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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Analysis and Grading of the Test Performance of PS Modules for the CMS Phase-II Outer Tracker Upgrade

The Outer Tracker detector of the Compact Muon Solenoid (CMS) experiment provides information about the trajectory of charged particles produced in proton-proton collisions at the Large Hadron Collider (LHC). During the High Luminosity LHC upgrade, scheduled for the late 2020s, the Outer Tracker will be replaced with new modules capable of transmitting data to the L1 Trigger. These modules are being assembled at several facilities around the world, including Fermilab, necessitating coordinated standards of module quality. Here I discuss the development of POTATO (Phase-II Outer Tracker Analyzer of Test Outputs), a C++ software which provides a standardized procedure for analyzing and grading test results of the Outer Tracker modules. The particular focus of this paper is on the analysis and grading of the PS (pixel-strip) modules in POTATO.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Ultra-short pulse generation from mid-IR to THz range using plasma wakes and relativistic ionization fronts

In this work, we discuss numerical and experimental results on frequency downshifting and upshifting of a 10 μ m infrared (IR) laser to cover the entire wavelength (frequency) range from λ = 1 to 150 μ m ( ν = 300–2 THz) using two different plasma techniques. The first plasma technique utilizes frequency downshifting of the drive laser pulse in a nonlinear plasma wake. Based on this technique, we have proposed and demonstrated that in a tailored plasma structure, multi-millijoule energy, single-cycle, long-wavelength IR (3–20 μ m) pulses can be generated by using an 810 nm Ti:sapphire drive laser. Here, we extend this idea to the THz frequency regime. We show that sub-joule, terawatts, single-cycle terahertz (2–12 THz or 150–25 μ m) pulses can be generated by replacing the drive laser with a picosecond 10 μ m CO 2 laser and a different shaped plasma structure. The second plasma technique employs frequency upshifting by colliding a CO 2 laser with a rather sharp relativistic ionization front created by ionization of a gas in less than half cycle (17 fs) of the CO 2 laser. Even though the electrons in the ionization front carry no energy, the frequency of the CO 2 laser can be upshifted due to the relativistic Doppler effect as the CO 2 laser pulse enters the front. The wavelength can be tuned from 1 to 10 μ m by simply changing the electron density of the front. While the upshifted light with 5 < λ ( μ m ) < 10 propagates in the forward direction, that with 1 < λ ( μ m ) < 5 is back-reflected. These two plasma techniques seem extremely promising for covering the entire molecular fingerprint region.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

A synthetic cell density signal can drive proliferation in chick embryonic tendon cells and tendon cells from a full size rooster can produce high levels of procollagen in cell culture

Cell density signaling drives tendon morphogenesis by regulating both procollagen production and cell proliferation. The signal is composed of a small, highly conserved protein (SNZR P) tightly bound to a tissue-specific, unique lipid (SNZR L). This allows the complex (SNZR PL) to bind to the membrane of the cell and locally diffuse over a radius of ~1 mm. The cell produces low levels of this signal but the binding to the membrane increases with the number of tendon cells in the local environment. In this article SNZR P was produced in E.coli and SNZR L was chemically synthesized. The two bind together when heated to 60 °C in the presence of Ca ++ and Mg ++ and the synthesized SNZR PL at ng/ml levels can replace serum. Adding SNZR PL to the medium was also tested on primary tendon cells from adult roosters. The older cells were in a maintenance state in vivo and in cell culture they proliferate more slowly than embryonic cells. Nevertheless, after reaching a moderately high cell density, they produced high levels of procollagen similar to the embryonic cells. This data was not expected from older cells but suggests that adult tendon cells can regenerate the tissue after injury when given the correct signals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Integrative Additive Design for Robust SEI Formation in NMC811||Silicon Batteries

Silicon (Si) is considered a promising replacement for graphite anodes in lithium-ion batteries (LIBs) due to its high abundance and exceptional specific capacity, but its widespread commercialization has been hindered by poor electrochemical performance. Among various strategies, the use of functional additives has emerged as one of the most effective and cost-efficient methods to enhance the electrochemical properties of LIBs. In this study, several additives—vinylene carbonate (VC), vinyl ethylene carbonate (VEC), lithium difluorophosphate (LiDFP), lithium difluoro(oxalato)borate (LiDFOB), lithium tetrafluorooxalatophosphate (LiTFOP), and lithium difluorobis(oxalato)phosphate (LiDFBOP)—were systematically investigated in LiNi₀.₈Mn₀.₁Co₀.₁O₂ (NMC811)||Si full cells. Notably, LiDFBOP, a lithium salt containing two oxalate groups, outperformed all other additives, delivering the best capacity retention after 300 cycles. Comprehensive characterizations, including FTIR, SEM, and XPS, revealed that LiDFBOP's superior performance stems from its ability to form a more stable solid electrolyte interphase (SEI) on the Si anode, owing to its favorable molecular structure that integrates the beneficial features of the other additives.

25 ENERGY STORAGE↗
DOE OSTI2024

Covalent Triazine-Based Frameworks with Ru-tda Based Catalyst Anchored via Coordination Bond for Photoinduced Water Oxidation

Light-induced water splitting (hν-WS) for the production of hydrogen as a solar fuel is considered a promising sustainable strategy for the replacement of fossil fuels. An efficient system for hν-WS involves a photoactive material that, upon shining light, is capable of separating and transferring charges to catalysts for the hydrogen and oxygen evolution processes. Covalent triazine-based frameworks (CTFs) represent an interesting class of 2D organic light-absorbing materials that have recently emerged thanks to their tunable structural, optical and morphological properties. Typically, catalysts (Cat) are metallic nanoparticles generated in situ after photoelectroreduction of metal precursors or directly drop-casted on top of the CTF material to generate Cat-CTF assemblies. Here, in this work, the synthesis, characterization and photocatalytic performance of a novel hybrid material, Ru-CTF, is reported, based on a CTF structure featuring dangling pyridyl groups that allow the Ru-tda (tda is [2,2':6',2'“-terpyridine]-6,6'”-dicarboxylic acid) water oxidation catalyst (WOC) unit to coordinate via covalent bond. The Ru-CTF molecular hybrid material can carry out the light-induced water oxidation reaction efficiently at neutral pH, reaching values of maximum TOF of 17 h -1 and TONs in the range of 220 using sodium persulfate as a sacrificial electron acceptor.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Mechanistic Study of the Li–Air Battery with a Co 3 O 4 Cathode and Dimethyl Sulfoxide Electrolyte

The lithium–air battery, a powerful competitor to replace the traditional lithium-ion battery, has attracted increasing attention due to its extremely high theoretical energy density. However, its development is limited by the cathode and electrolyte properties, which should include high stability, conductivity, and electrocatalytic properties in oxygen-rich environments. Here, we employ a systematic first-principles study of Li–O 2 discharge and charge reactions on the Co 3 O 4 -based cathode with the assistance of dimethyl sulfoxide (DMSO) electrolyte. The structure, stability, and electronic properties of different surface reconstructions of the Co 3 O 4 (100) facet are investigated. In addition, the mechanisms and thermodynamic overpotentials of multi-step reactions between Li + /e – and O 2 are provided, where lithium suboxide products (Li 2 O 2 or Li 3 O 2 ) are formed on the different Co 3 O 4 (100) terminations. The solvation shell of Li + components in explicit DMSO solvent is investigated through ab initio molecular dynamics simulations. In general, we find that the Co 3 O 4 (100)-O (oxidized) surface is the most stable one under standard conditions, and the stable Li + solvation structure is found in a tetrahedral Li(DMSO) 4 + shell in the DMSO-based electrolyte. Moreover, in the system of the Co 3 O 4 (100)-O cathode and DMSO electrolyte, the solution model pathway is energetically favorable for the Li–O 2 discharge reaction. It provides a low constant overpotential of 0.17 V during a long-term discharging process, thus causing the final toroid Li 2 O 2 formation on the cathode. During the charging process, an overpotential of 0.36 V is required to rapidly decompose Li 2 O 2 .

25 ENERGY STORAGE↗
DOE OSTI2024

Cycloalkane-rich sustainable aviation fuel production via hydrotreating lignocellulosic biomass-derived catalytic fast pyrolysis oils

Sustainable aviation fuel (SAF) produced from lignocellulosic biomass is emerging as an ideal alternative to conventional jet fuel for aviation sector decarbonization. Catalytic fast pyrolysis (CFP) can convert lignocellulosic biomass into relatively stable bio-oil that can be selectively transformed to various transportation fuels through hydroprocessing under conditions of different severities. In this contribution, two CFP oils produced from pine-based feedstocks over different types of catalysts (i.e., ZSM-5 and Pt/TiO 2 catalysts) were hydrotreated at 125 bar in a non-isothermal process with a maximum temperature of 385 °C over a sulfided NiMo/Al 2 O 3 catalyst to produce SAF with high cycloalkane concentrations of 89–92 wt%. Cycloalkanes are an important component of jet fuel with advantageous fuel properties, such as high energy density, low sooting, and potential for replacing aromatic hydrocarbons to provide good seal swelling properties. The hydrotreating process successfully converted 91–92% of the biogenic carbon in the CFP oil intermediates to liquid-phase hydrotreated products. Through distillation, 39–40 wt% of the hydrotreated oils were collected in the jet-fuel range as SAF fractions. The rest of the hydrotreated product could be valorized as fuels (e.g., diesel) or chemicals. The SAF fractions with oxygen contents below the detection limit (<0.01 wt%) met ASTM D7566 finished fuel blend and D4054 Tier 1 specifications with respect to density, lower heating value (LHV), volatility, flash point, and freeze point. These results indicate hydrotreating lignocellulosic biomass-derived CFP oil as a promising pathway to produce high-quality SAF rich in cycloalkanes. Continued research is required to increase the SAF yield by process improvements, such as increased CFP oil yields, and an enhanced production of SAF-range molecules via e.g., cracking of high-molecular weight compounds either during CFP or hydrotreating, as well as evaluation of a broader range of jet fuel properties and performance requirements.

09 BIOMASS FUELS↗
DOE OSTI2023

Green Needle Coke Production from Pyrolysis Biocrude toward Bio-based Anode Material Manufacture: Biochar Fines Addition Effect as “Physical Template” on the Crystalline Order

Here, a new method for producing green needle coke (GNC) is developed by replacing the “heavy fraction” of petroleum pitch delayed coking with fast pyrolysis biocrude. A series of alternative biocrude distillation, carbonization, and calcination conditions were investigated to determine the influence of these processing parameters onto the crystalline structure of the resulting graphitized material. For the first time, the addition of biochar fines was found to serve as a “physical template” to increase the graphitic nature of the final product. During the initial biocrude carbonization (350–450 °C), volatile compounds are released, and aromatics in pyrolysis biocrude experience condensation, resulting in GNC solids with carbon contents above 95 wt % and some early lamellar structure. In the second stage of the thermal process (25–1500 °C), there are additional thermal decomposition reactions with an increase in the aromatic nature of the graphitized solid. It was found that systematic addition of biochar fines induces a nucleating effect during the GNC development. Thermogravimetric analysis suggests that biochar fines promote polycondensation reactions by modifying the biopitch structure and molecular weight, while elemental analysis (CHN) shows a reduction in both H/C and O/C ratios which are consistent with the increase in aromaticity and removal of oxygenated compounds as thermal treatment evolves. The effects of different bio-based pitch materials (after distillation) and GNC intermediates were evaluated by pyrolysis-gas chromatography mass spectrometry and Fourier transform infrared, displaying slight changes on product yields and quality. X-ray diffraction patterns taken after graphitization evidence an increase in the graphitic order with the addition of biochar fines. Transmittance electron microscopy depicts an improvement on graphitic morphology as biochar fine content increases. The use of biochar fines showed a significant increase in graphitic ordering at addition levels above 0.01 wt %. These results show that thermally treated biocrude/biochar fine systems can produce graphitic structures (hard carbon-like) that might be suitable for the manufacture of sodium-ion batteries.

09 BIOMASS FUELS↗
DOE OSTI2022

Analytic gradients for compressed multistate pair-density functional theory

Photochemical reactions often involve states that are closely coupled due to near degeneracies, for example by proximity to conical intersections. Therefore, a multistate method is used to accurately describe these states; for example, ordinary perturbation theory is replaced by quasidegenerate perturbation theory. Multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to approximate the full dynamical correlation energy of strongly correlated systems, and we recently proposed compressed multistate pair-density functional theory (CMS-PDFT) to treat closely coupled states. In the present paper, we report the implementation of analytic gradients for CMS-PDFT in both OpenMolcas and PySCF, and here we illustrate the use of these gradients by applying the method to the excited states of formaldehyde and phenol.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Superconductivity in CH 4 and BH – 4 containing compounds derived from the high-pressure superhydrides

Inspired by the synthesis of the high-pressure Fm3m LaH 10 superconducting superhydride, systematic density functional theory (DFT) calculations are performed to study ternaries that could be derived from it by replacing two of the hydrogen atoms with boron or carbon and varying the identity of the electropositive element. Though many of the resulting alkali-metal and alkaline-earth MC 2 H 8 phases are predicted to be dynamically stable at mild pressures, their superconducting critical temperatures (T c s) are low because their metallicity results from the filling of an electride-like band. Substitution with a trivalent element leads to phases with substantial metal d- character at the Fermi level whose T c s are typically above 40 K. Here, among the MB 2 H 8 phases examined, KB 2 H 8 , RbB 2 H 8 and CsB 2 H 8 are predicted to be dynamically stable at very mild pressures, and their stability is rationalized by a DFT-Chemical Pressure analysis that elucidates the role of the M atom size. Quantum anharmonic effects strongly affect the properties of KB 2 H 8 , the highest predicted T c compound, near 10 GPa, but molecular dynamics simulations reveal it would decompose below its T c at this pressure. Nonetheless, at ca. 50 GPa KB 2 H 8 is predicted to be thermally stable with a superconducting figure of merit surpassing that of the recently synthesized LaBeH 8 .

36 MATERIALS SCIENCE↗
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 OSTI2023

Near-infrared absorbing acceptor with suppressed triplet exciton generation enabling high performance tandem organic solar cells

Reducing the energy loss of sub-cells is critical for high performance tandem organic solar cells, while it is limited by the severe non-radiative voltage loss via the formation of non-emissive triplet excitons. Herein, we develop an ultra-narrow bandgap acceptor BTPSeV-4F through replacement of terminal thiophene by selenophene in the central fused ring of BTPSV-4F, for constructing efficient tandem organic solar cells. The selenophene substitution further decrease the optical bandgap of BTPSV-4F to 1.17 eV and suppress the formation of triplet exciton in the BTPSV-4F-based devices. The organic solar cells with BTPSeV-4F as acceptor demonstrate a higher power conversion efficiency of 14.2% with a record high short-circuit current density of 30.1 mA cm –2 and low energy loss of 0.55 eV benefitted from the low non-radiative energy loss due to the suppression of triplet exciton formation. We also develop a high-performance medium bandgap acceptor O1-Br for front cells. By integrating the PM6:O1-Br based front cells with the PTB7-Th:BTPSeV-4F based rear cells, the tandem organic solar cell demonstrates a power conversion efficiency of 19%. The results indicate that the suppression of triplet excitons formation in the near-infrared-absorbing acceptor by molecular design is an effective way to improve the photovoltaic performance of the tandem organic solar cells.

14 SOLAR ENERGY↗
DOE OSTI2020

Magnetic, thermal, and electronic-transport properties of EuMg 2 Bi 2 single crystals

The trigonal compound EuMg 2 Bi 2 has recently been discussed in terms of its topological band properties. These are intertwined with its magnetic properties. In this paper detailed studies of the magnetic, thermal, and electronic-transport properties of EuMg 2 Bi 2 single crystals are presented. The Eu + 2 spins 7/2 in EuMg 2 Bi 2 exhibit an antiferromagnetic (AFM) transition at a temperature T N = 6.7 K, as previously reported. By analyzing the anisotropic magnetic susceptibility χ data below T N in terms of molecular-field theory (MFT), the AFM structure is inferred to be a c -axis helix, where the ordered moments in the hexagonal a b -plane layers are aligned ferromagnetically in the a b plane with a turn angle between the moments in adjacent moment planes along the c axis of ≈ 120 ° . An alternate but less likely magnetic structure is a planar structure with nearest-neighbor Eu spins aligned at ≈ 120 ° with respect to each other, where these ordered-moment layers are stacked along the c axis. The magnetic heat capacity exhibits a λ anomaly at T N with evidence of dynamic short-range magnetic fluctuations both above and below T N . The high- T limit of the magnetic entropy is close to the theoretical value for spins 7/2. The in-plane electrical resistivity ρ ( T ) data indicate metallic character with a mild and disorder-sensitive upturn below T min = 23 K. An anomalous rapid drop in ρ ( T ) on cooling below T N as found in zero field is replaced by a two-step decrease in magnetic fields. The ρ ( T ) measurements also reveal an additional transition below T N in applied fields of unknown origin that is not observed in the other measurements and may be associated with an incommensurate to commensurate AFM transition. The dependence of T N on the c -axis magnetic field H ⊥ was derived from the field-dependent χ ( T ) , C p ( T ) , and ρ ( T ) measurements. This T N ( H ⊥ ) was found to be consistent with the prediction of MFT for a c -axis helix with S = 7 / 2 and was used to generate a phase diagram in the H ⊥ – T plane.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Computational study of TATB

We have performed a computational study of TATB. The study is composed of two parts, one where we perform static T = 0 K calculations with several different DFT functionals, to investigate structural properties and obtain a cold curve. Even though the functionals used in this study give poor results at ambient pressure, they perform much better at compression, when the dominance of the van der Waals’ forces in the binding is replaced by more normal interactions. In particular AM05 gives good results, mainly because it doesn’t include any “faulty” van der Waals’. Indeed the van der Waals’ corrected functional (PBE+D2) results shows the worst performance on structural properties. For the cold curve the PBE+D2 functional gives the best results compared to experiments (room temperature) but since the structural properties were bad with this functional we cannot for sure say that this is in any way a validation. It is shown that scaling the AM05 results with a common factor reproduces the experimental data. We leave the question on why to a follow up study but speculate that maybe the experiment and our calculations do not represent the same system set-up. From the structural properties we identify a site in the TATB lattice that contains a high concentration of oxygen and hydrogen. The consequences of this finding, if any, are left to a future project. In the second part of the study we perform extensive high-quality DFT-MD (molecular dynamics with DFT forces) calculations to obtain points on the Hugoniot. This part of the study did not get finished within this project and a more extensive summary of this part will be given in a follow up report at a future date. However, we show that obtaining calculated data is essential for equations of state development since the existing experimental Hugoniot data barely deviates from room temperature isotherm data and thus give no information of the high temperature dependency of materials properties. Our conclusion so far in the project is that being able to calculate materials properties is essential for high explosives since experiments are unable to give information in the high temperature part of phase space. While blind use of DFT cannot (yet) give unambiguous answers, we can still explore qualitatively and use such information to guide us in EOS development. However, the main conclusion is that we need better functionals in DFT to easily extract needed properties from calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Sn-modified BaTiO 3 thin film with enhanced polarization

Hybrid molecular beam epitaxy (MBE) growth of Sn-modified BaTiO 3 films was realized with varying domain structures and crystal symmetries across the entire composition space. Macroscopic and microscopic structures and the crystal symmetry of these thin films were determined using a combination of optical second harmonic generation (SHG) polarimetry and scanning transmission electron microscopy (STEM). SHG polarimetry revealed a variation in the global crystal symmetry of the films from tetragonal (P4mm) to cubic (PM3¯m) across the composition range, x = 0 to 1 in BaTi 1–x Sn x O 3 (BTSO). STEM imaging shows that the long-range polar order observed when the Sn content is low (x = 0.09) transformed to a short-range polar order as the Sn content increased (x = 0.48). Consistent with atomic displacement measurements from STEM, the largest polarization was obtained at the lowest Sn content of x = 0.09 in Sn-modified BaTiO 3 as determined by SHG. Furthermore, these results agree with recent bulk ceramic reports and further identify this material system as a potential replacement for Pb-containing relaxor-based thin film devices.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Deep learning for NLTE spectral opacities

Computer simulations of high energy density science experiments are computationally challenging, consisting of multiple physics calculations including radiation transport, hydrodynamics, atomic physics, nuclear reactions, laser–plasma interactions, and more. To simulate inertial confinement fusion (ICF) experiments at high fidelity, each of these physics calculations should be as detailed as possible. However, this quickly becomes too computationally expensive even for modern supercomputers, and thus many simplifying assumptions are made to reduce the required computational time. Much of the research has focused on acceleration techniques for the various packages in multiphysics codes. In this work, we explore a novel method for accelerating physics packages via machine learning. The non-local thermodynamic equilibrium (NLTE) package is one of the most expensive calculations in the simulations of indirect drive inertial confinement fusion, taking several tens of percent of the total wall clock time. We explore the use of machine learning to accelerate this package, by essentially replacing the physics calculation with a deep neural network that has been trained to emulate the physics code. Overall, we demonstrate the feasibility of this approach on a simple problem and perform a side-by-side comparison of the physics calculation and the neural network inline in an ICF Hohlraum simulation. We show that the neural network achieves a 10× speed up in NLTE computational time while achieving good agreement with the physics code for several quantities of interest.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Diastereomers and Low-Temperature Oxidation

Diastereomers have historically been ignored when building kinetic mechanisms for combustion. Low-temperature oxidation kinetics, which continues to gain interest in both combustion and atmospheric communities, may be affected by the inclusion of diastereomers in radical chain-branching pathways. In this work, key intermediates and transition states lacking stereochemical specification in an existing diethyl ether low-temperature oxidation mechanism were replaced with their diastereomeric counterparts. Rate coefficients for reactions involving diastereomers were computed with ab initio transition state theory master equation calculations. The presence of diastereomers increased rate coefficients by factors of 1.2-1.6 across various temperatures and pressures. Ignition delay simulations incorporating these revised rate coefficients indicate that the diastereomers enhanced the overall reactivity of the mechanism by almost 15% and increased the peak ketohydroperoxide concentration by 30% in the negative temperature coefficient region at combustion-relevant pressures. Furthermore, these results provide an illustrative indication of the important role of stereomeric effects in oxidation kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The ChiS-Family DNA-Binding Domain Contains a Cryptic Helix-Turn-Helix Variant

Sequence-specific DNA-binding domains (DBDs) are conserved in all domains of life. These proteins carry out a variety of cellular functions, and there are a number of distinct structural domains already described that allow for sequence-specific DNA binding, including the ubiquitous helix-turn-helix (HTH) domain. In the facultative pathogen Vibrio cholerae, the chitin sensor ChiS is a transcriptional regulator that is critical for the survival of this organism in its marine reservoir. We recently showed that ChiS contains a cryptic DBD in its C terminus. This domain is not homologous to any known DBD, but it is a conserved domain present in other bacterial proteins. Here, we present the crystal structure of the ChiS DBD at a resolution of 1.28 Å. We find that the ChiS DBD contains an HTH domain that is structurally similar to those found in other DNA-binding proteins, like the LacI repressor. However, one striking difference observed in the ChiS DBD is that the canonical tight turn of the HTH is replaced with an insertion containing a β-sheet, a variant which we term the helix-sheet-helix. Through systematic mutagenesis of all positively charged residues within the ChiS DBD, we show that residues within and proximal to the ChiS helix-sheet-helix are critical for DNA binding. Finally, through phylogenetic analyses we show that the ChiS DBD is found in diverse proteobacterial proteins that exhibit distinct domain architectures. Together, these results suggest that the structure described here represents the prototypical member of the ChiS-family of DBDs.

59 BASIC BIOLOGICAL SCIENCES↗