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Results for “structural plasticity”

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At least 19 records

All sources NASA NTRS DOE OSTI

DOE OSTI2025

Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site

Abstract Thefralocus ofSalmonella entericaencodes five genes for metabolism of fructose‐asparagine, an Amadori product formed by condensation of asparagine with glucose. In the last step of this pathway, the FraB deglycase cleaves 6‐phospho‐fructose‐aspartate into glucose‐6‐phosphate and aspartate. In homology models, FraB forms a homodimer with two equivalent active sites located at the dimer interface. E214 and H230, two invariant residues essential for catalysis, project into each active site cleft from opposing subunits of the dimer. Here, we have determined six crystal structures of FraB, three of a variant containing an N‐terminal His 6 tag and two mutations needed for crystallization (hereafter referred to as WT′), two with additional mutations to active site residues (E214A and P232A), and one of a variant with C‐terminal residues 313–325 deleted. Surprisingly, in the WT′ FraB structure, the two catalytic residues, E214 (general base) and H230 (general acid), are positioned ~22 Å apart. In the E214A and C‐terminus‐truncated FraB variants, however, a conformational change in the E214‐residing helix brings E214 and H230* to ~7 Å (* indicates residue from the second protomer that creates the inter‐subunit catalytic center). The loop bearing H230 also exhibits significant variation, ranging from being completely disordered to adopting open or closed states, with the nearby P232* residue being eithercisortrans. The C‐terminal residues 313–325 form a flexible “C‐tail” that can be fully disordered, bind in the active site to block access of substrate, or angle across the active site to wrap across the other subunit of the dimer and potentially close over substrate. Collectively, these structures reveal that FraB is a conformational heterodimer with two chemically identical subunits that are constrained to adopt different structures as they come together for catalysis. This plasticity likely involves correlated opening and closure of the two active sites for their respective binding and release of substrates and ligands.

Biochemistry & Molecular Biology↗

DOE OSTI2024

A spatially-resolved model of neutron-irradiated tungsten coupling stochastic cluster dynamics and finite deformation plasticity

Structural materials used in nuclear reactors face severe degradation in mechanical properties, such as hardening and embrittlement. At the microscopic scale, this occurs due to creation and accumulation of irradiation-induced defects and their interaction with system dislocations. Although techniques exist which can model evolution of irradiation defects, for instance kinetic transport theory-based models, their interaction with mechanical deformation of the bulk material has not been investigated extensively. In this work, we demonstrate a novel spatially-resolved multiscale coupling between microscopic irradiation defect evolution, modeled using Stochastic Cluster Dynamics (SCD) and macroscopic mechanical deformation modeled using a finite-deformation plasticity model. SCD is used to determine the statistically averaged defect cluster spacing, dependent on operating conditions such as irradiation dose and temperature. This acts as an initial condition that governs the critical resolved shear stress of dislocation glide in the macroscopic plasticity model. This framework is used to predict mechanical behavior in post-mortem test of irradiated Tungsten samples, which has found its importance as structural material used in nuclear reactors. The results obtained using the coupled approach are in good agreement with experimental data of uniaxial tension tests. The model is able to capture the effect of temperature and irradiation dose on the material hardening. Two methods are proposed to estimate hardness – using Tabor's Law relating uniaxial yield stress to hardness and from flat-punch simulations. The results are in reasonable agreement with hardness data from micro-indentation experiments of irradiated Tungsten samples. Finally, the model is also able to reveal microstructural details such as spatial variation in defect density and local stress.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF‐Trap

The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Structural characterization of influenza group 1 chimeric hemagglutinins as broad vaccine immunogens

Chimeric hemagglutinins (cHA) appear to be promising for the design and development of universal influenza vaccines. Influenza A group 1 cHAs, cH5/1, cH8/1, and cH11/1, comprising an H1 stem attached to either an H5, H8, or H11 globular head, have been used sequentially as vaccine immunogens in human clinical trials and induced high levels of broadly protective antibodies. Using X-ray crystallography and negative-stain electron microscopy, we determined structures of cH5/1, cH8/1, and cH11/1 HAs in their apo (unliganded) and antibody Fab-bound states. Stem-reactive antibodies 3E1 and 31.b.09 recognize their cognate epitopes in cH5/1, cH8/1, and cH11/1 HAs. However, with cH5/1, the head domains are rotated by 35 to 45° around the threefold axis of the HA trimer compared to native HA with a more splayed-open conformation at the stem base. cH11/1 with 3E1 is structurally more native-like but resembles cH5/1 with 31.b.09, whereas cH8/1 with 31.b.09 exhibited a range of closed-to-open stem configurations with some separation of head and stem domains. Furthermore, all of these group 1 cHAs effectively bound a broad head trimer interface antibody and other broad stem antibodies. Thus, the cHAs exhibit structural plasticity without compromising the stem and head trimer interface epitopes for elicitation of influenza A group 1 cross-reactive antibodies.

Science & Technology - Other Topics↗

DOE OSTI2025

Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study

The structural analysis of catechol 1,2 dioxygenase from Stutzerimonas frequens GOM2, SfC12DO, was conducted using various structural techniques. SEC-SAXS experiments revealed that SfC12DO, after lyophilization and reconstitution processes, can form multiple enzymatically active oligomers, including dimers, tetramers, and octamers. These findings differ from previous studies, which reported active dimers in homologous counterparts with available crystallographic structures, or trimers observed exclusively in solution for SfC12DO and its homologous isoA C12DO from Acinetobacter radioresistens under low ionic strength conditions. In some cases, tetramers were also reported, such as for the Rodococcus erythropolis C12DO. The combined results of Small-Angle X-ray Scattering, Dynamic Light Scattering, and Transmission Electron Microscopy experiments provided additional insights into these active oligomers’ shape and molecular organization in an aqueous solution. These results highlight the oligomeric structural plasticity of SfC12DO, proving that it can exist in different oligomeric forms depending on the physicochemical characteristics of the solutions in which the experiments were performed. Remarkably, regardless of its oligomeric state, SfC12DO maintains its enzymatic activity even after prior lyophilization. All these characteristics make SfC12DO a putative candidate for bioremediation applications in polluted soils or waters.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Structural properties of plastically deformed SrTiO 3 and KTaO 3

Dislocation engineering has the potential to open new avenues toward the exploration and modification of the properties of quantum materials. Strontium titanate (SrTi⁢O 3 , STO) and potassium tantalate (KTa⁢O 3 , KTO) are incipient ferroelectrics that show metallization and superconductivity at extremely low charge-carrier concentrations and have been the subject of resurgent interest. These materials also exhibit remarkable ambient-temperature ductility, and thus represent exceptional platforms for studies of the effects of deformation-induced dislocation structures on electronic properties. Recent work on plastically deformed STO revealed an enhancement of the superconducting transition temperature and the emergence of local ferroelectricity and magnetism near self-organized dislocation walls. Here, in this work, we present a comprehensive structural analysis of plastically deformed STO and KTO, employing specially designed strain cells, diffuse neutron and x-ray scattering, Raman scattering, and nuclear magnetic resonance (NMR). Diffuse scattering and NMR provide insight into the dislocation configurations and densities and their dependence on strain. As in the prior work on STO, Raman scattering reveals evidence for local ferroelectric order near dislocation walls in plastically deformed KTO. Our findings provide valuable information about the self-organized defect structures in both materials, and they position KTO as a second model system in which to explore the associated emergent physics.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Unified Stress-Strain Model for Plasticity to the Structural Instability

A unified model for the work hardening Θσ Θ(σ) and stress-strain σε σ(ε) behavior is presented that accounts for deformation under tensile loading, from the onset of yielding at the proportional limit up to the ultimate strength as defined at the structural instability. The origin of this approach is based on a negative exponential formulation for an asymptotic-curvilinear work-hardening model that accounts for the rapid strengthening of metals as well as the continuation of steady-state deformation to the instability.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Structure-dependent mechanisms for plastic degradation in the marine environment

The visible and invisible accumulation of waste plastic in our oceans is a consequence of rapidly increasing inputs and very slow degradation rates. In general, this combination of effects results in long residence times. Nevertheless, the abiological degradation rate of a specific synthetic plastic varies widely, depending on its structural characteristics at the molecular, mesoscopic, and macroscopic levels. This chapter summarizes factors that determine these rates of degradation, and describes their principal mechanisms, for several of the major types of waste plastic found in the oceans. Mechanical forces cause cracking and flaking that break macroplastics into microplastics and even smaller fragments with increasing surface-to-volume ratios. Chemical degradation rates increase with surface area, influenced by intrinsic variations in crystallinity and the presence of additives, as well as extrinsic factors such as temperature, pH, and UV light intensity. Since polyolefin-based plastics are less dense than seawater and lack hydrolysable bonds in their polymer backbones, they accumulate close to the surface of the ocean where photo-oxidation is the principal cause of C–C bond cleavage in the polymer backbone. In contrast, polyesters and polyamides are denser than seawater and they sink, experiencing less exposure to solar irradiation. However, they can also degrade by slow hydrolysis of the C–O or C–N bonds intrinsic to the polymer structures.

Maciulis, Nicholas A.↗

DOE OSTI2025

Towards a multiscale approach for understanding irradiation induced swelling and creep in 316 stainless steels - A coupled cluster dynamics and crystal plasticity approach

Structural materials undergo mechanical degradation, in part due to irradiation-induced swelling and creep, under nuclear reactor conditions. While swelling results from the migration and clustering of irradiation-induced atomic-scale mobile defects, the interaction of mesoscale dislocations with these defects causes creep deformation. A coupled crystal plasticity (CP) and mean-field cluster dynamics (CD) approach is presented to investigate the effect of irradiation on the long-term mechanical behavior of 316 stainless steel, which are under consideration for use in nuclear reactors. The temporal evolution of Frenkel pairs and extended defect population, under a chosen irradiation flux and temperature, is predicted using the CD model. The impact of the irradiation defects on the stress state, and the resulting dislocation-mediated inelastic deformation, is modeled concurrently with the CP model. The inelastic deformation is irradiation flux dependent, and early-stage defect evolution determines the later-stage mechanical behavior in 316 stainless steel.

36 - MATERIALS SCIENCE↗

DOE OSTI2026

Emerging hierarchical dislocation structures: Insights from scanning electron microscopy-electron backscatter diffraction in situ tensile testing and multifractal analysis

Understanding the evolution of dislocation structures during plastic deformation is critical for predicting the mechanical performance of metallic materials. In this work, we applied in situ scanning electron microscopy/electron backscatter diffraction tensile testing combined with multifractal (MF) analysis to assess deformation-induced dislocation structure evolution in solution-annealed 304 L stainless steel, both in its as-received and neutron-irradiated states (5.4 displacements per atom). The analysis of kernel average misorientation patterns revealed the formation of hierarchical dislocation arrangements that exhibit clear MF scaling behavior. Despite pronounced visual differences between nonirradiated and irradiated specimens—most notably, the appearance of dislocation channels after irradiation—the singularity spectra suggest that both conditions give rise to similar underlying hierarchical structures. MF analysis provides a quantitative measure of the spatial complexity and self-organization of dislocation patterns, highlighting the accelerated emergence and evolution of the dislocation structures in irradiated polycrystalline materials, as well as the limitation of their spatial extent. The findings indicate that irradiation not only modifies microstructure but also alters correlation-driven dislocation organization. More generally, they demonstrate that MF analysis is a powerful tool for probing mesoscale deformation mechanisms.

Dislocation structures↗

DOE OSTI2025

Shaping Peptide Assemblies Using Multifaceted Cyclic Tectons

Constructing distinct biomacromolecular assemblies typically necessitates target-specific selection and engineering of building blocks alongside optimization of assembly conditions. The challenge lies in achieving diverse morphological outcomes using simple, shared modules under identical conditions, a hallmark of natural systems that remains elusive in synthetic approaches. Here, in this work, we present a molecular scaffold-based strategy to instruct the coassembly of the same set of peptides into a variety of nanostructures across multiple dimensions. We create trifaceted cyclic scaffolds to manipulate two pairs of dimeric coiled-coil peptides prior to coassembly. These scaffolds, with addressable and orthogonal modules, allow controlled exposure of their cohesive faces, directing the formation of nanotriangles and fibrillar and lamellar assemblies. By tuning interpeptide arrangements that dictate scaffold geometry, we construct nonstraight fibrils with tunable curvature, which are rarely observed before. Notably, these scaffolds exhibit plasticity in adapting the sizes and orientations of cohesive faces to different assembly morphologies. The resultant nanostructures are consistent with the design and simulation results, demonstrating the reliability and predictability of this approach. Multifaceted cyclic scaffolds bridge the intellectual and physical gaps between building peptides and assemblies, holding promise for endowing various existing assembly systems with high tunability and versatility.

assembly morphology↗

DOE OSTI2026

Topology-Informed Design Rules for Deconstructable Thermoset Copolymer Networks

Existing models of thermoset deconstruction facilitated by incorporating cleavable comonomers rely on a mean-field reverse gel point paradigm, which predicts network dissolution once cleavable bonds reach a critical stoichiometric threshold, but does not account for where those bonds reside within the network architecture. Using reactive coarse-grained molecular dynamics simulations coupled with graph-theoretic analysis, we extend this stoichiometric picture to show that deconstructability is governed by the curing-imprinted network topology rather than stoichiometry alone. This topological organization is hierarchical: at the local scale, the elastic effectiveness of cross-link junctions determines which cross-links constitute the load-bearing scaffold; at the mesoscale, the cross-linking rate kinetically templates that scaffold into topologically modular communities─densely cross-linked clusters connected by sparse bridging strands that sustain network connectivity. Using betweenness centrality to identify nodes that disproportionately lie on intercommunity shortest paths, we demonstrate that effective deconstruction of the network into macromolecular fragments requires cleavable comonomers to intercept these high-centrality bridging strands. We further find that under uniform, disassortative comonomer incorporation, this topological requirement provides a mechanistic basis for extending the reverse gel point to incorporate network topology. We also show that modularity imposes a fundamental limit on fragment uniformity that persists even when the centrality requirement is met. Finally, we demonstrate that chain stiffness provides a nearly independent lever to suppress mechanically redundant cross-links and raise the glass transition temperature without significantly altering the deconstruction outcome. Together, these findings reframe the thermoset design space around network topology and provide actionable guidelines for engineering thermoset copolymers with predictable deconstructability and targeted thermomechanical performance.

coarse-grained molecular dynamics↗

DOE OSTI2026

Chain entanglements enable regeneration of high-performance thermosets

Thermoset plastics underpin structural materials, electronics and transportation, yet the permanent covalent networks that prevent flow and provide dimensional stability also make them difficult to recycle without sacrificing performance. In this work we show that high-performance thermosets can be built around dense chain entanglements, the physical interlacing of long polymer strands, rather than dense permanent crosslinks, with only a small number of selectively cleavable junctions preserving connectivity. Long, rigid, entangled polyolefin backbones generated by frontal polymerization form glassy polymers with high stiffness, high toughness and excellent creep suppression yet can be fully deconstructed into soluble, linear oligomers. Varying oligomer length and end-group chemistry enables their reuse as re-entangling building blocks that regenerate thermosets with thermal and mechanical properties that remain unchanged across generations. The strategy further extends to high-temperature fibre-reinforced composite matrices and additively manufactured structures, establishing chain entanglement as a design principle for durable, regenerable thermosets.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction

Abstract The Rev response element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 (human immunodeficiency virus type 1) infection. However, the structures and mechanisms underlying this process remain largely unknown. Here, we determined the crystal structure of the HIV-1 RRE stem-loop II (SLII), revealing a unique three-way junction architecture in which the base stem (IIa) bifurcates into the stem-loops (IIb and IIc) to compose Rev binding sites. The crystal structures of various SLII mutants demonstrated that while some mutants retain the same “compact” fold as the wild type, other single-nucleotide mutants induce drastic conformational changes, forming an “extended” SLII structure. Through in vitro Rev binding assays and Rev activity measurements in HIV-1-infected cells using structure-guided SLII mutants designed to favor specific conformers, we showed that while the compact fold represents a functional SLII, the alternative extended conformation inhibits Rev binding and oligomerization and consequently stimulates HIV-1 RNA nuclear export dysfunction. The propensity of SLII to adopt multiple conformations as captured in crystal structures and their influence on Rev oligomerization illuminate emerging perspectives on RRE structural plasticity-based regulation of HIV-1 nuclear export and provide opportunities for developing anti-HIV drugs targeting specific RRE conformations.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Tailoring the Properties of Chemically Recyclable Polyethylene‐Like Multiblock Polymers by Modulating the Branch Structure

Abstract Developing plastics that fill the need of polyolefins yet are more easily recyclable is a critical need to address the plastic waste crisis. However, most efforts in this vein have focused on high‐density polyethylene (PE), while many different types of PE exist. To create broadly sustainable PE with modular properties, we present the synthesis, characterization, and demonstration of materials applications for chemically recyclable PE‐like multiblock polymers prepared from distinct hard and soft blocks using ruthenium‐catalyzed dehydrogenative polymerization. By altering the branching pattern within the soft blocks, a series of PE‐like multiblock polymers were synthesized with tunable glass transition temperatures ( T g ) while maintaining consistent high melting temperatures ( T m ). A clear U‐shape trend between T g and mechanical properties was found, showcasing their potential as sustainable materials with tailored properties spanning commercial linear low‐density polyethylene (LLDPE) and low‐density polyethylene (LDPE). These materials offer adjustable adhesive strength to metal and demonstrate chemical recyclability and selective depolymerization in mixed plastic streams, promoting circularity and separation.

Zhao, Yucheng↗

DOE OSTI2024

Tailoring the Properties of Chemically Recyclable Polyethylene‐Like Multiblock Polymers by Modulating the Branch Structure

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Investigating PVC polymer–plasticizer interactions with atomistic MD simulations and potential of mean force calculations

For this work, atomistic molecular dynamics (MD) simulations coupled with potential of mean force (PMF) calculations were employed to investigate the interactions between PVC polymer chains containing 6–20 repeating units and various plasticizers, with the goal of identifying potential replacements for the toxic plasticizer di(2-ethylhexyl)phthalate (DEHP) used in blood bags. The selected plasticizers belong to various chemical families, such as orthophthalates, citrates, adipates, and the terephthalate DEHT. Both the polymer and the plasticizers lack ionizable groups, and their interactions are primarily governed by van der Waals and electrostatic forces. A model correlating PMF profiles with interaction forces was developed and validated across polyvinyl chloride (PVC) polymers of different lengths and all investigated plasticizers. This model provides insight into how structural variations in plasticizers influence their respective PMF values. The study ranks the investigated plasticizers based on binding affinity, identifying TOTM (tris(2-ethylhexyl) trimellitate, TEHTM), BTHC (butyryl trihexyl citrate, Citroflex B-6), ATHC (acetyl trihexyl citrate, Citroflex A-6, CA-6), and DEHT (bis(2-ethylhexyl)terephthalate, DOTP/DEHTP) as promising alternatives for further investigation. This comprehensive study encompasses PVC polymers of four different lengths and 14 plasticizers, with all data averaged over 30 independent simulations. The approach provides a deeper understanding of molecular interactions, enabling the tailoring of polymer–plasticizer systems for diverse applications, including extractables and leachables, with relevance spanning materials science to biomedical engineering, and also serves as a basis for developing coarse-grained simulation protocols. Overall, this study provides valuable insights for designing safer and more efficient plasticizer substitutes and is well supported by other studies.

Shet, Sai Athmeeya G. [Sri Sathya Sai Institute of↗

DOE OSTI2024

The Effects of Polyolefin Structure and Source on Pyrolysis-Derived Plastic Oil Composition

Seven types of plastics were pyrolyzed in a fluidized bed reactor: post-consumer recycled (PCR) high-density polyethylene (HDPE), PCR polypropylene (PP), virgin resins of varying molecular weights of HDPE, virgin resins of low-density polyethylene (LDPE), linear low-density polyethylene (LLDPE), and (PP). Pyrolysis produced non-condensable gases (C1-C3), liquid phase products (C4-C40), and solids (C40+ and chars), with alkane, alkene, alkadiene, aromatic, and multi-cycloaromatics as the predominant compounds. Polymer structure had the greatest impact on product distribution, with minimal influence from molecular weight. Branches in polyethylene (PE) acted as thermal defects initiating degradation. Higher branch density in PE led to increased concentrations of aromatics, branched alkanes, and internal alkenes. PP and PE exhibited distinct degradation mechanisms, with PP requiring less energy for decomposition and yielding more oil. Here, pyrolysis oil from PCR HDPE and PCR PP contained a higher proportion of branched compounds. Additives in PCR plastics may promote isomerization during pyrolysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗