving bed technology for industrial separation of these isomers. Herein, we report a stacked one-dimensional coordination polymer {[Mn(dhbq)(H 2 O) 2 ], H 2 dhbq = 2,5-dihydroxy-1,4-benzoquinone} that exhibits an ideal molecular recognition and sieving of xylene isomers. Its distinct temperature-adsorbate–dependent adsorption behavior enables full separation of p -, m -, and o -xylene isomers in both vapor and liquid phases. The delicate stimuli-responsive swelling of the structure imparts this porous material with exceptionally high flexibility and stability, well-balanced adsorption capacity, high selectivity, and fast kinetics at conditions mimicking industrial settings. This study may offer an alternative approach for energy-efficient and adsorption-based industrial xylene separation and purification processes.
In this work, a series of ionic liquids with symmetric, macrocyclic cations composed of N-heterocycles connected by alkyl or ether linkages coupled with bis(trifluoromethylsulfonyl)imide or bis(pentafluoroethanesulfonyl)amide anions were synthesized to explore their application in CO 2 separation. These novel ionic liquids showed selective physical absorption of CO 2 compared to N 2 making them potential candidates for carbon capture. We examined the effect of cation structure on the physicochemical and separations properties of the ionic liquid and showed that these ionic liquids exhibit an inverse relationship between molar volume and CO 2 sorption capacity following the trend predicted by models based on regular solution theory. The fractional free volumes of the ionic liquids were lower than typical alkyl-imidazolium ionic liquids despite the cyclic structure of the cations which could be related to the flexibility of the alkyl and ether linkages. These results provide added insight into our understanding of structure–property relationships in CO 2 solubility in ionic liquids and afford a path toward enhancing the separations properties based on structure.
To cope with legacy greenhouse gas emissions and to achieve net-zero emissions by 2050, the U.S. Department of Energy (DOE) is funding efforts to develop direct air capture (DAC), a method for removing CO2 directly from air. Metal organic frameworks (MOFs) have been studied as DAC sorbent materials because of their structural and chemical diversity. Thermodynamic calculations using classical force fields are often used to screen MOFs for their performance in separations such as CO2 capture. Machine-learned force fields (MLFFs) can use machine learning to form quantitative relationships between a material’s chemical structure and the forces and energies predicted by more accurate quantum mechanical calculations, such as dispersion-corrected density functional theory (DFT). These descriptions of forces and energies can be used to improve the accuracy of adsorption calculations. In this work, MLFF models were developed for MOFs to achieve DFT-level accuracy for the forces and energies associated with MOF flexibility and CO2 adsorption. These methods were parametrized based on thousands of DFT calculations of CO2 in flexible MOFs and used to predict MOF structural properties as well as CO2 adsorption properties.
Low-dimensional hybrid inorganic–organic perovskites are excellent candidates for stable optoelectronic devices. The dimensionality of these perovskites depends largely on the organic and inorganic compositions, as well as the synthetic conditions. We report five new hybrid iodides, (ETU) 4 Ge 5 I 18 , (ETU)GeI 4 , (ETU)SnI 4 , (ETU)PbI 4 , and (ETU) 3 Pb 2 I 10 using only one type of organic cation, namely, S-(2-aminoethyl)isothiouronium (ETU). (ETU)GeI 4 and (ETU)SnI 4 belong to the (110)-oriented structure-type with “3 × 3” sawtooth corrugated layers and crystallize in a structure with the orthorhombic space group Pbca. (ETU) 4 Ge 5 I 18 crystallizes in a structure with the triclinic space group P$\bar{1}$with combining macron], featuring a 2D layered structure with combinations of corner, edge, and face-sharing [GeI 6 ] octahedra. For the Pb-based series, (ETU)PbI 4 has the conventional (100) – oriented 2D type whereas (ETU) 3 Pb 2 I 10 has a unique 0D structure. Remarkably, the unstable 2D orange-phase (ETU)PbI 4 transforms to a stable 0D yellow phase (ETU) 3 Pb 2 I 10 , accompanied by the reduction of the C–S–C angle of the organic cation ETU. The optical band gaps are largely regulated by the diverse types of structure and are in the range of 1.8 eV to 2.8 eV. (ETU)SnI 4 is the only material showing notable photoluminescence at room-temperature. Our work showcases the flexibility of the organic cation in determining the structural dimensionality and provides a new strategy in generating new hybrid materials.
Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.