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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

An optogenetic toolkit for light-inducible antibiotic resistance

Abstract Antibiotics are a key control mechanism for synthetic biology and microbiology. Resistance genes are used to select desired cells and regulate bacterial populations, however their use to-date has been largely static. Precise spatiotemporal control of antibiotic resistance could enable a wide variety of applications that require dynamic control of susceptibility and survival. Here, we use light-inducible Cre recombinase to activate expression of drug resistance genes in Escherichia coli . We demonstrate light-activated resistance to four antibiotics: carbenicillin, kanamycin, chloramphenicol, and tetracycline. Cells exposed to blue light survive in the presence of lethal antibiotic concentrations, while those kept in the dark do not. To optimize resistance induction, we vary promoter, ribosome binding site, and enzyme variant strength using chromosome and plasmid-based constructs. We then link inducible resistance to expression of a heterologous fatty acid enzyme to increase production of octanoic acid. These optogenetic resistance tools pave the way for spatiotemporal control of cell survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Yu-Shiba-Rusinov states and ordering of magnetic impurities near the boundary of a superconducting nanowire

We theoretically study the spectrum induced by one and two magnetic impurities near the boundary of a one-dimensional nanowire in proximity to a conventional s-wave superconductor and extract the ground-state magnetic configuration. We show that the energies of the subgap states, supported by the magnetic impurities, are strongly affected by the boundary for distances less than the superconducting coherence length. In particular, when the impurity is moved towards the boundary, multiple quantum phase transitions periodically occur in which the parity of the superconducting condensate oscillates between even and odd. We find that the magnetic ground-state configuration of two magnetic impurities depends not only on the distance between them, but also explicitly on their distance away from the boundary of the nanowire. As a consequence, the magnetic ground state can switch from ferromagnetic to antiferromagnetic while keeping the interimpurity distance unaltered by simultaneously moving both impurities away from the boundary. The ground-state magnetic configuration of two impurities is found analytically in the weak coupling regime and exactly for an arbitrary impurity coupling strength using numerical tight-binding simulations.

1-dimensional systems↗
DOE OSTI2022

Hybridized Exciton-Photon-Phonon States in a Transition Metal Dichalcogenide van der Waals Heterostructure Microcavity

Excitons in atomically thin transition-metal dichalcogenides (TMDs) have been established as an attractive platform to explore polaritonic physics, owing to their enormous binding energies and giant oscillator strength. Basic spectral features of exciton polaritons in TMD microcavities, thus far, were conventionally explained via two-coupled-oscillator models. This ignores, however, the impact of phonons on the polariton energy structure. Here we establish and quantify the threefold coupling between excitons, cavity photons, and phonons. For this purpose, we employ energy-momentum-resolved photoluminescence and spatially resolved coherent two-dimensional spectroscopy to investigate the spectral properties of a high-quality-factor microcavity with an embedded WSe 2 van der Waals heterostructure at room temperature. Our approach reveals a rich multibranch structure which thus far has not been captured in previous experiments. Simulation of the data reveals hybridized exciton-photon-phonon states, providing new physical insight into the exciton polariton system based on layered TMDs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects

The identity of metal ions surrounding DNA is key to its biological function and materials applications. In this work, we compare atomistic molecular dynamics simulations of double strand DNA (dsDNA) with four alkaline earth metal ions (Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ ) to elucidate the physical interactions that govern DNA–ion binding. Simulations accurately model the ion–phosphate distance of Mg 2+ and reproduce ion counting experiments for Ca 2+ , Sr 2+ , and Ba 2+ . Our analysis shows that alkaline earth metal ions prefer to bind at the phosphate backbone compared to the major groove and negligible binding occurs in the minor groove. Larger alkaline earth metal ions with variable first solvation shells (Ca 2+ , Sr 2+ , and Ba 2+ ) show both direct and indirect binding, where indirect binding increases with ion size. Mg 2+ does not fit this trend because the strength of its first solvation shell predicts indirect binding only. Ions bound to the phosphate backbone form fewer contacts per ion compared to the major groove. Within the major groove, metal ions preferentially bind to guanine–cystosine base pairs and form simultaneous contacts with the N7 and O6 atoms of guanine. Overall, we find that the interplay among ion size, DNA–ion interaction, and the size and flexibility of the first solvation shell are key to predicting how alkaline earth metal ions interact with DNA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Effect of Ionic Strength and Anion Identity on Rare‐Earth Element Chelation by Poly(acrylic acid)

Abstract Rare‐earth elements (REEs) are critical components of many modern technologies, but their efficient separation and purification continue to pose significant challenges. Metal‐binding polymers may enable the development of promising alternative approaches to conventional separation techniques (e.g., solvent extraction), and insights into the interactions between the metal ions and polymers in solution are crucial to such development. In this work, the effect of ionic strength on the chelation of REEs by poly(acrylic acid) is investigated using isothermal titration calorimetry (ITC) to measure the metal‐binding thermodynamics. ITC experiments revealed that when ionic strength increases from increasing the sodium acetate buffer strength, polymer‐REE binding becomes increasingly disfavored. However, when ionic strength is increased by the addition of sodium chloride, binding again becomes increasingly disfavored, but to a lesser extent than when ionic strength increases from increasing the buffer strength. Additionally, the reduction in binding affinity is enthalpically driven when ionic strength is raised with sodium chloride, while it is entropically driven when raised with sodium acetate buffer, suggesting competive binding by the acetate ions. These results highlight the importance of ionic strength in polymer‐metal binding thermodynamics and will guide the development of new processes for the purification of critical metals.

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

The intrinsic mechanical properties of hydromagnesite, Mg 5 (CO 3 ) 4 (OH) 2 ·4H 2 O, a key phase of reactive MgO carbonate cement

To potentially enable CO 2 sequestration, reactive MgO carbonate cement is emerging as an alternative binder to Portland cement. Understanding the mechanical properties of its binding phase is critical for understanding the strength development and performing materials design for reactive MgO cement systems; however, the intrinsic mechanical properties of hydromagnesite (Mg 5 (CO 3 ) 4 (OH) 2 ·4H 2 O), a key binding phase, remain unexplored. Here the present study utilized synchrotron-based high-pressure X-ray diffraction to determine the unit cell-scale, intrinsic mechanical properties of hydromagnesite for the first time. Up to hydrostatic loading of 7.7 GPa, the bulk modulus of hydromagnesite was determined as 59 GPa or 71 GPa fitted using the second-order or third-order Birch-Murnaghan equation of state, which we contextualize with binding phases in various cement systems. The experiment results are applicable in materials design of low-carbon concrete and valuable for the validation and calibration of atomistic models.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Exciton–Polaritons in CsPbBr 3 Crystals Revealed by Optical Reflectivity in High Magnetic Fields and Two-Photon Spectroscopy

Cesium lead bromide (CsPbBr3) is a representative material of the emerging class of lead halide perovskite semiconductors that possess remarkable optoelectronic properties. Its optical properties in the vicinity of the bandgap energy are greatly contributed by excitons, which form exciton polaritons due to strong light–matter interactions. Exciton–polaritons in solution-grown CsPbBr 3 crystals are examined by means of circularly polarized reflection spectroscopy measured in high magnetic fields up to 60 T. The excited 2P exciton state is measured by two-photon absorption. Comprehensive modeling and analysis provides detailed quantitative information about the exciton–polariton parameters: exciton binding energy of 32.5 meV, oscillator strength characterized by longitudinal–transverse splitting of 5.3 meV, damping of 6.7 meV, reduced exciton mass of 0.18$m$ 0 , exciton diamagnetic shift of 1.6 μeV T -2 , and exciton Landé factor $g$ x = + 2.35. It is shown that the exciton states can be described within a hydrogen-like model with an effective dielectric constant of 8.7. From the measured exciton longitudinal–transverse splitting, Kane energy of E p = 15 eV is evaluated, which is in reasonable agreement with values of 11.8–12.5 eV derived from the carrier effective masses.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry

Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO 2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor

Inhibition of the SARS-CoV-2 main protease (M pro ) is a major focus of drug discovery efforts against COVID-19. Here we report a hit expansion of non-covalent inhibitors of M pro . Starting from a recently discovered scaffold (The COVID Moonshot Consortium. Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics. bioRxiv 2020.10.29.339317) represented by an isoquinoline series, we searched a database of over a billion compounds using a cheminformatics molecular fingerprinting approach. We identified and tested 48 compounds in enzyme inhibition assays, of which 21 exhibited inhibitory activity above 50% at 20 μM. Among these, four compounds with IC 50 values around 1 μM were found. Interestingly, despite the large search space, the isoquinolone motif was conserved in each of these four strongest binders. Room-temperature X-ray structures of co-crystallized protein–inhibitor complexes were determined up to 1.9 Å resolution for two of these compounds as well as one of the stronger inhibitors in the original isoquinoline series, revealing essential interactions with the binding site and water molecules. Molecular dynamics simulations and quantum chemical calculations further elucidate the binding interactions as well as electrostatic effects on ligand binding. The results help explain the strength of this new non-covalent scaffold for M pro inhibition and inform lead optimization efforts for this series, while demonstrating the effectiveness of a high-throughput computational approach to expanding a pharmacophore library.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Formation of the skyrmionic polaron by Rashba and Dresselhaus spin-orbit coupling

Skyrmions in reduced dimensions such as thin layers and interfaces are of both fundamental and technological importance. In these systems, itinerant electrons are often present together with the Rashba and Dresselhaus spin-orbit coupling (SOC). Here, in this study, we show that an itinerant electron in the presence of these interactions can nucleate the skyrmion state, even when the standard Dzyaloshinskii-Moriya interaction (DMI) is absent, and the electron can become self-trapped in the skyrmion core, forming the “skyrmionic polaron” (SkP). The formation of the SkP is investigated from a continuum model of the electron, exchange coupled to the lattice spins, by solving the appropriate Euler-Lagrange equations. The skyrmion (antiskyrmion) texture is favored by the Rashba (Dresselhaus) SOC, with the binding energy increasing quadratically with the strength of the interaction. In contrast, if the skyrmion is already formed due to a nonzero DMI, the electron is delocalized and avoids the skyrmion core until the strength of the Rashba or Dresselhaus SOC exceeds a critical value. Below this critical value, the electron is not bound to the skyrmion core, the polaron does not form, and the electron has little effect on the skyrmion state. Our work envisions the possibility of manipulating the skyrmion state in device applications by altering the strength of the Rashba or Dresselhaus interactions, e.g., by an external electric field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing

Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Buckybowls as gas adsorbents: binding of gaseous pollutants and their electric-field induced release

Here, the adsorption of nitric oxide and nitrogen dioxide (NO x ) to the Buckybowls sumanene and corannulene was investigated. Binding energies were up to 1.8x larger than for coronene as the planar analogue, demonstrating the advantages of Buckybowls for gas adsorption. In agreement with previous reports on carbon dioxide and methane adsorption, the favorable binding energies for NO x were shown to be associated with the curvature of the Buckybowls. It is shown that applying an electric field along the bowl symmetry axis modifies the bowl curvatures and impacts adsorbate binding energies, including the potential to desorb adsorbates. As a proof of concept, it is shown that applying electric fields of different strengths and orientations selectively controls sumanene's preference to bind nitric oxide, nitrogen dioxide, and carbon dioxide, suggesting potential applications for dynamically tunable gas adsorption. Moreover, it is demonstrated that adsorbates can be desorbed by applying suitable electric field strengths, allowing cleaning of the Buckybowls for renewed usage.

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

Dipole Strength Distribution of 8 He and Decay Characteristics

The weak binding and spatially extended neutron densities characteristic of drip-line nuclei give rise to a distinctive low-energy dipole response. The drip-line nucleus 8 He is the most neutron-rich bound nucleus with a mass-to-charge ratio of 𝐴/𝑍 = 4. We measure the dipole response of 8 He, including for the first time the four-neutron decay channel. A total dipole strength of ∑𝐵⁡(𝐸⁢1)(𝐸*< 15 MeV) = 0.95⁢(16)⁢𝑒 2 fm 2 and a dipole polarizability of 𝛼 𝐷 = 0.61⁢(1) fm 3 are extracted from the differential Coulomb-excitation cross section and compared to state-of-the-art theoretical calculations employing coupled cluster and three-body approaches. We find that the dipole continuum is dominated, even at high excitation energies well above the 4⁢𝑛 decay threshold, by two-neutron emission, pointing to a 6 He + 2⁢𝑛 structure of the excited dipole mode. No indication was found for a 4⁢𝑛 final-state correlation, while pronounced 𝑛⁢𝑛 and 6 He−𝑛 final-state correlations are apparent.

Lehr, C. [Technical University of Darmstadt (Germa↗
DOE OSTI2021

Hot Carrier Redistribution, Electron-Phonon Interaction, and Their Role in Carrier Relaxation in Thin Film Metal-Halide Perovskites

Temperature dependent (4–295 K) photoluminescence and transmission spectra are analyzed to study the effect of changing the different components of a perovskite compound, be it A, B, or X. Four different films are compared: FAMAPbSnI3, FAPbI3, FAMAPbI3, and FAPbBr3. The low temperature results highlight the changes that occur, especially underlying ones that are easily masked at room temperature. The overall Stokes shift is of similar magnitude at room temperature for the three Pb only based samples. This is governed by the interaction strength GLO, phonon energy ELO, and exciton binding energy Eex. One exception to this behavior is the Sn based FAMAPbSnI3 film, which shows a lack of Stokes shift between the absorption and photoluminescence. However, the strong absorption (more than 100 meV) below the band gap is indicative of an excitonic feature that has a large density of states. Transient absorption measurements confirm the trends observed in continuous wave (CW) measurements; the three Pb only films all show the convolution of an excitonic feature within 20 meV of the band gap as a contributing factor to the photobleach along with a region of high energy photoinduced absorption (PIA). However, the behavior for the Sn based film is notably different (just as it is in the CW measurements) with an unusual low energy PIA and a lack of high energy PIA. The large unusual low energy PIA is attributed to the large sub-band-gap absorption observed in the CW transmission/absorption measurements. Notably, regardless of interchanging components, the slow cooling of carriers in metal-halide perovskites shows little effect of GLO, ELO, and Eex. As such, here it is proposed that while the initial cooling of carriers is attributed to LO phonons, the overall cooling of carriers is dominated by the intrinsic low thermal conductivity of all metal-halide perovskites, which limits the dissipation of acoustic phonons in these systems

2D perovskites↗
DOE OSTI2021

Intertwined charge, spin, and pairing orders in doped iron ladders

Motivated by recent experimental progress on iron-based ladder compounds, we study the doped two-orbital Hubbard model for the two-leg ladder BaFe2S3. The model is constructed by using ab initio hopping parameters and the ground state properties are investigated using the density matrix renormalization group method. We show that the (π,0) magnetic ordering at half filling, with ferromagnetic rungs and antiferromagnetic legs, becomes incommensurate upon hole doping. Moreover, depending on the strength of the Hubbard U coupling, other magnetic patterns, such as (0,π), are also stabilized. We found that the binding energy for two holes becomes negative for intermediate Hubbard interaction strength, indicating hole pairing. Due to the crystal-field split among orbitals, the holes primarily reside in one orbital, with the other one remaining half filled. This resembles orbital selective Mott states. The formation of tight hole pairs continues with increasing hole density, as long as the magnetic order remains antiferromagnetic in one direction. The study of pair-pair correlations indicates the dominance of the intraorbital spin-singlet channel, as opposed to other pairing channels. Although in a range of hole doping pairing correlations decay slowly, our results can also be interpreted as corresponding to a charge density wave made of pairs, a precursor of eventual superconductivity after interladder couplings are included. Such a scenario of intertwined orders has been extensively discussed before in the cuprates, and our results suggest a similar physics could exist in ladder iron-based superconductors. Finally, we also show that a robust Hund's coupling is needed for pairing to occur.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

The Effect of Calcium on the Cohesive Strength and Flexural Properties of Low-Methoxyl Pectin Biopolymers

Pectin binds the mesothelial glycocalyx of visceral organs, suggesting its potential role as a mesothelial sealant. To assess the mechanical properties of pectin films, we compared pectin films with a less than 50% degree of methyl esterification (low-methoxyl pectin, LMP) to films with greater than 50% methyl esterification (high-methoxyl pectin, HMP). LMP and HMP polymers were prepared by step-wise dissolution and high-shear mixing. Both LMP and HMP films demonstrated a comparable clear appearance. Fracture mechanics demonstrated that the LMP films had a lower burst strength than HMP films at a variety of calcium concentrations and hydration states. The water content also influenced the extensibility of the LMP films with increased extensibility (probe distance) with an increasing water content. Similar to the burst strength, the extensibility of the LMP films was less than that of HMP films. Flexural properties, demonstrated with the 3-point bend test, showed that the force required to displace the LMP films increased with an increased calcium concentration ( p < 0.01). Toughness, here reflecting deformability (ductility), was variable, but increased with an increased calcium concentration. Similarly, titrations of calcium concentrations demonstrated LMP films with a decreased cohesive strength and increased stiffness. We conclude that LMP films, particularly with the addition of calcium up to 10 mM concentrations, demonstrate lower strength and toughness than comparable HMP films. These physical properties suggest that HMP has superior physical properties to LMP for selected biomedical applications.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Unveiling Unusual Reactivity of SO 2 and Unusual Type of S–X Long Bonds

A new reactivity of SO 2 to form unusual stable M−X−SO 2 (X = F, Cl, H) complexes is unveiled in this study. Moreover, a new type of S−X long bonds, which are significantly longer than traditional S−X covalent bonds, has been discovered. The P,N-ligated Ni−F complex model 1A can bind a SO 2 molecule through the new F−S long bond (2.207 Å), and a stable Ni−F−SO 2 complex 1B is generated, being exergonic by 2.2 kcal/mol. According to natural localized molecular orbital analysis, the new S−F long bond has a unique p(F) → π*(O=S=O) bonding interaction, which is shown to arise from the long S−F length. In comparison, the strength of the new F−S long bond (−2.2 kcal/mol) is found to be significantly stronger than common noncovalent interactions such as the hydrogen and halogen bond. The substituent modulations suggest that the electron-donating groups can increase the strength of new F−S bonds and enhance binding free energies ΔG bind . The scope of possible M−X complexes was explored, and various metals and X (F, Cl, and H) ligands were found to form stable M−X−SO 2 complexes. Specifically, the anionic M−X complexes display much higher ΔG bind values, ranging from −8 to −10 kcal/mol. The study paves the way for a green, recyclable, and adjustable SO 2 absorption method.

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

Tunable exciton binding energy in 2D hybrid layered perovskites through donor–acceptor interactions within the organic layer

The strength of electrostatic interactions within semiconductors strongly affects their performance in optoelectronic devices. An important target is the tuning of a material’s exciton binding energy—the energy binding an electron–hole pair through the electrostatic Coulomb force—independent of its electronic band gap. Here, we report on the doping of a family of two-dimensional hybrid perovskites, in which inorganic lead halide sheets alternate with naphthalene-based organic layers, with tetrachloro-1,2-benzoquinone (TCBQ). For four out of seven n = 1 perovskites, the incorporation of the electron-accepting TCBQ dopant into the organic sublattice containing the electron-donating naphthalene species enabled the tuning of the materials’ 1s exciton binding energy. The naphthalene–TCBQ electron donor–acceptor interactions increased the electrostatic screening of the exciton, in turn lowering its binding energy relative to the undoped perovskite—by almost 50% in one system. Structural and optical characterization showed that the inorganic lattice is not significantly perturbed even though the layer-to-layer spacing increases upon molecular dopant incorporation.

36 MATERIALS SCIENCE↗