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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Harnessing Heterologous Bacterial Two-Component Systems as Biosensors to Address Challenges in Fermentation Scale-Up

Scaling up bacterial fermentation from bench to industrial scale often results in unpredictable performance losses, possibly in part due to changes in microenvironmental conditions such as pH. To investigate this, we developed a suite of pH-sensitive biosensors from bacterial two-component systems (TCSs) that provide a dynamic, fluorescent readout in response to extracellular pH changes. TCSs consist of a periplasmic sensor histidine kinase (HK) that, in response to an extracellular stimulus, autophosphorylates intracellularly and subsequently transfers the phosphate to a cognate response regulator (RR) that modulates transcription of target genes. We utilized three pH-responsive TCSs (referred to here as CVJ1, CVJ30, and CVJ79) and linked their output to GFP. This was achieved by placing the RR promoter upstream of GFP or by constructing a chimeric RR composed of the native receiver domain and the DNA-binding domain of another well-characterized RR with a defined promoter. All components - HK, RR (native or chimeric), and GFP under its corresponding promoter - were cloned into a broad-host-range plasmid. Sensors were validated in Escherichia coli and Pseudomonas putida, including the muconic acid-producing strain P. putida TL207. All three biosensors successfully reported pH, with fluorescence (normalized to optical density) correlating strongly with media pH. Among the native sensors, CVJ79 showed the most robust performance while CVJ1 also performed best in its native form; CVJ30 exhibited improved functionality as a chimera, suggesting that modular RR design can enhance compatibility in some heterologous hosts. Further, CVJ79 was activated by alkaline conditions, while CVJ30 responded to acidic environments. Notably, CVJ1 was induced by high pH in wild-type E. coli and P. putida, but low pH in TL207. The observed differences in sensor activation between strains - particularly the divergent response of CVJ1 - suggest that host-specific regulatory pathways may influence how cells perceive and adapt to pH stress. Moving forward, these biosensors can be used to guide the rational design of more robust strains, optimize process conditions in real time, and inform strategies to minimize physiological heterogeneity during scale-up. Integrating these tools into high-throughput screening and bioreactors will be a key step toward improving predictability and performance in industrial bioprocesses.

09 BIOMASS FUELS↗
DOE OSTI2025

Emerging supersolidity in photonic-crystal polariton condensates

A supersolid is a counter-intuitive phase of matter in which its constituent particles are arranged into a crystalline structure, yet they are free to flow without friction. This requires the particles to share a global macroscopic phase while being able to reduce their total energy by spontaneous, spatial self-organization. The existence of the supersolid phase of matter was speculated more than 50 years ago1, 2, 3–4. However, only recently has there been convincing experimental evidence, mainly using ultracold atomic Bose–Einstein condensates (BECs) coupled to electromagnetic fields. There, various guises of the supersolid were created using atoms coupled to high-finesse cavities5,6, with large magnetic dipole moments7, 8, 9, 10, 11, 12–13, and spin–orbit-coupled, two-component systems showing stripe phases14, 15–16. Here we provide experimental evidence of a new implementation of the supersolid phase in a driven-dissipative, non-equilibrium context based on exciton–polaritons condensed in a topologically non-trivial, bound state in the continuum (BiC) with exceptionally low losses, realized in a photonic-crystal waveguide. We measure the density modulation of the polaritonic state indicating the breaking of translational symmetry with a precision of several parts in a thousand. Direct access to the phase of the wavefunction allows us to also measure the local coherence of the supersolid. We demonstrate the potential of our synthetic photonic material to host phonon dynamics and a multimode excitation spectrum.

Trypogeorgos, Dimitrios↗
DOE OSTI2025

Architecture, catalysis and regulation of methylthio-alkane reductase for bacterial sulfur acquisition from volatile organic compounds

Bacteria utilize methylthio-alkane reductase (MAR) to acquire sulfur from volatile organic sulfur compounds. Reductive cleavage of methylthio-ethanol and dimethylsulfide liberates methanethiol for methionine synthesis and concomitantly releases ethylene and methane, respectively. Here we show that the native MAR of Rhodospirillum rubrum is a two-component system composed of a MarH ATP-dependent reductase and a MarDK catalytic core, whose architecture parallels nitrogenase. MarS complexes with MarDK to downregulate MAR activity during cellular sulfate influx, based on chromatographic and activity analyses. MarDK possesses complex metallocofactors resembling, but not identical to, nitrogenase P- and iron-only M-clusters, designated as mar1 and mar2 clusters based on metal, spectroscopic and mutagenesis analyses. They exhibit electronic features similar to the iron-only nitrogenase under turnover and, remarkably, are matured by MarB or nitrogenase NifB, resulting in maturase-dependent activity profiles. Altogether, this suggests a broader scope of reactivity, mechanisms and regulation in microbial metabolism for the nitrogenase-like family of enzymes than previously considered.

09 BIOMASS FUELS↗
DOE OSTI2026

From photosynthetic electron flow to gene regulation: redox signal transduction in cyanobacteria

In cyanobacteria, the free-living ancestors of chloroplasts, photosynthesis simultaneously sustains growth and generates reactive oxygen species (ROS) that damage proteins, lipids, and DNA when light capture outpaces carbon fixation. Maintaining redox balance, therefore, requires cells to read photosynthetic electron flow as a signal that continuously tunes gene expression and protein activity. This review traces how these redox signals are transduced to transcription machinery through three routes: membrane-localized sensors, cytoplasmic redox sensors downstream of photosystem I, and ROS generated when electron sinks are saturated. Membrane-bound histidine kinases (two-component systems) relay the redox state of the plastoquinone pool to control photosystem remodeling, pigment biosynthesis, and circadian timing. Cytoplasmic one-component regulators, by contrast, sense redox directly through thiol-disulfide switches, glutathionylation, iron-sulfur clusters, and metal-catalyzed oxidation to control photosystem-cofactor, electron-carrier, and transition-metal homeostasis. Because many of these regulators persist in algal and plant chloroplasts, cyanobacteria illuminate principles of redox control across photosynthetic eukaryotes. Post-transcriptional and translational control further shapes redox-dependent gene expression programs through transcript stability, ribosome assembly, and translation initiation, extending redox regulation beyond transcription to every step of protein synthesis and even activity modulation. Finally, we connect redox regulation to photosynthetic physiology, stress resilience, and the rational engineering of cyanobacteria for sustainable bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural analysis of the NifL-NifA complex reveals the molecular basis of anti-activation of nitrogen fixation gene expression in Azotobacter vinelandii

Understanding the molecular basis of regulated nitrogen (N 2 ) fixation is essential for engineering N 2 -fixing bacteria that fulfill the demand of crop plants for fixed nitrogen, reducing our reliance on synthetic nitrogen fertilizers. In Azotobacter vinelandii and many other members of Proteobacteria, the two-component system comprising the anti-activator protein (NifL) and the Nif-specific transcriptional activator (NifA)controls the expression of nif genes, encoding the nitrogen fixation machinery. The NifL-NifA system evolved the ability to integrate several environmental cues, such as oxygen, nitrogen, and carbon availability. The nitrogen fixation machinery is thereby only activated under strictly favorable conditions, enabling diazotrophs to thrive in competitive environments. While genetic and biochemical studies have enlightened our understanding of how NifL represses NifA, the molecular basis of NifA sequestration by NifL depends on structural information on their interaction. Here, we present mechanistic insights into how nitrogen fixation is regulated by combining biochemical and genetic approaches with a low-resolution cryo-electron microscopy (cryo-EM) map of the oxidized NifL-NifA complex. Our findings define the interaction surface between NifL and NifA and reveal how this interaction can be manipulated to generate bacterial strains with increased nitrogen fixation rates able to secrete surplus nitrogen outside the cell, a crucial step in engineering improved nitrogen delivery to crop plants.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Battery Failure Databank

The Battery Failure Databank contains thermal runaway results gathered from nearly 300 small format fractional thermal runaway calorimetry (S-FTRC) experiments. A majority of these experiments were conducted at synchrotron facilities where high-speed x-ray videography was conducted of the cell while tested inside of the S-FTRC. The databank is a two-component system which consists of a Microsoft ExcelTM spreadsheet which provides S-FTRC results in tabular format and a radiographic video library containing the high-speed x-ray videos. Overall, the databank provides thermal results from S-FTRC experiments conducted on a mixture of commercially available lithium-ion (Li-ion) cells and specialized Li-ion test cells with varying cell format (18650, 21700, and D-cell) and trigger mechanism (heaters, heaters plus internal short circuiting device, and nail penetration). The radiography video component provides insight into the initiation and propagation of TR in the cells, in addition to consequences of TR measured by the FTRC. Fractions of mass ejected for the cell types are separated into regimes based on the different failure modes of the cells, such as purely venting, partial ejection, and total ejection. With knowledge of the rate and characterization of the internal degradation of the cells during TR, and the amounts of mass ejected and unrecovered, the extent of TR, and therefore the mitigation of TR, is revealed relative to cell types and failure modes.

Lithium-ion battery↗
DOE OSTI2025

Mapping in situ the assembly and dynamics in aqueous supramolecular polymers

Supramolecular polymers, bonded through directional non-covalent interactions, closely mimic dynamic behaviors of biological nanofibers. However, the complexity of assembly pathways makes it highly challenging to unravel the nature of supramolecular dynamics in aqueous environments. Here we introduce a precise combinatorial titration methodology to probe in situ the assembly of peptide amphiphiles (PAs). This approach reveals a binary assembly mechanism governed by equilibrium between spheroidal micelles and β-sheet polymers. Weakening hydrogen bonding shifts the equilibrium towards micelles and decreases the internal structural order of filamentous polymers, promoting supramolecular dynamics. Extending this methodology to two-component copolymerization systems, we find a surprising tendency to form blocky nanostructures with reduced internal phase separation as the mismatch in peptide sequence decreases. Interestingly, while well-mixed copolymers acquire different dynamics, mismatched ones retain the characteristic supramolecular motion of their homopolymer counterparts. These critical insights into supramolecular dynamics offer strategies to tailor the dynamic functions of supramolecular nanomaterials.

Molecular self-assembly↗
DOE OSTI2025

Rewiring Aromatic Compound Consumption: Chromosomal Amplification and Evolution of a Foreign Pathway in Acinetobacter baylyi ADP1

Rational engineering strategies that seek to harness the remarkable diversity of microbial metabolism can be limited by incomplete biological knowledge. As described here, a novel approach to address this challenge involved replacing a native pathway for degrading lignin-derived aromatic compounds via ortho cleavage of protocatechuate in Acinetobacter baylyi ADP1 with a foreign meta-cleavage pathway that uses different enzymes, metabolites, and redox carriers. This alteration may improve lignin valorization and coordinate catabolism with bioproduction strategies. When a 14-kbp region of foreign DNA was inserted in the chromosome, the heterologous genes failed to confer growth on target substrates. Regional gene dosage was increased using a synthetic DNA fragment to promote recombination, and higher copy number enabled growth. During adaptive laboratory evolution, compensatory mutations arose that permit growth with one copy of the foreign genes. This complex metabolic remodeling was accomplished without assumptions about the impediments that initially prevented growth. To understand the changes that emerged, a novel transformation assay identified a combination of mutations sufficient for the new phenotype. Three unexpected changes were revealed: loss of one foreign enzyme, loss of one native enzyme, and loss of a two-component transcriptional regulatory system. This study establishes that large multicopy tandem arrays of poorly adapted pathway genes can confer new functions and improve understanding of metabolism.

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

Two-component dynamics in supercritical $\text {CO}_2$ from inelastic X-ray scattering

Supercritical fluids are characterized by unique thermodynamic properties. One of these properties is the existence of two-component dynamics that is associated with distinct low-frequency and high-frequency vibrational responses of the fluid. However, the origin of this behavior remains unknown. By combining inelastic X-ray scattering and molecular dynamics simulations, we show that this behavior can be connected to density heterogeneities arising from molecular clusters. Analyses of measurements and molecular trajectories suggest that the two-component dynamics emerges due to distinct momentum fluctuations of clustered and unbound molecules. This connection between clusters and two-component dynamics highlights the importance of molecular-structural heterogeneities in supercritical fluids, colloids, and condensed-matter systems.

biophysics↗
DOE OSTI2026

Gaunt and Breit two-electron contributions to mean-field transformations and fine structure splitting

Materials utilized by novel energy systems are often studied using weakly correlated mean-field theories. However, if these systems incorporate heavy elements, relativistic effects must be included. Therefore, a Kramers unrestricted coupled cluster with singles and doubles excitation formalism within a molecular mean-field exact two-component framework (X2C mmf ) using a four-component Dirac–Hartree–Fock (DHF) reference state is presented. The exact X2C mmf transformed normal-order Hamiltonian incorporates all one-electron and two-electron (2e) contributions from the Coulomb, Gaunt, and Breit operators and is used with the equation of motion method to calculate the excitation energies of the alkali group of elements. Using this framework, the effects of 2e Gaunt and Breit integrals are studied. Results demonstrate growing contributions from these integrals to the generated X2C mmf mean-fields and electronic fine structure calculations with increasing atomic number. Overall, this paper outlines the method, its effect within the X2C mmf approach, and lays the foundation for future theoretical development of relativistic calculations within this framework.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

One-Step Relativistic Driven Similarity Renormalization Group Multireference Perturbation Theory

We present an efficient implementation of a one-step relativistic second-order multireference perturbation theory based on the multireference driven similarity renormalization group (MR-DSRG) using the exact two-component (X2C) Hamiltonian, which we denote X2C-DSRG-MRPT2. We show that the X2C-DSRG-MRPT2 method can accurately capture spin–orbit coupling (SOC) effects in the electronic structure of strongly correlated systems containing elements across the periodic table. We further demonstrate that the X2C-DSRG-MRPT2 method, through its variational treatment of SOC effects, can yield spin–orbit splittings with mean absolute percentage errors consistently below 7% with respect to experimental values for systems containing up to sixth row elements. With its modest computational scaling (fourth power in system size for the perturbative step) and high accuracy, X2C-DSRG-MRPT2 provides a promising avenue for the routine treatment of relativistic effects in strongly correlated molecular systems.

Hamiltonians↗
DOE OSTI2025

Heterologous synthesis of a simplified nitrogenase analog in Escherichia coli

The heterologous synthesis of a nitrogen-fixing system in a non-diazotrophic organism is a long-sought-after goal because of the crucial importance of nitrogenase for agronomy, energy, and the environment. Here, we report the heterologous synthesis of a two-component nitrogenase analog fromAzotobacter vinelandii, which consists of the reductase component (NifH) and the cofactor maturase (NifEN), inEscherichia coli. Metal, electron paramagnetic resonance, and activity analyses verify the cluster composition and functional competence of the heterologously expressed NifH and NifEN. Nuclear magnetic resonance, nanoscale secondary ion mass spectrometry, and growth experiments further illustrate the ability of the NifH/NifEN system to reduce N 2 and incorporate the reduced N into the cellular mass. These results establish NifEN/NifH as a simplified nitrogenase analog that could be optimized and engineered to facilitate transgenic expression and biotechnological adaptations of this important metalloenzyme.

Science & Technology - Other Topics↗
DOE OSTI2026

Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens.

Bacteriophages are being cataloged at an accelerating pace and are recognized as key players in nutrient and energy cycling across ecosystems. Yet the bacterial genetic determinants that govern phage-host specificity and infection success remain poorly understood, particularly in clinically and ecologically important genera such as Klebsiella where prior receptor characterization has been almost entirely limited to capsulated strains. Here we used a randomly barcoded, genome-wide, loss-of-function transposon mutant library (RB-TnSeq) of Klebsiella sp. M5al, a naturally acapsular, nitrogen-fixing rhizobacterium, to generate the first systematic, cross-family map of phage receptor gene dependencies in Klebsiella. Challenging the library against 25 double-stranded DNA phages spanning five families in 213 parallel assays, we identified 42 bacterial genes associated with phage infection, of which 15 had no prior association with phage infection in any bacterial system. Disruption of surface receptor biosynthesis genes conferred cross-resistance across multiple phage families, while intracellular gene disruptions had predominantly phage-specific effects. Clonal validation of eight genes confirmed LPS outer core biosynthesis genes as primary receptor determinants alongside additional host factors spanning outer membrane transport, cofactor biosynthesis, and two-component signaling. Comparative analysis across all 25 phages revealed that phage genus rather than family is the stronger predictor of host gene dependency profiles, a finding with direct implications for the functional annotation of uncharacterized phage isolates and rational phage cocktail design. Together, these findings provide a community resource for linking phage genomic diversity to functional host interaction space in this ecologically and clinically important genus.

Gittrich, Marissa R↗
DOE OSTI2025

Hetero-Orbital Two-Component Fractional Quantum Hall States in Bilayer Graphene

A two-dimensional electron system exposed to a strong magnetic field produces a plethora of strongly interacting fractional quantum Hall (FQH) states, the complex topological orders of which are revealed through exotic emergent particles, such as composite fermions, and fractionally charged Abelian and non-Abelian anyons. Much insight has been gained by the study of multicomponent FQH states, where spin and pseudospin indices of the electron contribute additional correlation. Traditional multicomponent FQH states develop in situations where the components share the same orbital states and the resulting interactions are pseudospin independent; this homo-orbital nature is also crucial to their theoretical understanding. Here, we study “hetero-orbital” two-component FQH states, in which the orbital index is part of the pseudospin, rendering the multicomponent interactions strongly SU(2) anisotropic in the pseudospin space. Such states, obtained in bilayer graphene at the isospin transition between 𝑁 = 0 and 𝑁 = 1 electron Landau levels, are markedly different from previous homo-orbital two-component FQH states. In particular, we observe strikingly different behaviors for the parallel-vortex and reverse-vortex attachment composite fermion states, and an anomalously strong two-component 2/5 state over a wide range of magnetic field before it abruptly disappears at a high field. Our findings, combined with detailed theoretical calculations, reveal the surprising robustness of the hetero-orbital FQH effects, significantly enriching our understanding of FQH physics in this novel regime.

Bilayer graphene↗
DOE OSTI2025

Observation of Vortex Stripes in UTe 2

In conventional type-II superconductors, quantum vortices determine the magnetic response of the system and tend to form regular lattices. UTe 2 is a recently discovered heavy Fermion superconductor exhibiting many anomalous macroscopic behaviors, but whether it has a multicomponent order parameter remains open. Here, in this work, we study the vortices of UTe 2 by employing scanning superconducting quantum interference device microscopy. While a small out-of-plane magnetic field produces typical isolated vortices, a higher field generates vortex stripe patterns that evolve with the vortex density. The stripes form at different locations and along different directions in the surface plane when the field is along the b or c axis. The behavior is reproduced by our simulation based on an anisotropic two-component order parameter. This study shows that UTe 2 has a nontrivial disparity of multiple length scales, placing constraints on the multicomponent superconductivity.

UTe2↗
DOE OSTI2025

Tunable pairing with local spin-dependent Rydberg molecule potentials in an atomic Fermi superfluid

We explore the energy spectrum and eigenstates of two-component atomic Fermi superfluids with tunable pairing interactions in the presence of spin-dependent ultralong-range Rydberg molecule (ULRM) potentials, within the Bogoliubov–de Gennes formalism. The attractive ULRM potentials lead to local-density accumulation, while their difference results in a local polarization potential and induces the in-gap Yu-Shiba-Rusinov (YSR) states whose energies lie below the bulk energy gap. A transition from equal population to population imbalance occurs as the pairing strength falls below a critical value, accompanied by the emergence of local Fulde-Ferrell-Larkin-Ovchinnikov (FFLO)–like states characterized by out-of-phase wave functions and lower energies compared to the YSR states. The negative contribution emanating from the FFLO-like states also causes a sign change in the gap function within the ULRM potentials. Depending on the Rydberg excitation, the transition towards population imbalance can be on either the BCS or the Bose-Einstein condensation side of the Fermi superfluid. Additionally, spin-polarized bound states arise along with oscillatory “clumpy states” to compensate for the local-density difference. Here, we discuss possible experimental realizations of the composite Rydberg-atom–Fermi-superfluid system.

Cold and ultracold molecules↗
DOE OSTI2026

SAP-X2C: Optimally-Simple Two-Component Relativistic Hamiltonian with Size-Intensive Picture Change

We present a simple relativistic exact 2-component (X2C) Hamiltonian that models two-electron picture-change effects using Lehtola’s superposition of atomic potentials (SAP) [S. Lehtola, J. Chem. Theory Comput. 15, 1593−1604 (2019)]. The SAP-X2C approach retains the low cost and technical simplicity of the popular 1-electron X2C (1eX2C) predecessor but is significantly more accurate and has a well-defined thermodynamic limit, making it applicable to extended systems (such as large molecules and periodic crystals). The assessment of the SAP-X2C-based Hartree−Fock total and spinor energies, spin−orbit splittings, equilibrium bond distances, and harmonic vibrational frequencies suggests that SAP-X2C is similar to the more complex atomic meanfield (AMF) X2C counterparts in its ability to approximate the 4-component Dirac−Hartree−Fock reference.

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

Relativistic Exact Two-Component Theory in the Generalized Pseudospectral Representation

We present a formulation and implementation of exact two-component (X2C) relativistic theory in the generalized pseudospectral representation. When combined with the Hartree-Fock-Slater framework, this approach enables efficient and accurate treatments of scalar-relativistic and spin-orbit effects in atomic electronic structures without the computational overhead of four-component methods. Benchmark calculations across light and heavy elements demonstrate that the our X2C scheme yields substantially more accurate relativistic corrections to core-electron binding energies than perturbational Breit-Pauli treatments while converging more rapidly with respect to basis size. The method provides an improved computational framework for modeling ultrafast x-ray-induced processes in heavy-element systems.

Wang, Xubo↗