Engineering PapersSearch

SEARCH · Engineering Papers

Results for “structure-function”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

31 records · Page 2

Microscopic Imprints of Learned Solutions in Tunable Networks

In physical networks trained using supervised learning, physical parameters are adjusted to produce desired responses to inputs. An example is an electrical contrastive local learning network of nodes connected by edges that adjust their conductances during training. When an edge conductance changes, it upsets the current balance of every node. In response, physics adjusts the node voltages to minimize the dissipated power. Learning in these systems is therefore a coupled double-optimization process, in which the network descends both a cost landscape in the high-dimensional space of edge conductances and a physical landscape—the power dissipation—in the high-dimensional space of node voltages. Because of this coupling, the physical landscape of a trained network contains information about the learned task. Here, we derive a structure-function relation for trained tunable networks and demonstrate that all the physical information relevant to the trained input-output relation can be captured by a tuning susceptibility, an experimentally measurable quantity. We supplement our theoretical results with simulations to show that the tuning susceptibility is correlated with functional importance and that we can extract physical insight into how the system performs the task from the conductances of highly susceptible edges. Our analysis is general and can be applied directly to mechanical networks, such as networks trained for protein-inspired function such as allostery.

36 MATERIALS SCIENCE

Secure biosystems design in Saccharomyces cerevisiae establishes effective biocontainment strategies and mechanisms of escape

The widespread application of recombinant DNA and synthetic biology approaches for microbial metabolic engineering pursuits has motivated the development of biocontainment strategies, targeting safe and secure deployment of genetically modified microorganisms (GMMs). However, the design rules and mechanistic drivers governing biocontainment efficacy, as well as impacts of biocontainment upon microbial fitness, remain to be comprehensively evaluated, hindering predictive design and application of these strategies. We have developed a platform for high-resolution analysis of a transactivated kill switch in laboratory and industrial strains of Saccharomyces cerevisiae to assess modes of biocontainment escape and establish design rules for development of kill switch systems in diverse microbes. A camphor-regulated, RelE toxin system was systematically deployed to assess the impacts of differential kill switch copy number and ploidy in laboratory vs industrial strains. CRISPR-mediated integration of the biocontainment system at various loci revealed rapid escape events driven, in part, by mutations to both the Cam-transactivator (cam-TA) and RelE toxin. Genetic engineering enabled recapitulation of escape phenotypes, confirming mechanisms of escape and establishing structure-function relationships in the cam-TA system. Interestingly, genomic resequencing of escape mutants also revealed a series of off-target mutations, implicating additional modes of kill switch escape. Multi-copy integration of the kill switch system mitigated these effects by orders of magnitude, without compromising the biosynthetic capacity of the microbes, but proved insufficient to establish sustained biocontainment. The resultant data define a series of key design rules for next-generation biocontainment strategies and add to a growing foundational knowledge base targeting establishment of secure biosystems designs.

59 BASIC BIOLOGICAL SCIENCES

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology

A Bottom-Up Approach to Rational Design of Crystalline Materials: Investigation of Vibronic Coherences Underlying Exciton Dynamics in Semiconductors

In this project we uncovered structure-function relationships of donor-acceptor co-crystals used to develop next-generation optoelectronic devices. Unraveling the photodynamics of molecular crystalline materials poses many challenges for spectroscopy due to broad, overlapping features representing numerous underlying dynamical processes. This leads researchers to make many assumptions about the dynamics of a system in choosing an appropriate kinetic fitting model. Computationally, electronic structure methods are either prohibitively expensive or underdeveloped for computing the excited state structure of molecular materials, especially states that exhibit charge transfer. Researchers must therefore perform calculations of excited electronic states using truncated models of molecular materials. Here we present a joint experimental-theoretical approach to bridging the gap between the photodynamics of a molecular material and its constituent molecules. We focus our efforts on quantifying the timescales and mechanisms of photoexcitation in donor-acceptor co-crystals and donor-acceptor dimers where the lowest-lying excited state is characterized by charge transfer from the donor to the acceptor. We employ ultrafast UV pump, UV-Vis probe transient absorption spectroscopy to unravel the time-resolved spectroscopic signatures of the photodynamics in both the crystalline material and donor-acceptor dimers in solution. We perform electronic structure and excited state dynamics calculations of the dimers to inform kinetic fitting models and assign the spectral features. The photodynamics of the crystal vs. dimer systems have many similarities, enabling unprecedented insights into the formation and evolution of charge transfer excitons in the crystalline systems.

36 MATERIALS SCIENCE

Proton Spin from Small-x With Constraints from the Valence Quark Model

We apply the valence quark model to constrain the non-perturbative initial condition for the small-x helicity evolution. The remaining free parameters are constrained by performing a global analysis to the available polarized small-x deep inelastic scattering data. A good description of the world data is obtained with only 8 free parameters. The model parameters are tightly constrained by the data, allowing us to predict the proton polarized structure-function to be negative at small x. Furthermore, we obtain the small-x quark and gluon spins, depending on the applied running coupling prescription.

Adamiak, Daniel [Thomas Jefferson National Acceler

Uniting Theory and Experiment to Deliver Flexible MOFS for Superior Methane (NG) Storage

The objective of the project was to use previous insights developed through synthesis and quantitative modeling of rigid metal–organic frameworks (MOFs) in an established synergistic theoretical/experimental team to create, modify, and evaluate flexible MOFs (FlexMOFs) for natural gas (NG) storage and release at practically useful pressures and transform the NG storage economy. The goal was reduced pressure absorbed natural gas (ANG) FlexMOF storage at operating pressures less than 100 bar with physisorption exploiting the favorable thermodynamics and kinetics of flexible porous material opening in response to adsorption. Hydrogen behavior in this context was also considered. The specific aim of the project was to design and develop a standard computational modeling methodology for, first, detailed atomistic retrodiction of FlexMOF gating behavior and ultimately prediction of the effects of functionalization and/or substitution on structural transitioning. The project was also geared towards the establishment of the interaction of methane with the framework and binding sites using modeling and the FlexMOF will be both internally and external validated as a SMART metric. This has value to the scientific community both from the obvious standpoint of providing a better understanding of the promising test case systems (CdIF-13 and the MIL-53(Al) series of MOFs), but also in providing an avenue of obtaining insight into these FlexMOF systems in general, which is of particular interest given the tendency of structure-function correlation to lag behind synthesis methodology (making the latter a hit or miss proposition for applications). This gap remains significant for FlexMOF systems whose gate opening behaviors complicate computational examination. The computational methodologies are relatively inexpensive in terms of both money and computational resources enhancing the general viability of these methodologies. The ultimate gain to the public will be in the application of these techniques to design systems for natural gas storage and use to cut down on green-house emissions.

03 NATURAL GAS

Cross-species analysis of FcγRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque

Introduction Antibodies play a critical role in immunity in part by mediating clearance of pathogens and infected cells by antibody-dependent cellular phagocytosis (ADCP) through engagement of Fc gamma receptors (FcγRs) on innate immune cells. Among these, FcγRIIa (CD32a) is a key activating receptor expressed on macrophages, dendritic cells, and other antigen-presenting cells. Its affinity for IgG and ability to mediate ADCP is influenced by allelic polymorphisms. In humans, a single amino acid polymorphism at position 131, where histidine (H) is substituted with arginine (R), leads to decreased IgG1 and IgG2 subclass binding affinity and, consequently, lower efficiency of phagocytic responses. Rhesus macaques ( Macaca mulatta ), which are widely used as nonhuman primate models, exhibit a similar polymorphism at position 131 of FcγRIIa, but with arginine replaced by proline (P). Here, we investigated structure-function relationships associated with the FcγRIIa polymorphism at position 131 in both species, specifically with respect to IgG1 and IgG2. Methods We determined the structures of complexes formed by each variant with IgG1 Fc and those formed by the higher affinity variant with IgG2 Fc for both species by x-ray crystallography and linked these structures to affinity and activity using SPR and an ADCP assay. We also determined the structure of human inhibitory FcγRIIb (CD32b) in complex with IgG1 Fc by x-ray crystallography. Results Through analysis of these structures, our studies reveal that FcγRIIa engagement is minimally influenced by Fc glycan composition, distinguishing it from FcγRIIIa whose affinity is strongly influenced by glycan-composition. Comparative structures of human and macaque FcγRIIa variants demonstrate species- and allele-specific differences in Fc binding, but our functional assays showed only minimal allele-specific effects in humans. In contrast, allele-specific effects in macaques were highly significant; the macaque P 131 variant showing uniformly reduced IgG affinity. Conclusion These insights highlight fundamental interspecies and allelic distinctions that are critical for interpreting FcγRIIa-mediated effector functions in macaque models and for optimizing translational antibody and vaccine design.

Tolbert, William D.

Current understanding of Oxidative Coupling of Methane (OCM) reaction over supported Mn-Na 2 WO 4 catalysts

This perspective reviews the current understanding of the Oxidative Coupling of Methane (OCM) reaction over the supported Mn-Na 2 WO 4 /SiO 2 catalyst, with a focus on recent insights gained from state-of-the-art in-situ and operando spectroscopic characterization and chemical probe experiments under controlled environments. The supported Mn-Na 2 WO 4 /SiO 2 catalyst exhibits dynamic structural changes during the OCM reaction, involving multiple reactive lattice and adsorbed oxygen species, each associated with different oxide phases. These oxygen species play distinct roles in various steps of the OCM mechanism. The catalytic active sites for activation of CH 4 are associated with isolated surface Na-WO x sites on the SiO 2 support and the role of surface MnO x sites on SiO 2 is to oxidatively dehydrogenate C 2 H 6 to C 2 H 4 . Furthermore, this paper provides a detailed discussion of these roles and also introduces new experimental data from Temporal Analysis of Products (TAP) studies to clarify the ongoing debate in the literature regarding the contributions of lattice versus adsorbed oxygen species in OCM reaction product formation. Additionally, recommendations are offered for optimizing the performance of supported Mn-Na 2 WO 4 /SiO 2 catalysts to enhance CH 4 activation and C 2 product selectivity.

03 - NATURAL GAS

Thermally Stable Co@C3N4 Single-Atom Catalysts for CO Oxidation: Atomic-Level Insights into Structure and Activity

Single Co atoms supported on C3N4 (Co@C3N4) have demonstrated high activity and selectivity in photocatalysis. However, the investigation of structure–function relationships and reaction mechanisms under photocatalytic conditions is very challenging due to the complex conditions of light absorption, charge transfer, and catalysis. In this study, we employed thermal CO oxidation as a prototypical probe reaction to benchmark the intrinsic catalytic performance and track the active-site evolution of Co@C3N4. Single Co atoms were identified and shown to be the catalytically active sites for CO oxidation based on control experiments and isotope-labeling experiments. The Co sites remained atomically dispersed before, during, and after the reaction with temperatures up to 400 °C, as established by in situ X-ray absorption fine structure (XAFS) combined with density functional theory (DFT), FDMNES simulations, and dynamic-time-warping (DTW)-assisted X-ray absorption near edge structure (XANES) matching. Together with theoretical calculations, the integrated analysis reveals a stable coordination environment under reaction conditions, which correlates with sustained activity, establishing Co@C3N4 single-atom catalysts as thermally stable CO oxidation catalysts. Beyond these findings, the current study provides a workflow for unambiguously assigning active sites in Co@C3N4 for thermal CO oxidation. This workflow will aid the understanding of their behavior in photocatalysis in the future, where light-driven dynamics obscure direct structure–function links. Notably, this study provides fundamental insights for the rational design of robust single-atom catalysts and a foundation for the broader application of Co@C3N4 catalysts in oxidation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Rubisco kinetic acclimation at the holoenzyme level

Kinetic acclimation enables proteins to adjust their activity in response to environmental perturbations. For the CO 2 -fixing enzyme Rubisco, kinetic acclimation may be conferred by its small subunits. Plants express multiple small subunits and vary their expression with temperature. Here, we demonstrate that different small subunits can bind to the same Rubisco to form a heterogeneous holoenzyme. These small subunits had distinct kinetic effects which aligned with changes in holoenzyme structure and stability. Our findings indicate that small subunits enable Rubisco kinetic acclimation via manipulation of flexibility. By assembling a more rigid active site in higher temperatures and a more flexible one in lower temperatures, plants maximize the efficiency of their Rubisco, and thus photosynthesis, over a wide range of temperatures.

CO2 fixation

In anaerobic reactors the microbial community structure depends on feed type, with no “keystone” species tied to COD removal

Two-stage anaerobic digestion (AD) systems provide treatment for high strength wastewater with high stability and performance. Encapsulation technology can intensify AD to facilitate the separation of the solids retention time from the hydraulic retention time (HRT), offering lower HRTs, smaller reactors, and high effluent quality. To support successful deployment, however, the encapsulated community must contain all the needed microorganisms for successful treatment and be flexible enough to treat a variety of wastewaters. Here, a two-stage system was investigated in which microbial cultures were enriched on various high-strength wastewaters in suspended flow-through systems to determine how feed type influenced performance and microbial community structure. The hypothesis was that specific genera, or so-called “keystone species” would positively correlate to organic carbon degradation for a given feed, enabling construction of a well-functioning community for encapsulation. Results showed that the number of total bacteria (as 16S rRNA gene copies) did not correlate to soluble chemical oxygen demand (sCOD) removal, indicating that the community structure and/or members were important for good performance. Results also showed that feed type strongly influenced carbon removal and microbial community structure for 1st-stage fermenting communities, but not 2nd-stage methanogenic communities. In this study, the “core” community members were defined as organisms common to all of either the 1st- or 2nd-stage reactors irrespective of the feed they received and were present in at least 50% of the samples throughout the entire experiment. “Unique” community members were specific to a single feed, and hence, only present in either the 1st- or 2nd-stage reactors receiving that feed. In both 1st- and 2nd-stage communities, only one core genera and no unique genera were positively and significantly correlated to sCOD removal. Verification experiments performed with encapsulated communities showed that organisms identified in flow-through system and correlated with carbon degradation, though not significantly, seemed to be important for performance. Our results suggest that one cannot construct a community containing specific populations in lieu of enrichment. Nevertheless, a single diverse encapsulated anaerobic community should provide good (>80%) carbon removal when fed a variety of influents, if time is provided for enrichment after deployment.

54 ENVIRONMENTAL SCIENCES

Structural insights into binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean

Tetrahydrofolate and its derivatives participate in one-carbon transfer reactions in all organisms. The cellular form of tetrahydrofolate (THF) is modified by multiple glutamate residues and polyglutamylation plays a key role in organellar and cellular folate homeostasis. In addition, polyglutamylation of THF is known to increase the binding affinity to enzymes in the folate cycle, many of which can utilize polyglutamylated THF as a substrate. Here, we use X-ray crystallography to provide a high-resolution view of interactions between the enzyme serine hydroxymethyltransferase (SHMT), which provides one carbon precursors for the folate cycle, and a polyglutamylated form of THF. Our 1.7 Å crystal structure of soybean SHMT8 in complex with diglutamylated 5-formyl-THF reveals, for the first time, a structural rearrangement of a loop at the entrance to the folate binding site accompanied by the formation of novel specific interactions between the enzyme and the diglutamyl tail of the ligand. Biochemical assays show that additional glutamate moieties on the folate ligand increase both enzyme stability and binding affinity. Together these studies provide new information on SHMT structure and function and inform the design of anti-folate agents.

59 BASIC BIOLOGICAL SCIENCES