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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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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.

archaea↗
DOE OSTI2018

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

Herein, we present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases. Published by AIP Publishing.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Decoupling Thin Film CdTe Growth from Packaging: Toward Record Specific Power in Low Cost Polycrystalline PV

There are critical material and scientific barriers to producing high efficiency, flexible, lightweight solar cells that maximize specific power in a cost-effective manner. III-V solar cells have produced the highest specific power of any photovoltaic technology due to their extremely high efficiency, however, they are also among the most expensive to produce. This work explores a novel lift-off approach with thin-film solar cells, particularly CdTe, to achieve high specific power at low costs. Thin-film devices can be delaminated from their heavy, glass growth substrates post-growth by exploiting a mismatch in coefficient of thermal expansion between the two. This allows thin-film PV to be decoupled from high temperature growth requirements and repackaged using lightweight materials. In this work we evaluate different materials and approaches for achieving large area delamination of CdTe films from their glass superstrates. It is found that epoxy bonded to a rigid handle provides robust and reproducible delamination at the TCO/CdS interface upon submersion in liquid nitrogen. Following delamination, a transparent front contact is re-deposited and selectively etched to expose the back contact to produce a functioning device. Effects of delamination and contributions to device functionality from CdCl 2 and CdS layers are discussed. Reproducible delamination of high efficiency, thin-film solar cells over large areas will enable work to further improve device efficiency through passivation and reconstruction of the previously buried interface between the transparent contact and CdS.

14 SOLAR ENERGY↗
DOE OSTI2017

Hierarchical Self-Organization of AB n Dendron-like Molecules into a Supramolecular Lattice Sequence

To understand the hierarchical self-organization behaviors of soft materials as well as their dependence on molecular geometry, a series of ABn dendron-type giant molecules based on polyhedral oligomeric silsesquioxane (POSS) nanoparticles were designed and synthesized. The apex of these molecules is a hydrophilic POSS cage with fourteen hydroxyl groups (denoted DPOSS). At its periphery, there are different numbers (n = 1–8) of hydrophobic POSS cages with seven isobutyl groups (denoted BPOSS), connected to the apical DPOSS via flexible dendron type linker(s). With varying the BPOSS number from one to seven, a supramolecular lattice formation sequence ranging from lamella (DPOSS-BPOSS), double gyroid (space group of Ia3d, DPOSS-BPOSS2), hexagonal cylinder (space group of P6mm, DPOSS-BPOSS3), Frank-Kasper A15 (space group of Pm3n, DPOSS-BPOSS4, DPOSS-BPOSS5, and DPOSS-BPOSS6), to Frank-Kasper sigma (space group of P42/mnm, DPOSS-BPOSS7) phases can be observed. The nanostructure formations in this series of ABn dendron-type giant molecules are mainly directed by the macromolecular geometric shapes. Furthermore, within each spherical motif, the soft spherical core is consisted of hydrophilic DPOSS cages with flexible linkages, while the hydrophobic BPOSS cages form the relative rigid shell and contact with neighbors to provide decreased interfaces among the spherical motifs for constructing final polyhedral motifs in these Frank-Kasper lattices. This study provides the design principle of macromolecules with specific geometric shapes and functional groups to achieve anticipated structures and macroscopic properties.

Feng, Xueyan↗
DOE OSTI2019

High thermoelectric performance in BaAgYTe 3 via low lattice thermal conductivity induced by bonding heterogeneity

Solid-state technology based on thermoelectric (TE) materials enables the conversion of heat into electricity offering an environmentally friendly solution to energy conservation. Here, we use density functional theory calculations to show that BaAgYTe 3 , a layered semiconductor, exhibits low lattice thermal conductivity (κ l ) and a high thermoelectric figure of merit. Our calculations reveal that the presence of bonding inhomogeneity, resulting from the coexisting rigid and fluctuating sublattices, favorably helps in both the electronic and phonon transports. We show that low κ l in this compound mainly originates from (a) the small group velocities of the acoustic modes, (b) quasilocalized low-frequency optical phonons that give rise to multiple scattering channels, and (c) strong lattice anharmonicity. While the calculations of the atomic displacement parameters and bonding analysis reveal relatively weaker bonding of Ag atoms and establish the heterogeneity in the chemical bonding, the strong anharmonicity is manifested in the large mode Gruneisen parameters. Thus, our work provides a theoretical prediction that warrants experimental verification and should encourage further exploration of potential TE materials in the same crystal family.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Decoupling of ion conductivity from segmental dynamics in oligomeric ethylene oxide functionalized oxanorbornene dicarboximide homopolymers

Here, in order to design more effective solid polymer electrolytes, it is important to decouple ion conductivityfrom polymer segmental motion. To that end, novel polymers based on oxanorbornene dicarboximidemonomers with varying lengths of oligomeric ethylene oxide side chains have been synthesized usingring opening metathesis polymerization. These unique polymers have a fairly rigid and bulky backboneand were used to investigate the decoupling of ion motion from polymer segmental dynamics. Ionconductivity was measured using broadband dielectric spectroscopy for varying levels of added lithiumsalt. The conductivity data demonstrate six to seven orders of separation in timescale of ion conductivityfrom polymer segmental motion for polymers with shorter ethylene oxide side chains. However,commensurate changes in the glass transition temperatures T g reduce the effect of decoupling in ionconductivity and lead to lower conductivity at ambient conditions. These results suggest that both anincrease in decoupling and a reduction in T g might be required to develop solid polymer electrolytes withhigh ion conductivity at room temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Highly Coupled Heterobicycle‐Fused Porphyrin Dimers: Excitonic Coupling and Charge Separation with Coordinated Fullerene, C 60

Abstract Porphyrin dimers have been widely explored and studied owing to their importance in photosynthetic systems. A vast variety of dimers linked by different groups and at different angles have been synthesized and studied; however, the means by which to synthesize rigidly fused porphyrins with direct conjugation of the chromophores remains limited. Such a class of porphyrins may possess interesting properties that unconjugated or stacked dimers may not exhibit. In this study, bisbenzimidazole‐fused porphyrin dimers and their mono‐ and bis−zinc derivatives are synthesized and characterized. As a consequence of excitonic coupling, these dimers exhibit a split Soret band irrespective of the metal ion in the porphyrin cavity. Steady‐state fluorescence and excitation spectra followed by femtosecond transient absorption spectral studies of the heterometallated dimer, (free‐base and zinc porphyrin) reveals the occurrence of efficient singlet‐singlet energy transfer (>95 % efficiency and rate constant >10 12 s −1 ) within the dyad. Further, donor‐acceptor conjugates were formed by metal‐ligand axial coordination of phenyl imidazole functionalized C 60 and were characterized by a variety of physicochemical techniques. Excited state charge separation from both singlet and triplet excited states of ZnP in the conjugates has been established. The lifetime of the final charge‐separated state was in the 30–40 μs range revealing charge stabilization. Interestingly, no charge separation in the conjugate derived from the heterometallated dimer was observed wherein excitation transfer dominated the process. The present study brings out the importance of the rigid π‐spacer connecting porphyrin dimers in governing the energy and electron transfer events when coupled with an electron acceptor.

Chemistry↗
DOE OSTI2022

Accurate tight-binding model for twisted bilayer graphene describes topological flat bands without geometric relaxation

A major hurdle in understanding the phase diagram of twisted bilayer graphene is the roles of lattice relaxation and electronic structure on isolated band flattening near magic twist angles. Here in this work, the authors develop an accurate local environment tight-binding model fit to tight-binding parameters computed from ab initio density-functional theory calculations across many atomic configurations. With the accurate parametrization, it is found that the magic angle shifts to slightly lower angles than often quoted, from around 1.05° to around 0.99°, and that isolated flat bands appear for rigidly rotated graphene layers, with enhancement of the flat bands when the layers are allowed to distort. Study of the orbital localization supports the emergence of fragile topology in the isolated flat bands without the need for lattice relaxation.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Beyond the Rigid Lid: Baroclinic Modes in a Structured Atmosphere

Abstract The baroclinic-mode decomposition is a fixture of the tropical-dynamics literature because of its simplicity and apparent usefulness in understanding a wide range of atmospheric phenomena. However, its derivation relies on the assumption that the tropopause is a rigid lid that artificially restricts the vertical propagation of wave energy. This causes tropospheric buoyancy anomalies of a single vertical mode to remain coherent for all time in the absence of dissipation. Here, the authors derive the Green’s functions for these baroclinic modes in a two-dimensional troposphere (or, equivalently, a three-dimensional troposphere with one translational symmetry) that is overlain by a stratosphere. These Green’s functions quantify the propagation and spreading of gravity waves generated by a horizontally localized heating, and they can be used to reconstruct the evolution of any tropospheric heating. For a first-baroclinic two-dimensional right-moving or left-moving gravity wave with a characteristic width of 100 km, its initial horizontal shape becomes unrecognizable after 4 h, at which point its initial amplitude has also been reduced by a factor of 1/π. After this time, the gravity wave assumes a universal shape that widens linearly in time. For gravity waves on a periodic domain the length of Earth’s circumference, it takes only 10 days for the gravity waves to spread their buoyancy throughout the entire domain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Oxygen vacancy induced site-selective Mott transition in LaNiO 3

While defects such as oxygen vacancies in correlated materials can modify their electronic properties dramatically, understanding the microscopic origin of electronic correlations in materials with defects has been elusive. Lanthanum nickelate with oxygen vacancies, LaNiO 3 - x , exhibits the metal-to-insulator transition as the oxygen vacancy level x increases from the stoichiometric LaNiO 3 . In particular, LaNiO 2.5 exhibits a paramagnetic insulating phase, also stabilizing an antiferromagnetic state below T N ≃ 152 K . Here, we study the electronic structure and energetics of LaNiO 3 - x using first principles. We find that LaNiO 2.5 exhibits a “site-selective” paramagnetic Mott insulating state at T ≃ 290 K as obtained using density functional theory plus dynamical mean field theory ( DFT + DMFT ). The Ni octahedron site develops a Mott insulating state with strong correlations as the Ni e g orbital is half-filled while the Ni square-planar site with apical oxygen vacancies becomes a band insulator. Overall, our oxygen vacancy results cannot be explained by the pure change of the Ni oxidation state alone within the rigid band-shift approximation. Our DFT + DMFT density of states explains that the peak splitting of unoccupied states in LaNiO 3 - x measured by the experimental x-ray absorption spectra originates from two nonequivalent Ni ions in the vacancy-ordered structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Implicit mesh discontinuous Galerkin methods and interfacial gauge methods for high-order accurate interface dynamics, with applications to surface tension dynamics, rigid body fluid–structure interaction, and free surface flow: Part I

In this two-part paper, a high-order accurate implicit mesh discontinuous Galerkin (dG) framework is developed for fluid interface dynamics, facilitating precise computation of interfacial fluid flow in evolving geometries. The framework uses implicitly defined meshes—wherein a reference quadtree or octree grid is combined with an implicit representation of evolving interfaces and moving domain boundaries—and allows physically prescribed interfacial jump conditions to be imposed or captured with high-order accuracy. Part one discusses the design of the framework, including: (i) high-order quadrature for implicitly defined elements and faces; (ii) high-order accurate discretisation of scalar and vector-valued elliptic partial differential equations with interfacial jumps in ellipticity coefficient, leading to optimal-order accuracy in the maximum norm and discrete linear systems that are symmetric positive (semi)definite; (iii) the design of incompressible fluid flow projection operators, which except for the influence of small penalty parameters, are discretely idempotent; and (iv) the design of geometric multigrid methods for elliptic interface problems on implicitly defined meshes and their use as preconditioners for the conjugate gradient method. Also discussed is a variety of aspects relating to moving interfaces, including: (v) dG discretisations of the level set method on implicitly defined meshes; (vi) transferring state between evolving implicit meshes; (vii) preserving mesh topology to accurately compute temporal derivatives; (viii) high-order accurate reinitialisation of level set functions; and (ix) the integration of adaptive mesh refinement. In part two, several applications of the implicit mesh dG framework in two and three dimensions are presented, including examples of single phase flow in nontrivial geometry, surface tension-driven two phase flow with phase-dependent fluid density and viscosity, rigid body fluid–structure interaction, and free surface flow. A class of techniques known as interfacial gauge methods is adopted to solve the corresponding incompressible Navier–Stokes equations, which, compared to archetypical projection methods, have a weaker coupling between fluid velocity, pressure, and interface position, and allow high-order accurate numerical methods to be developed more easily. Convergence analyses conducted throughout the work demonstrate high-order accuracy in the maximum norm for all of the applications considered; for example, fourth-order spatial accuracy in fluid velocity, pressure, and interface location is demonstrated for surface tension-driven two phase flow in 2D and 3D. Specific application examples include: vortex shedding in nontrivial geometry, capillary wave dynamics revealing fine-scale flow features, falling rigid bodies tumbling in unsteady flow, and free surface flow over a submersed obstacle, as well as high Reynolds number soap bubble oscillation dynamics and vortex shedding induced by a type of Plateau–Rayleigh instability in water ripple free surface flow. In conclusion, these last two examples compare numerical results with experimental data and serve as an additional means of validation; they also reveal physical phenomena not visible in the experiments, highlight how small-scale interfacial features develop and affect macroscopic dynamics, and demonstrate the wide range of spatial scales often at play in interfacial fluid flow.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Implicit mesh discontinuous Galerkin methods and interfacial gauge methods for high-order accurate interface dynamics, with applications to surface tension dynamics, rigid body fluid–structure interaction, and free surface flow: Part II

Here, in this two-part paper, a high-order accurate implicit mesh discontinuous Galerkin (dG) framework is developed for fluid interface dynamics, facilitating precise computation of interfacial fluid flow in evolving geometries. The framework uses implicitly defined meshes—wherein a reference quadtree or octree grid is combined with an implicit representation of evolving interfaces and moving domain boundaries—and allows physically prescribed interfacial jump conditions to be imposed or captured with high-order accuracy. Part one discusses the design of the framework, including: (i) high-order quadrature for implicitly defined elements and faces; (ii) high-order accurate discretisation of scalar and vector-valued elliptic partial differential equations with interfacial jumps in ellipticity coefficient, leading to optimal-order accuracy in the maximum norm and discrete linear systems that are symmetric positive (semi)definite; (iii) the design of incompressible fluid flow projection operators, which except for the influence of small penalty parameters, are discretely idempotent; and (iv) the design of geometric multigrid methods for elliptic interface problems on implicitly defined meshes and their use as preconditioners for the conjugate gradient method. Also discussed is a variety of aspects relating to moving interfaces, including: (v) dG discretisations of the level set method on implicitly defined meshes; (vi) transferring state between evolving implicit meshes; (vii) preserving mesh topology to accurately compute temporal derivatives; (viii) high-order accurate reinitialisation of level set functions; and (ix) the integration of adaptive mesh refinement. In part two, several applications of the implicit mesh dG framework in two and three dimensions are presented, including examples of single phase flow in nontrivial geometry, surface tension-driven two phase flow with phase-dependent fluid density and viscosity, rigid body fluid–structure interaction, and free surface flow. A class of techniques known as interfacial gauge methods is adopted to solve the corresponding incompressible Navier–Stokes equations, which, compared to archetypical projection methods, have a weaker coupling between fluid velocity, pressure, and interface position, and allow high-order accurate numerical methods to be developed more easily. Convergence analyses conducted throughout the work demonstrate high-order accuracy in the maximum norm for all of the applications considered; for example, fourth-order spatial accuracy in fluid velocity, pressure, and interface location is demonstrated for surface tension-driven two phase flow in 2D and 3D. Specific application examples include: vortex shedding in nontrivial geometry, capillary wave dynamics revealing fine-scale flow features, falling rigid bodies tumbling in unsteady flow, and free surface flow over a submersed obstacle, as well as high Reynolds number soap bubble oscillation dynamics and vortex shedding induced by a type of Plateau–Rayleigh instability in water ripple free surface flow. In these last two examples compare numerical results with experimental data and serve as an additional means of validation; they also reveal physical phenomena not visible in the experiments, highlight how small-scale interfacial features develop and affect macroscopic dynamics, and demonstrate the wide range of spatial scales often at play in interfacial fluid flow.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Making the most of your electrons: Challenges and opportunities in characterizing hybrid interfaces with STEM

Inspired by the unique architectures composed of hard and soft materials in natural and biological systems, synthetic hybrid structures and associated hard-soft interfaces have recently evoked significant interest. Soft matter is typically dominated by structural fluctuations even at room temperature, while hard matter is governed by rigid mechanical behavior. This dichotomy offers considerable opportunities to leverage the disparate properties offered by these components across a wide spectrum spanning from basic science to engineering insights with significant technological overtones. Such hybrid structures, which include polymer nanocomposites, DNA functionalized nanoparticle superlattices, and metal organic frameworks to name a few, have delivered promising insights into the technologically relevant applications such as catalysis, environmental remediation, optoelectronics, and medicine. The interfacial structure between the hard and soft phases demonstrates features across a variety of length scales and often strongly influence the functionality of hybrid systems. While scanning/transmission electron microscopy (S/TEM) has proven to be a valuable tool for acquiring intricate molecular and nanoscale details of these interfaces, the unusual nature of hybrid composites presents a suite of challenges that make assessing or establishing structure–property relationships especially difficult. There are additional considerations at all stages of sample analysis from preparing electron-transparent samples to obtaining sufficient contrast to resolve the interface between dissimilar materials given the dose sensitivity of soft materials. Here, we discuss each of these challenges and supplement a review of recent developments in the field with additional experimental investigations and simulations to present solutions for attaining a nano or molecular-level understanding of these interfaces. These solutions present a host of opportunities for investigating the role interfaces play in this unique class of functional materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Synthesis and Characterization of Pyridine Dipyrrolide Uranyl Complexes

The first actinide complexes of the pyridine dipyrrolide (PDP) ligand class, ( Mes PDP Ph )UO 2 (THF) and ( Cl2Ph PDP Ph )UO 2 (THF), are reported as the U VI uranyl adducts of the bulky aryl substituted pincers ( Mes PDP Ph ) 2– and ( Cl2Ph PDP Ph ) 2– (derived from 2,6-bis(5-(2,4,6-trimethylphenyl)-3-phenyl-1H-pyrrol-2-yl)pyridine (H 2 Mes PDP Ph , Mes = 2,4,6-trimethylphenyl), and 2,6-bis(5-(2,6-dichlorophenyl)-3-phenyl-1H-pyrrol-2-yl)pyridine (H 2 Cl2Ph PDP Ph , Cl 2 Ph = 2,6-dichlorophenyl), respectively). Following the in situ deprotonation of the proligand with lithium hexamethyldisilazide to generate the corresponding dilithium salts (e.g., Li 2 Ar PDP Ph , Ar = Mes of Cl 2 Ph), salt metathesis with [UO 2 Cl 2 (THF) 2 ] 2 afforded both compounds in moderate yields. The characterization of each species has been undertaken by a combination of solid- and solution-state methods, including combustion analysis, infrared, electronic absorption, and NMR spectroscopies. In both complexes, single-crystal X-ray diffraction has revealed a distorted octahedral geometry in the solid state, enforced by the bite angle of the rigid meridional ( Ar PDP Ph ) 2– pincer ligand. The electrochemical analysis of both compounds by cyclic voltammetry in tetrahydrofuran (THF) reveals rich redox profiles, including events assigned as U VI /U V redox couples. Here, a time-dependent density functional theory study has been performed on ( Mes PDP Ph )UO 2 (THF) and provides insight into the nature of the transitions that comprise its electronic absorption spectrum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Ultrasonic-Assisted Extrusion Processing for Enhancing Physical Properties of High-Density Polyethylene by Flow-Induced Crystallization

The evolution of crystallinity resulting from stress imposed on a melt, known as flow-induced crystallinity, can strongly influence the mechanical and physical properties of semicrystalline polymers. This study investigates shear-induced crystallization by applying an ultrasonic field to the melt flow as it passes through dies with various geometries. A custom-built sonication die is employed for controlling the dynamic temperature and shear environment, resulting in molecular alignment and potential for flow-induced crystallization. Application of both conventional and ultrasonic shear rates at the equilibrium melt temperature of high-density polyethylene (HDPE) was investigated to accelerate crystallinity and manipulate the crystal morphology across the film in pursuit of improved mechanical and gas barrier properties without the need for additives or other polymer layers. The relationships among ultrasonic-assisted extrusion processing, polymer structure, and performance were analyzed using wide- and small-angle X-ray scattering (WAXS and SAXS), tensile testing, and oxygen transmission rate (OTR) analysis. Multiple linear regression models were implemented to predict the correlation among HDPE structure, process, and properties. Structural analysis revealed that both conventional and ultrasonic shear rates had the most significant influence on lamellar spacing and redistribution of rigid and soft amorphous fractions within the crystalline domains, ultimately dictating the mechanical and physical properties of the films. The goal is to explore the potential of the ultrasonic-assisted high crystallinity monolayer that can replace some of the functionality of complex, heterogeneous multilayer packaging with a single-material film having enhanced oxygen barrier properties.

crystallinity↗
DOE OSTI2024

Patterning of multicomponent elastic shells by gaussian curvature

Recent findings suggest that shell protein distribution and the morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. Here, we explore how the morphology and component patterning are coupled through the competition of mean and gaussian bending energies in multicomponent elastic shells that form three-component irregular polyhedra. We observe two softer components with lower bending rigidities allocated on the edges and vertices while the harder component occupies the faces. When subjected to a nonzero interfacial line tension, the two softer components further separate and pattern into subdomains that are mediated by the gaussian curvature. We find that this degree of fractionation is maximized when there is a weaker line tension and when the ratio of bending rigidities between the two softer domains ≈2. Our results reveal a patterning mechanism in multicomponent shells that can capture the observed morphologies of bacterial microcompartments, and moreover, can be realized in synthetic vesicles.

Monte Carlo methods↗
DOE OSTI2024

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗
DOE OSTI2023

Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway

Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron–sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron–sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.

59 BASIC BIOLOGICAL SCIENCES↗