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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites

Trichoderma spp. are ubiquitous rhizosphere fungi capable of producing several classes of secondary metabolites that can modify the dynamics of the plant-associated microbiome. However, the bacterial-fungal mechanisms that mediate these interactions have not been fully characterized. Here, a random barcode transposon-site sequencing (RB-TnSeq) approach was employed to identify bacterial genes important for fitness in the presence of Trichoderma atroviride exudates. We selected three rhizosphere bacteria with RB-TnSeq mutant libraries that can promote plant growth: the nitrogen fixers Klebsiella michiganensis M5aI and Herbaspirillum seropedicae SmR1, and Pseudomonas simiae WCS417. As a non-rhizosphere species, Pseudomonas putida KT2440 was also included. From the RB-TnSeq data, nitrogen-fixing bacteria competed mainly for iron and required the siderophore transport system TonB/ExbB for optimal fitness in the presence of T . atroviride exudates. In contrast, P . simiae and P . putida were highly dependent on mechanisms associated with membrane lipid modification that are required for resistance to cationic antimicrobial peptides (CAMPs). A mutant in the Hog1-MAP kinase (Δ tmk 3) gene of T . atroviride showed altered expression patterns of many nonribosomal peptide synthetase (NRPS) biosynthetic gene clusters with potential antibiotic activity. In contrast to exudates from wild-type T . atroviride , bacterial mutants containing lesions in genes associated with resistance to antibiotics did not show fitness defects when RB-TnSeq libraries were exposed to exudates from the Δ tmk3 mutant. Unexpectedly, exudates from wild-type T . atroviride and the Δ tmk 3 mutant rescued purine auxotrophic mutants of H . seropedicae , K . michiganensis and P . simiae . Metabolomic analysis on exudates from wild-type T . atroviride and the Δ tmk 3 mutant showed that both strains excrete purines and complex metabolites; functional Tmk3 is required to produce some of these metabolites. This study highlights the complex interplay between Trichoderma -metabolites and soil bacteria, revealing both beneficial and antagonistic effects, and underscoring the intricate and multifaceted nature of this relationship.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

IBR Digital Supply Chain Gap Analysis and Recommendations

The adoption of clean energy technologies, including solar photovoltaics, continues to introduce non-traditional stakeholders to the operations and planning of the electric system. Stakeholders such as manufacturers, vendors, owners, aggregators, and others are enabling the adoption, integration, and optimum operations of solar technologies at accelerated rates. Inverters form the foundation of many digitally controlled energy sources for clean energy technologies, including Solar, Battery Energy Storage Systems, Hybrid Systems, and Hydrogen Fuel Cells. Their supply chain is complex, a series of microchips, electronic switches and other components making up its primary functions. The complexity of this space and the growing digitization associated with these components can create supply chain cyber risks. One measure to mitigate cybersecurity attacks is proper digital supply chain security. The U.S. Department of Energy (DOE) Solar Energy Technologies Office (SETO), in partnership with the Cybersecurity, Energy, Security, and Emergency Response (CESER) office, is hosting a workshop to bring together solar vendors and services providers to discuss digital supply chain security for solar systems and challenges and opportunities in the transitioning to a fully domestic supply chain for solar energy in the U.S. This workshop will support the Securing Solar for the Grid (S2G) and Energy Cyber Sense program activities. During the workshop, industry experts and researchers from DOE National Laboratories will discuss the current solar supply chain landscape and the transition to domestic manufacturing of solar components in the U.S. Tools and techniques to better manage and secure the digital supply chain of solar devices and systems will be discussed.

cybersecurity↗
DOE OSTI2023

Spin-state gaps and self-interaction-corrected density functional approximations: Octahedral Fe(II) complexes as case study

Accurate prediction of a spin-state energy difference is crucial for understanding the spin crossover phenomena and is very challenging for density functional approximations, especially for local and semi-local approximations due to delocalization errors. Here, we investigate the effect of the self-interaction error removal from the local spin density approximation (LSDA) and Perdew–Burke–Ernzerhof generalized gradient approximation on the spin-state gaps of Fe(II) complexes with various ligands using recently developed locally scaled self-interaction correction (LSIC) by Zope et al. [J. Chem. Phys. 151, 214108 (2019)]. The LSIC method is exact for one-electron density, recovers the uniform electron gas limit of the underlying functional, and approaches the well-known Perdew–Zunger self-interaction correction (PZSIC) as a particular case when the scaling factor is set to unity. Our results, when compared with reference diffusion Monte Carlo results, show that the PZSIC method significantly overestimates spin-state gaps favoring low spin states for all ligands and does not improve upon density functional approximations. The perturbative LSIC-LSDA using PZSIC densities significantly improves the gaps with a mean absolute error of 0.51 eV but slightly overcorrects for the stronger CO ligands. Finally, the quasi-self-consistent LSIC-LSDA, such as coupled-cluster single double and perturbative triple [CCSD(T)], gives a correct sign of spin-state gaps for all ligands with a mean absolute error of 0.56 eV, comparable to that of CCSD(T) (0.49 eV).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Molecular Dynamics Simulations of Complexation of Am(III) with a Preorganized Dicationic Ligand in an Ionic Liquid

Preorganized ligands with imidazolium arms have been found to be highly selective in extracting Am(III) into ionic liquids (ILs), but the detailed structure and mechanism of the complexation process in the ionic solvation environment are unclear. Here, we carry out molecular dynamics simulation of the complexation of Am(III) with a preorganized 1,10-phenanthroline-2,9-dicarboxamide complexant (L) functionalized with alkyl chains and imidazolium cations in the butylmethylimidazolium bistriflimide ([BMIM][NTf 2 ]) IL. Both Am:L (1:1) and Am:L 2 (1:2) complexes are examined. In the absence of the ligand, Am(III) is found to be coordinated by six NTf 2 anions via nine O donors in the first solvation shell. In the Am:L complex, Am(III) is coordinated to the ligand via two O donors and four NTf 2 anions via seven O donors in the first coordination shell. In the Am:L 2 complex, Am(III) is coordinated to the two ligands via four O donors and four NTf 2 anions via five O donors. The imidazolium arms of the ligands play an important role in the secondary solvation environment by attracting NTf 2 anions closer to the metal center. As a result, we find that the binding free energy for the second L 2+ ligand is twice that for the first L 2+ ligand, making the Am:L 2 complex significantly more stable than the Am:L complex. This study highlights the multiple factors and tunability in using preorganized ligands with charged functional groups in an ionic solvation environment, which could hold the key to achieving desired selectivity in ion extraction efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Photocatalytic Transfer Hydrogenation in Water: Insight into Mechanism and Catalyst Speciation

Organometallic catalysts with strong metal-to-ligand charge-transfer (MLCT) optical transitions and reactive metal-hydride bonds provide opportunities for new excited-state reactivity. Toward this end, we have investigated photoinduced transfer hydrogenation reactions for a series of Cp*IrH complexes with functionalized bipyridyl ligands. Overcoming the baseline reactivity of this class of catalyst toward hydrogen evolution in aqueous media presents a major challenge for focusing this photochemical reactivity into desired transformations of more complex organic substrates. In this work, a photochemically induced aqueous ketone reduction catalyzed by [Cp*Ir(bpy)H][Cl] is reported and benchmarked to the competing hydrogen evolution reaction (HER). A detailed mechanistic study is conducted of the reduction of cyclohexanone with sodium formate delivering the reducing equivalent. Examining the kinetic profile of the cyclohexanone reduction revealed an unexpected induction period, suggesting a more complex underlying reaction mechanism where product selectivity was not simply a function of direct competition from a common excited-state reactive intermediate. The reaction kinetics were analyzed by variable time normalization analysis (VTNA), and the catalyst resting state was interrogated through operando light-emitting diode (LED) illumination H-1 NMR spectroscopy. Overall, these and other mechanistic studies provide insight into a photochemical reaction pathway to ketone reduction that is distinct from that previously reported for HER.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins

Here, we outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships - however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Chiral Spectroscopy of Nanostructures

Chirality is ubiquitous in the universe and in living creatures over detectable length scales from the subatomic to the galactic, as exemplified in the two extremes by subatomic particles (neutrinos) and spiral galaxies. Between them are living creatures that display multiple levels of chirality emerging from hierarchically assembled asymmetric building blocks. Not too far from the bottom of this pyramid are the foundational building blocks with chiral atomic centers on sp 3 carbon atoms exemplified by L-amino acids and D-sugars that are self-assembled into higher-order structures with increasing dimensions forming highly complex, amazingly functional, and energy-efficient living systems. The organization and materials employed in their construction inspired scientists to replicate complex living systems via the self-assembly of chiral components. Multiple studies pointed to unexpected and unique electromagnetic properties of chiral structures with nanoscale and microscale dimensions, including giant circular dichroism and collective circularly polarized scattering that their constituent units did not possess. To address the wide variety of chiral geometries observed in continuous materials, singular particles, and their complex systems, multiple analytic techniques are needed. Simultaneously, their spectroscopic properties create a pathway to multiple applications. For example, mirror-asymmetric vibrations at chiral centers formed by sp 3 carbon atoms lead to optical activity for the infrared (IR) wavelength regions. At the same time, understanding the optical activity in, for example, the IR region enables biomedical applications because multiple modalities of biomedical imaging and vibrational optical activity (VOA) of biomolecules are known for IR range. In turn, VOA can be realized in both absorption and emission modalities due to large magnetic transition moments, as vibrational circular dichroism (VCD) or Raman optical activity (ROA) spectroscopy. In addition to the VOA, in the range of longer wavelengths, lattice vibrational mode or phononic behavior occurs in chiral crystals and nanoassemblies, which can be readily detected by terahertz circular dichroism (TCD) spectroscopy. Meanwhile, chiral self-assembly can induce circularly polarized light emission (CPLE) regardless of the existence of chirality in coassembled fluorophores. The CPLE from self-assembled chiral materials is particularly interesting because the CPLE can originate from both circularly polarized luminescence and circularly polarized scattering (CPS). Furthermore, because self-assembled nanostructures often exhibit stronger optical activity than their building blocks owing to dimension and resonance effects, the optical activity of single assembled nanostructures can be investigated by using microscopic technology combined with chiral optics. Here, we describe the state of the art for spectroscopic methods for the comprehensive analysis of chiral nanomaterials at various photon wavelengths, addressed with special attention given to new tools emerging both for materials with self-organized hierarchical chirality and single-particle spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A structured RNA motif locks Argonaute2:miR-122 onto the 5’ end of the HCV genome

microRNAs (miRNAs) form regulatory networks in metazoans. Viruses engage miRNA networks in numerous ways, with Flaviviridae members exploiting direct interactions of their RNA genomes with host miRNAs. For hepatitis C virus (HCV), binding of liver-abundant miR-122 stabilizes the viral RNA and regulates viral translation. Here, we investigate the structural basis for these activities, taking into consideration that miRNAs function in complex with Argonaute (Ago) proteins. The crystal structure of the Ago2:miR-122:HCV complex reveals a structured RNA motif that traps Ago2 on the viral RNA, masking its 5’ end from enzymatic attack. The trapped Ago2 can recruit host factor PCBP2, implicated in viral translation, while binding of a second Ago2:miR-122 competes with PCBP2, creating a potential molecular switch for translational control. Combined results reveal a viral RNA structure that modulates Ago2:miR-122 dynamics and repurposes host proteins to generate a functional analog of the mRNA cap-binding complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF)

Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure—and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis , using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (Δ fadN ) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA- fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n 16:0 to a 15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

MSTor 2023 : A new version of the computer code for multistructural torsional anharmonicity, now with automatic torsional identification using redundant internal coordinates

The MSTor program is a computer program for calculating partition functions and thermodynamic functions of complex gas-phase molecules with multiple torsions; the multi-structural approximation with torsional anharmonicity (MS-T) can be used based on either a coupled torsional potential or an uncoupled torsional potential. The program can also carry out calculations in the multiple-structure local harmonic (MS-LH) approximation or multi-structural local quasiharmonic (MS-LQ) approximation or by the dual-level MS-T method. Furthermore, the program package includes eight utility codes that can be used as stand-alone programs to help the user to generate the input files for the code or to generate comparison results. The 2023 version of MSTor includes a new capability, namely automatic identification of torsional modes with redundant internal coordinates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Exploring the Relationship of Microstructure and Conductivity in Metal Halide Perovskites via Active Learning-Driven Automated Scanning Probe Microscopy

Electronic transport and hysteresis in metal halide perovskites (MHPs) are key to the applications in photovoltaics, light emitting devices, and light and chemical sensors. These phenomena are strongly affected by the materials microstructure including grain boundaries, ferroic domain walls, and secondary phase inclusions. Here, we demonstrate an active machine learning framework for “driving” an automated scanning probe microscope (SPM) to discover the microstructures responsible for specific aspects of transport behavior in MHPs. In our setup, the microscope can discover the microstructural elements that maximize the onset of conduction, hysteresis, or any other characteristic that can be derived from a set of current–voltage spectra. Furthermore, this approach opens new opportunities for exploring the origins of materials functionality in complex materials by SPM and can be integrated with other characterization techniques either before (prior knowledge) or after (identification of locations of interest for detail studies) functional probing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Atomic Layer Deposition for Materials-Based H2 Storage: Opportunities and Limitations

The transportation demands in our growing hydrogen (H2) economy requires robust storage systems. The current commercially implemented technology in fuel cell cars relies on the well-established technology of hydrogen gas compressed to 350-700 bar, depending on the application. The compressed gas tanks in use today are bulky and cost intensive. To address this challenge, material-based storage is one of the long-term alternatives considered and constitutes the focus of this talk. Material-based storage is broadly defined as hydrogen bound to solid materials, with its binding strength varying from physisorption to porous materials, such as zeolites and metal organic frameworks, to chemisorption in (complex) metal hydrides. The ultimate targets set by the U.S. Department of Energy for this technology include a system gravimetric capacity of 6.5 wt% and volumetric capacity of 40 g/L at 100 bar, operating temperatures ranging between -40 C and +40 C and adsorption/desorption timescales of < 5 min. Storage in the form of physisorbed or chemisorbed hydrogen has guided the materials research, which metal- organic framework and (complex) metal hydrides being the most promising materials classes. A variety of these materials have met one or more of the targets, but it has remained elusive for a single material system to meet all these stringent requirements. Nano-encapsulation and low-concentration chemical additives have previously been employed separately to overcome such challenges. Functionalization via atomic layer deposition (ALD), however, offers unique characteristics that make it suitable for both, nano-encapsulation and "doping" with low-concentration additives. This deposition technique has sub-monolayer thickness control, is highly conformal in high-surface area materials and is self-limiting, i.e., once the gas-phase precursor reacts with the available surface sites, the surface reactions stop. In this presentation, we will showcase examples where ALD, more generally vapor-phase functionalization, on (complex) metal hydrides and organic frameworks has improved the material properties for H2 storage. In our first study, Al2O3 was deposited on magnesium borohydride, Mg(BH4)2, at room temperature using trimethylaluminum (TMA) and water. From our findings, encouraging initial results were obtained: the H2 desorption temperature was lowered by 60-120 degrees C, the desorbed gravimetric H2 capacity at temperatures < 250 degrees C was doubled, and the desorption kinetics increased by a factor of ~6 compared to uncoated Mg(BH4)2. However, hydrolysis reactions caused by residual surface -OH groups from the ALD water-pulse degraded the sample substantially. Through this study, the use of TMA was observed to be highly reactive with the Mg(BH4)2 surface species, leading to the strategy of exposing the sample only to TMA. The relative mole fraction of the vapor-phase additive can be precisely controlled with the number of TMA pulses and pulse duration. By tuning these parameters, we show in our second study that 10 pulses of TMA at ambient conditions were able to decrease the H2 desorption temperature by ~100 degrees C while retaining <95 % of its H2 capacity. We applied this approach with other additives such as BBr3, TiCl4 and tetrahydrofuran, and demonstrate that this unique approach opens the door to a new class of molecular additives and catalysts which cannot easily be introduced with conventional mechano-chemical or solvent-based techniques for (complex) metal-hydrides. In the case of metal organic frameworks, ALD is a promising technique to functionalize the pores with metal atoms or functional groups able to tune the gas selectivity and binding energy, for which ~15 kJ/mol has been established as the optimal value for H2 storage in sorbent materials. Vapor-phase techniques such as ALD have numerous benefits over other functionalization tools for H2 storage materials opening innumerable opportunities to the field. To exploit these opportunities, the current limitations on room temperature and water-less ALD processes needs to be overcome which will greatly expand the possibilities of encapsulation and incorporation of additives for organic frameworks and (complex) metal hydrides.

atomic layer deposition↗
DOE OSTI2026

Beyond sequence similarity: toward function-based screening of nucleic acid synthesis

Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Growth of tetragonal PtO by molecular-beam epitaxy and its integration into β-Ga 2 O 3 Schottky diodes

We demonstrate the epitaxial growth of tetragonal platinum monoxide (PtO) on MgO, TiO 2 , and β-Ga 2 O 3 single-crystalline substrates by ozone molecular-beam epitaxy. We provide synthesis routes and derive a growth diagram under which PtO films can be synthesized by physical vapor deposition. A combination of electrical transport and photoemission spectroscopy measurements, in conjunction with density functional theory calculations, reveal PtO to be a degenerately doped p-type semiconductor with a bandgap of E g ≈ 1.6 eV. Spectroscopic ellipsometry measurements are used to extract the complex dielectric function spectra, indicating a transition from free-carrier absorption to higher photon energy transitions at E ≈ 1.6 eV. Using tetragonal PtO as an anode contact, we fabricate prototype Schottky diodes on n-type Sn-doped β-Ga 2 O 3 substrates and extract Schottky barrier heights of ϕ B > 2.2 eV.

Hensling, Felix V. E. [Cornell Univ., Ithaca, NY (↗
DOE OSTI2022

Illuminating the Photophysics of Oxygen Atom Transfer in Rare Earth Metal-Organic Complexes

Industrial separations of rare earth metals are reliant on selectivity based on ionic radii, which are time, energy, and resource consuming.1 The unique and discontinuous manifold of energy states associated with the f-electron configurations of the rare earth ions2 offer an opportunity to overcome some of these limitations by incorporating light into the separation process. Here, we use transient absorption spectroscopy to understand the differences in mechanism of light-initiated oxygen atom transfer (OAT) in yttrium (Y) and dysprosium (Dy) rare earth complexes. These metal-organic complexes are functionalized with hexfluoroacetyl-acetonate (hfac) and 4-methylmorpholine-N-oxide (NMMO). After light absorption in the presence of triphenyl phosphine (TPP), the NMMO in the Y-NMMO complex is replaced by the TPPO OAT reaction product. Because the Dy f-electron manifold is accessible to the ligand excited states, while there are no accessible states associated with f-electrons for Y, there are significant differences in reactivity. Transient absorption spectroscopy (TAS) was used to monitor changes after 340 nm photoexcitation of Dy/Y-NMMO or the product complex Dy/Y-TPPO. TAS is a pump-probe technique where a white light probe pulse is delayed relative to a visible pump pulse, which photoexcites a sample. Differences between the ground and excited states are monitored over time. With TAS, we access time scales from 100 fs-400 us to determine the photophysics of the complexes of interest. Photoexcitation of Y-NMMO (Fig. 1A) creates a broad photoinduced absorption (PIA) that evolves into a sharp positive feature over 4.2 ps centered at 450 nm. A secondary feature centered at 550 nm grows in with a 200 ps time constant and remains through the 5 ns time window of our experiment. Control experiments for Y-TPPO reveal that the feature at 450 nm is due to internal dynamics of the hfac ligand, while the 550 nm shoulder is due to the presence of the NMMO. Comparing kinetics at 550 nm for Y-NMMO and Dy-NMMO (Fig. 1B) shows that while Y exhibits a distinct growth in the NMMO feature, the Dy decays almost completely within 5 ns. Control experiments with Dy-TPPO prove that the ligand excited states centered on the hfac ligand are deactivated via energy transfer to the Dy manifold within 200 ps. This deactivation leads to significant differences in OAT reactivity between Y and Dy.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS↗
DOE OSTI2025

Leveraging dendritic complexity for neuromorphic computing

Abstract Beyond-von Neumann computing approaches are necessary to sustain the growth of microelectronics and the increasing appetite for artificial intelligence/machine learning algorithms. Neuromorphic computing is an emerging paradigm that takes inspiration from the brain to provide a path forward to improve the computational efficiency and computational density of next-generation computing architectures. In nature, we observe brains performing complex computations with a much smaller energy footprint than conventional computing approaches. Current neuromorphic systems are focused primarily on scalability, namely, increasing the number of computational units (neurons) and connections between units (synapses). However, for brain-like cognition and efficiency in next-generation computing hardware, we need increased complexity in function, as well as improved connection density for scalability. Here, we present our work that aims to incorporate dendrites for ‘compute-on-wire’ in neuromorphic architectures to increase the computational complexity (e.g. number of programmable parameters, nonlinear dynamics) as well as computational efficiency (energy/compute) of artificial neural networks (ANNs). We do this by showcasing neuromorphic dendrite elements that can be leveraged for various applications. We will present examples of neuroscience-inspired direction-selective circuits and an ANN with active dendrites leveraging shunting inhibition. We also demonstrate the benefits of using dendrites in deep neural networks. To conclude, we discuss how we can utilize emerging hardware devices in these systems and design next-generation neuromorphic architectures with dendrites.

Cardwell, Suma G. (ORCID:0000000226575545)↗
DOE OSTI2022

A critical comparison of CH∙∙∙π versus π∙∙∙π interactions in the benzene dimer: obtaining benchmarks at the CCSD(T) level and assessing the accuracy of lower scaling methods

In this study, we have established CCSD(T)/CBS (Complete Basis Set) limits for 3 stationary points on the benzene dimer potential energy surface, corresponding to the π∙∙∙π (parallel displaced or PD(C 2h ), minimum) and CH∙∙∙π (T-shaped or T(C 2v ), transition state) and tilted T-shaped (or TT(Cs), minimum) bonding scenarios considering both the structure and binding energy. The CCSD(T)/CBS binding energies are -2.65 ± 0.02 (PD), -2.74 ± 0.03 (T), and -2.83 ± 0.01 kcal mol -1 (TT). To this end, the CH∙∙∙π is ~0.2 kcal mol -1 stronger than the π∙∙∙π interaction, whereas the tilting of the CH donating benzene molecule with respect to the other benzene is worth 0.1 kcal mol -1 . As previously discussed in the literature, the MP2 level of theory does not provide a close match for either the energy or structure, yet the SCS-MP2 yields structures in excellent agreement with respect to the CCSD(T) result. It is found that the SCS-MI-MP2 also gives optimized structures very close to SCS-MP2 (within ~0.01 Å of the benchmark). Despite the closer match in structure, the spin-biased MP2 methods (SCS-, SCS-MI-, and SOS-MP2) incorrectly predict the relative stabilities of the isomers. That said, none of the spin biased MP2 methods offers a good compromise between energy and structure for the systems examined. Finally, the CCSD(T)/CBS benchmarks were used to assess the performance of 13 DFT functionals selected from different rungs of Jacob's ladder. Several functionals such as TPSS-D3, B3LYP-D3, B97-D, B97-D3, and B2PLYP-D3 provided a good description of the binding energies for both CH∙∙∙π and π∙∙∙π interactions, yielding values within 6% of the CCSD(T)/CBS benchmark values. Unlike the MP2 methods, these functionals correctly predict the relative stability of the PD(C 2h ) and T(C 2v ) dimers. Further, we find that there is no systematic improvement as Jacob's ladder is ascended (increased complexity of functional). The best functionals that result in a good compromise between structure and energy accuracy are B97-D3 and B2PLYP-D3 for both the CH∙∙∙π and π∙∙∙π interaction. Despite the impressive performance of these functionals, a challenge that remains is ensuring the transferability of these density functionals in accurately describing the interaction between dimers of larger aromatic molecules, the latter requiring high-level benchmarks for these systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structural and functional characterization of IgG- and non-IgG-based T-cell-engaging bispecific antibodies

Bispecific T-cell-engaging antibodies are a growing class of therapeutics with numerous molecules being tested in clinical trials and, currently, seven of them have received market approval. They are structurally complex and function as adaptors to redirect the cytotoxicity of T cells to kill tumor cells. T-cell-engaging bispecific antibodies can be generally divided into two categories: IgG/IgG-like and non-IgG-like formats. Different formats may have different intrinsic potencies and physiochemical properties, and comprehensive studies are needed to gain a better understanding of how the differences in formats impact on structural and functional characteristics. In this study, we designed and generated bispecific T-cell-engaging antibodies with IgG-like (DVD-Ig) and non-IgG (BiTE) formats. Both target the same pair of antigens (EGFR and CD3) to minimize the possible influence of targets on functional characterization. We performed a side-by-side comparison to assess differences in the physiochemical and biological properties of these two bispecific T-cell-engaging antibodies using a variety of breast and ovarian cancer cell-based functional assays to delineate the structural–functional relationships and anti-tumor activities/potency. We found that the Fc portion of T-cell-engaging bispecific antibodies can significantly impact antigen binding activity, potency, and stability in addition to eliciting different mechanisms of action that contribute the killing of cancer cells.

cluster of differentiation 3 (CD3)↗