Characterization of Water Structure and Phase Behavior within Metal–Organic Nanotubes
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Engineering topics
Yu, Ping
Publications and source records attributed to Yu, Ping.
Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state
The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered and most widespread riboswitches. Numerous structural studies have been reported for this riboswitch bound with various ligands. However, the ligand-free (apo) structure remains unknown. Here, we report a 3.1 Å resolution crystal structure of Escherichia coli TPP riboswitch in the apo state, which exhibits an extended, Y-shaped conformation further supported by small-angle X-ray scattering data and driven molecular dynamics simulations. The loss of ligand interactions results in helical uncoiling of P5 and disruption of the key tertiary interaction between the sensory domains. Opening of the aptamer propagates to the gene-regulatory P1 helix and generates the key conformational flexibility needed for the switching behavior. Much of the ligand-binding site at the three-way junction is unaltered, thereby maintaining a partially preformed pocket. Together, these results paint a dynamic picture of the ligand-induced conformational changes in TPP riboswitches that confer conditional gene regulation.
59 BASIC BIOLOGICAL SCIENCES↗
Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass ( Panicum virgatum )
Summary Switchgrass ( Panicum virgatum ) is a bioenergy model crop valued for its energy efficiency and drought tolerance. The related monocot species rice ( Oryza sativa ) and maize ( Zea mays ) deploy species‐specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown. To investigate specialized metabolic drought responses in switchgrass, we integrated tissue‐specific transcriptome and metabolite analyses of the genotypes Alamo and Cave‐in‐Rock that feature different drought tolerance. The more drought‐susceptible Cave‐in‐Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid‐biosynthetic genes showed drought‐inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype‐specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought‐induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis verified select drought‐responsive diterpenoids as oxygenated furanoditerpenoids. Drought‐dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass drought responses. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance.
transcriptomics↗
Weak magnetic field-dependent photoluminescence properties of lead bromide perovskites
The strong spin–orbit coupling (SOC) in lead halide perovskites, when inversion symmetry is lifted, has provided opportunities for investigating the Rashba effect in these systems. Moreover, the strong orbital moment, which, in turn, impacts the spin-pair in singlet and triplet electronic states, plays a significant role in enhancing the optoelectronic properties in the presence of external magnetic fields in lead halide perovskites. Here, we investigate the effect of weak magnetic fields (<1 T) on the photoluminescence (PL) properties of CsPbBr 3 nanocrystals with and without Ruddlesden–Popper (RP) faults and single crystals of CH 3 NH 3 PbBr 3 . Along with an enhancement in the PL intensity as a function of an external magnetic field, which is observed in both lead bromide perovskites, the PL emission red-shifts in CsPbBr 3 nanocrystals. Density-functional theory calculations of the electronic band-edge in CsPbBr 3 show almost no change in the energy gap as a function of the external magnetic field. The experimental results, thus, suggest the role of mixing of the triplet and singlet excitonic states under weak magnetic fields. This is further deduced from an enhancement in PL lifetimes as a function of the field in CsPbBr 3 . In CH 3 NH 3 PbBr 3 , an increase in PL intensity is observed under weak magnetic fields; however, no changes in the peak energy or PL lifetimes are observed. The internal magnetic fields due to SOC are characterized for all three samples and found to be the highest for CsPbBr 3 nanocrystals with RP faults.
36 MATERIALS SCIENCE↗
The mechanism driving a solid–solid phase transition in a biomacromolecular crystal
A solid-solid phase transition (SSPT) occurs between distinguishable crystalline forms. Because of its importance in application and theory in material science and condensed matter physics, SSPT has been studied most extensively in metallic alloys, inorganic salt or small organic molecular crystals, but much less so in biomacromolecular crystals. In general, the mechanism of SSPT at atomic and molecular levels is not well understood. Here, we describe the ordered molecular rearrangements in biomacromolecular crystals of the adenine riboswitch (riboA) aptamer using real-time serial crystallography and solution atomic force microscopy (AFM). The large, ligand-induced conformational changes drive the initial phase transition from the apo unit cell (AUC) to the trans unit cell 1 (TUC1). During this transition, coaxial stacking of P1 duplexes becomes the dominant packing interface, whereas P2-P2 interactions are almost completely disrupted, resulting in “floating” layers of molecules. The coupling points in TUC1 and their local conformational flexibility allow the molecules to reorganize to achieve the more densely packed and energetically favorable bound unit cell (BUC). Our study thus reveals the interplay between the conformational changes and the crystal phases—the underlying mechanism that drives the phase transition. Using polarized video microscopy (PVM) to monitor the SSPT in small crystals at high ligand concentration, we have identified the time window during which the major conformational changes take place, and simulated the in crystallo kinetics. Together, these results provide the spatiotemporal information necessary for informing time-resolved crystallography (TRX) experiments. Moreover, this study illustrates a practical approach to characterize SSPT in transparent crystals.
36 MATERIALS SCIENCE↗
Synchronous RNA conformational changes trigger ordered phase transitions in crystals
Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.
59 BASIC BIOLOGICAL SCIENCES↗
Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation
Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.
59 BASIC BIOLOGICAL SCIENCES↗
Development of Advanced ISS-WPA Catalysts for Organic Oxidation at Reduced Pressure/Temperature
The Water Processor Assembly (WPA) at International Space Station (ISS) processes a waste stream via multi-filtration beds, where inorganic and non-volatile organic contaminants are removed, and a catalytic reactor, where low molecular weight organics not removed by the adsorption process are oxidized at elevated pressure in the presence of oxygen and elevated temperature above the normal water boiling point. Operation at an elevated pressure requires a more complex system design compared to a reactor that could operate at ambient pressure. However, catalysts currently available have insufficient activity to achieve complete oxidation of the organic load at a temperature less than the water boiling point and ambient pressure. Therefore, it is highly desirable to develop a more active and efficient catalyst at ambient pressure and a moderate temperature that is less than water boiling temperature. This paper describes our efforts in developing high efficiency water processing catalysts. Different catalyst support structures and coating metals were investigated in subscale reactors and results were compared against the flight WPA catalyst. Detailed improvements achieved on alternate metal catalysts at ambient pressure and 200 F will also be presented in the paper.
Yu, Ping↗
Advanced Catalysts for the Ambient Temperature Oxidation of Carbon Monoxide and Formaldehyde
The primary applications for ambient temperature carbon monoxide (CO) oxidation catalysts include emergency breathing masks and confined volume life support systems, such as those employed on the Shuttle. While Hopcalite is typically used in emergency breathing masks for terrestrial applications, in the 1970s, NASA selected a 2% platinum (Pt) on carbon for use on the Shuttle since it is more active and also more tolerant to water vapor. In the last 10-15 years there have been significant advances in ambient temperature CO oxidation catalysts. Langley Research Center developed a monolithic catalyst for ambient temperature CO oxidation operating under stoichiometric conditions for closed loop carbon dioxide (CO2) laser applications which is also advertised as having the potential to oxidize formaldehyde (HCHO) at ambient temperatures. In the last decade it has been discovered that appropriate sized nano-particles of gold are highly active for CO oxidation, even at sub-ambient temperatures, and as a result there has been a wealth of data reported in the literature relating to ambient/low temperature CO oxidation. In the shorter term missions where CO concentrations are typically controlled via ambient temperature oxidation catalysts, formaldehyde is also a contaminant of concern, and requires specially treated carbons such as Calgon Formasorb as untreated activated carbon has effectively no HCHO capacity. This paper examines the activity of some of the newer ambient temperature CO and formaldehyde (HCHO) oxidation catalysts, and measures the performance of the catalysts relative to the NASA baseline Ambient Temperature Catalytic Oxidizer (ATCO) catalyst at conditions of interest for closed loop trace contaminant control systems.
Nalette, Tim↗
Time domain numerical calculations of unsteady vortical flows about a flat plate airfoil
A time domain numerical scheme is developed to solve for the unsteady flow about a flat plate airfoil due to imposed upstream, small amplitude, transverse velocity perturbations. The governing equation for the resulting unsteady potential is a homogeneous, constant coefficient, convective wave equation. Accurate solution of the problem requires the development of approximate boundary conditions which correctly model the physics of the unsteady flow in the far field. A uniformly valid far field boundary condition is developed, and numerical results are presented using this condition. The stability of the scheme is discussed, and the stability restriction for the scheme is established as a function of the Mach number. Finally, comparisons are made with the frequency domain calculation by Scott and Atassi, and the relative strengths and weaknesses of each approach are assessed.
Hariharan, S. I.↗
Linear and nonlinear acoustic wave propagation in the atmosphere
The investigation of the acoustic wave propagation theory and numerical implementation for the situation of an isothermal atmosphere is described. A one-dimensional model to validate an asymptotic theory and a 3-D situation to relate to a realistic situation are considered. In addition, nonlinear wave propagation and the numerical treatment are included. It is known that the gravitational effects play a crucial role in the low frequency acoustic wave propagation. They propagate large distances and, as such, the numerical treatment of those problems become difficult in terms of posing boundary conditions which are valid for all frequencies.
Hariharan, S. I.↗