Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structure formation”

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.

At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Signal sequences target enzymes and structural proteins to bacterial microcompartments and are critical for microcompartment formation

ABSTRACT Spatial organization of pathway enzymes has emerged as a promising tool to address several challenges in metabolic engineering, such as flux imbalances and off-target product formation. Bacterial microcompartments (MCPs) are a spatial organization strategy used natively by many bacteria to encapsulate metabolic pathways that produce toxic, volatile intermediates. Several recent studies have focused on engineering MCPs to encapsulate heterologous pathways of interest, but how this engineering affects MCP assembly and function is poorly understood. In this study, we investigated the role of signal sequences, short domains that target proteins to the MCP core, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterized two novel Pdu signal sequences on the structural proteins PduM and PduB, which constitute the first report of metabolosome signal sequences on structural proteins rather than enzymes. We then explored the role of enzymatic and structural Pdu signal sequences on MCP assembly by deleting their encoding sequences from the genome alone and in combination. Deleting enzymatic signal sequences decreased the MCP formation, but this defect could be recovered in some cases by overexpressing genes encoding the knocked-out signal sequence fused to a heterologous protein. By contrast, deleting structural signal sequences caused similar defects to knocking out the genes encoding the full-length PduM and PduB proteins. Our results contribute to a growing understanding of how MCPs form and function in bacteria and provide strategies to mitigate assembly disruption when encapsulating heterologous pathways in MCPs. IMPORTANCE Spatially organizing biosynthetic pathway enzymes is a promising strategy to increase pathway throughput and yield. Bacterial microcompartments (MCPs) are proteinaceous organelles that many bacteria natively use as a spatial organization strategy to encapsulate niche metabolic pathways, providing significant metabolic benefits. Encapsulating heterologous pathways of interest in MCPs could confer these benefits to industrially relevant pathways. Here, we investigate the role of signal sequences, short domains that target proteins for encapsulation in MCPs, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterize two novel signal sequences on structural proteins, constituting the first Pdu signal sequences found on structural proteins rather than enzymes, and perform knockout studies to compare the impacts of enzymatic and structural signal sequences on MCP assembly. Our results demonstrate that enzymatic and structural signal sequences play critical but distinct roles in Pdu MCP assembly and provide design rules for engineering MCPs while minimizing disruption to MCP assembly.

Johnson, Elizabeth R. (ORCID:0000000179236881)↗
DOE OSTI2022

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine

Ribosome serves as a universal molecular machine capable of synthesis of all the proteins in a cell. Small-molecule inhibitors, such as ribosome-targeting antibiotics, can compromise the catalytic versatility of the ribosome in a context-dependent fashion, preventing transpeptidation only between particular combinations of substrates. Classic peptidyl transferase center inhibitor chloramphenicol (CHL) fails to inhibit transpeptidation reaction when the incoming A site acceptor substrate is glycine, and the molecular basis for this phenomenon is unknown. Here, we present a set of high-resolution X-ray crystal structures that explain why CHL is unable to inhibit peptide bond formation between the incoming glycyl-tRNA and a nascent peptide that otherwise is conducive to the drug action. Our structures reveal that fully accommodated glycine residue can co-exist in the A site with the ribosome-bound CHL. Moreover, binding of CHL to a ribosome complex carrying glycyl-tRNA does not affect the positions of the reacting substrates, leaving the peptide bond formation reaction unperturbed. These data exemplify how small-molecule inhibitors can reshape the A-site amino acid binding pocket rendering it permissive only for specific amino acid residues and rejective for the other substrates extending our detailed understanding of the modes of action of ribosomal antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A classical molecular dynamics simulation method for the formation of “dry” gels from boro-aluminosilicate glass structures

In contact with water, glass transforms into amorphous and porous structures called gels. A simulation method based on classical molecular dynamics is proposed here to mimic “dry” gels forming from initial oxide glass structures. Six glass compositions were investigated. Two behaviours were evidenced depending on the initial glass composition, and in particular on the quantity of elements removed. If a large quantity of soluble elements (B, Na) was removed, it induced an increase in the average pore size within the gels, and the time needed to stabilise the gel structure increased because more local atomic rearrangements occurred. The gel network displayed a higher proportion of Si-Q4 at the expense of Si-Q3 and a lower average ring size compared to the glass network, irrespective of the glass composition. Surface effects were also highlighted in the dry gels, such as the presence of 3-coordinated Al and a decrease in the average angle Si-O-Si and Al-O-Al. Our findings will be compared to both wet gels and experimental data in further studies, to help find the best procedure to simulate such structures.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Galaxy formation with wave/fuzzy dark matter: The core-halo structure and the solitonic imprint

Dark matter-dominated cores have long been claimed for the well-studied local group dwarf galaxies. More recently, extended stellar halos have been uncovered around several of these dwarfs through deeper imaging and spectroscopy. Such core-halo structures (inner flat core and a characteristic r −3 asymptotic outer halo profile) are not a feature of conventional cold dark matter (CDM). In contrast, smooth and prominent dark matter cores are predicted for wave/fuzzy dark matter (ψDM). The question arises as to what extent the visible stellar profiles should reflect this dark matter core structure. Here we compare cosmological hydrodynamical simulations of CDM, “WDM” (model used as a proxy for ψDM) & ψDM, aiming to predict the stellar profiles for these three DM scenarios. We show that cores surrounded by extended halos are distinguishable for ψDM, where the stellar density is enhanced in the core due to the presence of the relatively dense soliton. Our analysis demonstrates that, in our simulations, a distinctive core-halo structure does not appear in the case of CDM in the DM, gas, or stars. Whereas we do find a core-halo transition for DM, gas, and stars for ψDM, and the scale of this transition is in line with the predicted core radius set by the soliton scale anticipated for the adopted boson mass of 2.5×10 −22 eV. The presence of a core-halo structure in the stellar profile for Galaxy 1 for ψDM is visible for the most massive and the first galaxy to form in the simulation. Clearly, further simulations are needed to establish how strict this possible relationship is between the DM and stellar core-halo profile as a potential observational discriminator. Furthermore, we observe the anticipated asymmetry for ψDM due to the soliton's motion (jumping and random walk), a distinctive characteristic not found in the symmetric distributions of stars in the warm and CDM models.

dark matter↗
DOE OSTI2021

Formation of a Ti–Cu(111) single atom alloy: Structure and CO binding

A single atom Ti–Cu(111) surface alloy can be generated by depositing small amounts of Ti onto Cu(111) at slightly elevated surface temperatures (~500 to 600 K). Here, scanning tunneling microscopy shows that small Ti-rich islands covered by a Cu single layer form preferentially on ascending step edges of Cu(111) during Ti deposition below about 400 K but that a Ti–Cu(111) alloy replaces these small islands during deposition between 500 and 600 K, producing an alloy in the brims of the steps. Larger partially Cu-covered Ti-containing islands also form on the Cu(111) terraces at temperatures between 300 and 700 K. After surface exposure to CO at low temperatures, reflection absorption infrared spectroscopy (RAIRS) reveals distinct C–O stretch bands at 2102 and 2050 cm –1 attributed to CO adsorbed on Cu-covered Ti-containing domains vs sites in the Ti–Cu(111) surface alloy. Calculations using density functional theory (DFT) suggest that the lower frequency C–O stretch band originates specifically from CO adsorbed on isolated Ti atoms in the Ti–Cu(111) surface alloy and predicts a higher C–O stretch frequency for CO adsorbed on Cu above subsurface Ti ensembles. DFT further predicts that CO preferentially adsorbs in flat-lying configurations on contiguous Ti surface structures with more than one Ti atom and thus that CO adsorbed on such structures should not be observed with RAIRS. The ability to generate a single atom Ti–Cu(111) alloy will provide future opportunities to investigate the surface chemistry promoted by a representative early transition metal dopant on a Cu(111) host surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Native glycosylated HIV-1 Env in silico ensemble

The computationally modeled datasets generated in this study, namely the natively glycosylated SOSIP Env and the uniform mannose-9 glycosylated SOSIP Env ensembles will be submitted as Mendeley dataset server as required by the journal publishers, for public availability. These include two sets of Protein Data Bank (PDB)ensembles of 1000 structures each. The files are in the standardized PDB format. Each of the constituent ensemble structures are separated by the ‘END’ tag within the files. Snapshots from the beginning and end of each data set are given here. The column descriptions are as follows: Col1 –ATOM tag; Col 2 –atom number; COL 3 –atom name; COL4 –residue name; COL 5 –chain identifier; COL 6 –residue number; COL. 7,8,9 –X,Y,Z coordinates of atom in 3Dspace; COL 10 –Occupancy Factor; COL 11 -Temperature factor; COL 12 –segment identifier; COL 13 –element symbol.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Iron-assisted growth of anisotropic ZnO nanostructures

Anisotropic nanostructures offer a promising pathway to modulate structure-function relationships of materials. However, the correlation between growth direction of high-quality anisotropic nanostructures, the synthesis conditions and mechanisms controlling their growth, and their magnetic and optical properties remain underexplored. In this study, we developed an iron-assisted anisotropic growth method to form zinc oxide nanostructures on the O-polar (0001̄) surface, resulting in two distinct ZnO-based nanostructures: hand-shaped nanostructures and truncated hexagonal nanopyramids. In contrast to most reports of anisotropic nanostructure synthesis, which primarily focus on morphology control through ligand-ligand interactions, the current study probes the effects of doping on anisotropic growth, and how doping, along with ligand-ligand interactions and facet-specific ligand binding, control nanostructure morphology. The reaction mechanisms leading to formation of these novel structures were thoroughly probed by systematically manipulating synthesis parameters. A two-step formation mechanism was identified: first, a hexagonal platform forms through an initial homogeneous nucleation process, followed by secondary heterogeneous nucleation, which results in metastable secondary nanostructures growing on the oxygen-rich template. Optical and magnetic properties of these Fe/ZnO nanostructures were characterized. Our findings provide a new strategy that uses a magnetic element as a dopant to build new nanostructures of ZnO with controllable size and shape growing on an oxygen-rich crystal plane. These materials could have applications in novel technologies where both optoelectronic and magnetic properties are of interest.

Xuan, Zhengxi↗
DOE OSTI2023

The Origin of Anomalous Density Behavior of Silica Glass

The anomalous density–temperature relationship of vitreous silica with low hydroxyl content is explained by the formation of medium-range ordering structure in the glass transition process. The ordered medium-range structure has the shape of a “nanoflake” and consists of two layers of SiO 4 tetrahedra, bonded by O atoms located in the middle of the structure. The nanoflakes interact with their surrounding structures through both covalent chemical bonds and van der Waals bonds. In the formation of the van der Waals bonds, the orientation of SiO 4 tetrahedra can change, which results in an increase in distance between the nanoflakes and their surrounding structures. Thus, there is a slight volume enlargement associated with the formation of nanoflakes. Since the nanoflakes’ formation starts at a temperature near 1480 °C, and the population of the nanoflakes grows continuously as temperature decreases until about 950 °C, the bulk volume of silica glass increases in the temperature range from about 1480 °C to 950 °C. Therefore, the density anomaly of silica glass can be explained as a byproduct of forming of medium-range ordering structure in the silica glass transition.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Shear-free mixing to achieve accurate temporospatial nanoscale kinetics through scanning-SAXS: ion-induced phase transition of dispersed cellulose nanocrystals

Time-resolved in situ characterization of well-defined mixing processes using small-angle X-ray scattering (SAXS) is usually challenging, especially if the process involves changes of material viscoelasticity. In specific, it can be difficult to create a continuous mixing experiment without shearing the material of interest; a desirable situation since shear flow both affects nanoscale structures and flow stability as well as resulting in unreliable time-resolved data. Here, we demonstrate a flow-focusing mixing device for in situ nanostructural characterization using scanning-SAXS. Given the interfacial tension and viscosity ratio between core and sheath fluids, the core material confined by sheath flows is completely detached from the walls and forms a zero-shear plug flow at the channel center, allowing for a trivial conversion of spatial coordinates to mixing times. With this technique, the time-resolved gel formation of dispersed cellulose nanocrystals (CNCs) was studied by mixing with a sodium chloride solution. It is observed how locally ordered regions, so called tactoids, are disrupted when the added monovalent ions affect the electrostatic interactions, which in turn leads to a loss of CNC alignment through enhanced rotary diffusion. The demonstrated flow-focusing scanning-SAXS technique can be used to unveil important kinetics during structural formation of nanocellulosic materials. However, the same technique is also applicable in many soft matter systems to provide new insights into the nanoscale dynamics during mixing.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Self-organization of photoionized plasmas via kinetic instabilities

Abstract Self-organization in an unmagnetized collisionless plasma (in this paper) refers to formation of transient coherent structures such as collective oscillations (electrostatic waves) or magnetic fields resulting from so-called kinetic effects in the plasma. This topical review provides a comprehensive analysis of the self-organization of strong-field photoionized, non-equilibrium plasmas through kinetic instabilities. The authors propose and demonstrate a novel experimental platform that enables the formation of dense plasmas with known highly anisotropic and non-thermal electron velocity distribution functions on a timescale on the order of an inverse electron plasma frequency. We then show that such plasmas are highly susceptible to a hierarchy of kinetic instabilities, including two-stream, current filamentation and Weibel, that convert a fraction of the electron kinetic energy into electric and/or magnetic energy stored in self-organized structures. The electrostatic waves so produced are measured using a collective light (Thomson) scattering technique with femtosecond resolution as the kinetic instabilities aided by collisions eventually thermalize the plasma electrons. In addition, we describe a novel experimental technique that has made it possible to map the temporal evolution of the wavenumber spectrum of the thermal Weibel instability with picosecond resolution, which leads to the formation of quasi-static coherent magnetic fields with different topologies in photoionized plasmas. Finally, the paper summarizes the important results and discusses future directions on this topic.

Zhang, Chaojie (ORCID:0000000180353014)↗
DOE OSTI2025

Effect of rare earth size on network structure and glass forming ability in binary aluminum garnets

Rare earth aluminate glasses are potentially useful for optical, luminescence, and laser applications. As reluctant glass formers, these materials exhibit unconventional atomic structures. To better understand how their structures correlate with glass formation, we investigate two rare earth aluminum garnet melts, La 3 Al 5 O 12 (LAG) and Yb 3 Al 5 O 12 (YbAG), which represent the relative extremes of good and poor glass forming ability in rare earth aluminates. Structural models have been refined to high-energy X-ray diffraction data over 1340–2740 K. Both melts contain mixtures of AlO 4 , AlO 5 , and AlO 6 polyhedra, with larger fractions of [5] Al and [6] Al in YbAG. Extrapolation of the Al–O coordination distributions to the glass transition match closely with 27 Al nuclear magnetic resonance measurements of (La 1−z Y z ) 3 Al 5 O 12 glasses, z = 0 to 1. During cooling, the mean coordination numbers increase for La–O in LAG from 6.45(8) to 6.98(8) and for Yb–O in YbAG from 6.02(8) to 6.21(8). Linkedness among Al–O polyhedra at ∼2450 K is mostly corner-sharing, with 9% edge-sharing in LAG and 19% in YbAG. Among [4] Al units, both melts have 6% edge-sharing that convert to all corner-sharing upon cooling. Network connectivity is compared using a newly defined metric, K n , that is similar to the Q n distribution but that accounts for the edge-sharing and triply bonded oxygen present in these melts. The lower glass forming ability in YbAG as compared to LAG correlates with more edge-sharing, associated with the larger fractions of [5] Al and [6] Al, and lower connectivity among [4] Al units.

Wilke, Stephen K. [Materials Development, Inc., Ar↗
DOE OSTI2025

Magnon thermal conductivity in multiferroics with spin cycloids

Multiferroic materials, characterized by the occurrence of two or more ferroic properties, hold potential in future technological applications and also exhibit intriguing phenomena caused by the interplay of multiple orders. One such example is the formation of spin-cycloid structures within multiferroic materials, which we investigate in this work by focusing on their magnon excitations and transport based on a general multiferroic Hamiltonian with an antiferromagnetic order. More specifically, we identify the ground state and explore the dynamics of magnon modes, revealing distinct in-plane and out-of-plane modes with anisotropic dispersion relations. The magnon modes include a massless excitation, known as the Goldstone boson, originating from the spontaneous breaking of the translational symmetry by the formation of the cycloid structures. By employing the Boltzmann transport formalism, the magnonic thermal conductivity with spin cycloids and low-temperature anisotropic behaviors is discussed. This work provides pathways to envision the spin-textured multiferroics, which may serve as a fertile ground to look for novel thermal and spin transport with the rich interplay of quasiparticles such as magnons and phonons.

Park, Hyeon Woo↗
DOE OSTI2025

Computationally guided experimental validation of divacancy defect formation in 4H-SiC

Recent research into solid-state qubits for quantum information science has focused on optically addressable spin defects such as the negatively charged nitrogen-vacancy center in diamond and the neutrally charged divacancy (VV) in 4H-SiC as scalable quantum sensors and networking qubits. Within this context, direct investigations of the structural origin and defect formation dynamics of a sub-set of the VV center in 4H-SiC remain lacking. Here, we take a systematic experimental approach guided by predictions from first-principles simulations to gain a thorough mechanistic understanding of the VV defect formation and control in 4H-SiC. We study the effect of annealing time and temperature on VV formation in high-purity semi-insulating 4H-SiC samples following electron irradiation. Three different temperatures (1123, 1273, and 1473 K) and annealing duration (from 0.5 to 72 h) are chosen to explore VV formation in different regions. We find that samples annealed at 1273 K give the highest VV-related photoluminescence (PL) intensities, in agreement with the prediction from first-principles calculations. Furthermore, the logarithmic dependence of VV-related PL intensities on the annealing duration at 1273 K indicates that 1273 K provides sufficient thermal energy for silicon vacancy migration but not for VV migration. Together, these results suggest that efficient VV formation occurs above the V Si migration temperature and below the VV migration threshold.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Rapid Access to Diverse Multicomponent Hierarchical Nanostructures from Mixed–Graft Block Copolymers

Multicomponent nanostructured materials assembled from molecular building blocks received wide attention due to their precisely integrated multifunctionalities. However, discovery of these materials with desirable composition and morphology was limited by their low synthetic scalability and narrow structural tuning window with given building blocks. Here, we report a scalable and diversity-oriented synthetic approach to hierarchically structured nanomaterials based on a few readily accessible building blocks. Mixed-graft block copolymers containing sequence-defined side chains were prepared through ring-opening metathesis copolymerization of three or four types of macromonomers. Intramolecularly defined interfaces promoted the formation of ordered hierarchical structures with lattice sizes tunable across multiple length scales. Finally, the same set of macromonomers were arranged and combined in different ways, providing access to diverse morphologies in the resultant structures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Dual‐Scale Nanostructures via Evaporative Assembly

Abstract Dual‐scale hierarchical structures with regular microscale patterns and varying degree of nanoscale crystalline order are synthesized on physically and chemically homogeneous substrates by evaporative self‐assembly with a suspension of DNA‐functionalized nanoparticles (NPs) with a charged core shell. For a certain NP concentration range, periodic concentric rings in a stripe‐like micropattern are produced over macroscale surface areas by an NP monolayer with hexagonal lattice structure at the nanoscale. The stripe width, spacing, and nanoparticle ordering can be controlled by varying the NP concentration. The results indicate that the interplay between “stick‐slip” motion of the droplet contact line and coulombic and steric NP interactions control the formation of the observed structures. A simple analytical model is proposed to account for the experimental observations and guide the future design of different nanostructure morphologies. This work demonstrates a simple cost‐effective mask‐free method for fabricating large‐area nanostructured 2D materials and metasurfaces for applications ranging from energy conversion/storage to optoelectronics and nanophotonics.

Srivastava, Sunita↗
DOE OSTI2025

Chromium segregation-induced oxide evolution in Ni-10Cr alloys during high-temperature oxidation

The oxidation behavior of a Ni-10(wt%)Cr alloy under high-temperature O 2 conditions is investigated using transmission electron microscopy and first-principles calculations. Results reveal that chromium segregation plays a central role in driving the evolution of complex oxide phase structures during oxidation. At low Cr concentrations, Cr preferentially segregates to NiO grain boundaries or internal pores, substituting for Ni atoms and forming Ni(Cr)O solid solutions. As Cr content increases, enhanced diffusion promotes Cr penetration into the NiO lattice, leading to the formation of multiphase oxide structures. First-principles modeling corroborates these findings: at low Cr concentrations, Cr atoms favor surface and grain-boundary segregation, while higher concentrations lead to Cr aggregation within the NiO bulk. Furthermore, the integrated experimental-theoretical approach provides atomistic insights into Cr-mediated mass transport mechanisms during alloy oxidation and offers valuable guidance for controlling oxide growth kinetics and phase stability in Ni-Cr alloys, with implications for improving oxidation resistance in high-temperature structural applications.

36 MATERIALS SCIENCE↗