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DOE OSTI2018

Crystal Structures of Candida albicans Phosphodiesterase 2 and Implications for Its Biological Functions

The cAMP signaling system plays important roles in the physiological processes of pathogen yeast Candida albicans, but its functional mechanism has not been well illustrated. Here, we report the enzymatic characterization and crystal structures of C. albicans phosphodiesterase 2 (caPDE2) in the unliganded and 3-isobutyl-1-methylxanthine-complexed forms. caPDE2 is a monomer in liquid and crystal states and specifically hydrolyzes cAMP with a K M of 35 nM. It does not effectively hydrolyze cGMP as shown by the 1.32 × 105-fold specificity of cAMP/cGMP. The crystal structure of caPDE2 shows significant differences from those of human PDEs. First, the N-terminal fragment of caPDE2 (residues 1–201) tightly associates with the catalytic domain to form a rigid molecular entity, implying its stable molecular conformation for C. albicans to resist environmental stresses. Second, the M-loop, a critical fragment for binding of the substrate and inhibitors to human PDEs, is not a part of the caPDE2 active site. In conclusion, this feature of caPDE2 may provide a structural basis for the design of selective inhibitors for the treatment of yeast infection.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

In Vitro and in Vivo Analyses of the Effects of Source, Length, and Charge on the Cytotoxicity and Immunocompatibility of Cellulose Nanocrystals

Cellulose nanocrystals (CNCs) are an emergent, sustainable nanomaterial which are bio-sourced, abundant, and biodegradable. On account of their high aspect ratio, low density, and mechanical rigidity, they have been employed in numerous areas of biomedical research including as reinforcing materials for bone or tissue scaffolds or as carriers in drug delivery systems. Given the promise of these materials for such use, characterizing and understanding their interactions with biological systems is an important step to prevent toxicity or inflammation. Reported herein are studies aimed at exploring the in-vitro and in-vivo effects that source, length, and charge of the CNCs have on cytotoxicity and immune response. In this study, CNCs from four different biosources (cotton, wood, Miscanthus x. Giganteus, and sea tunicate) were prepared and functionalized with positive or negative charges to obtain a small library of CNCs with a range of dimensions and surface charge. A method to remove endotoxic or other impurities on the CNC surface leftover from the isolation process was developed, and the biocompatibility of the CNCs was subsequently assayed in-vitro and in-vivo. After subcutaneous injection, it was found that unfunctionalized (uncharged) CNCs form aggregates at the site of injection, inducing splenomegaly and neutrophil infiltration, while charged CNCs having surface carboxylates, sulfate half-esters, or primary amines were biologically inert. No effect of particle source or length was observed in the in-vitro and in-vivo studies conducted. The lack of in-vitro or in-vivo immune response toward charged CNCs in these experiments supports their use in future biological studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Fast, clash-free RNA conformational morphing using molecular junctions

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2019

Aeroelastic Indicial Response Reduced-Order Modeling for Flexible Flight Vehicles

A reduced-order modeling method capable of providing computationally efficient predictions of the nonlinear, unsteady aerodynamics encountered by flexible flight vehicles under- going forced oscillations is presented. Models are developed using indicial response theory, which characterizes a vehicle’s dynamics through identification of time-accurate aerodynamic responses due to step changes in the vehicle-state parameters, e.g., angle-of-attack, pitch rate. A coupled computational fluid dynamics aeroelastic analysis is proposed for identifying step (indicial) responses of flexible vehicles. In this approach, aeroelastic indicial responses are simulated via prescribed rigid body motions, while fluid-structure interactions are captured at the subiterative level through coupling to a linear modal structural solver. A nonlinear extension of indicial response theory is applied through time-dependent linear interpolation of a database of locally linear aeroelastic step responses. Reduced-order models are then created using the mathematical principle of convolution applied to the interpolated aeroelastic indicial responses to predict the time-dependent aerodynamic response of a flexible vehicle to any arbitrary prescribed flight maneuver. The NASA FUN3D computational fluid dynamics solver is utilized for simulating full-order trajectories and indicial response functions. Aerodynamic predictions were generated for the X-56A aircraft undergoing a series of harmonic forced oscillations. The s are shown to provide a practical option for evaluating the unsteady aerodynamics of flexible vehicles using high-fidelity simulations.

Hiller, Brett↗

DOE OSTI2022

Temperature Effects in Flexible Adsorption Processes for Amorphous Microporous Polymers

A collection of atomistic molecular simulations is reported that illustrate the impact of adsorption temperature on species uptake and adsorbate-induced structural rearrangement for amorphous polymers of intrinsic microporosity. Temperature-sensitive structural rearrangement is evaluated by contrasting two methods: standard grand canonical Monte Carlo simulations using a rigid framework approximation and a combined Monte Carlo/molecular dynamics approach that fully incorporates framework flexibility. We report single-component gas phase adsorption isotherms for CH 4 , C 2 H 4 , C 2 H 6 , C 3 H 6 , C 3 H 8 , and CO 2 across a temperature range of 250–400 K for models of an archetypal polymer of intrinsic microporosity, PIM-1. A quadratic model is presented that captures two main mechanisms of temperature-dependent adsorption-induced deformation of PIM-1 up to a relative swelling of 1.15: thermal expansion and an increased propensity to swell as a function of species uptake. Two case studies are reported that highlight the critical role of operating temperature in industrial storage and separation applications. The first study focuses on methane storage and delivery applications using a pressure–temperature swing adsorption application (PTSA). We demonstrate that larger working capacities are accompanied by increased volumetric strain between adsorption–desorption steps. The second case study considers PIM-1 as an adsorbent to separate an exemplar ternary syngas mixture at operating temperatures ranging 300–550 K. Here, a temperature threshold of ~400 K is identified, beyond which adsorption-induced PIM-1 swelling is negligible and the solubility selectivity-loading curve transitions to exhibiting a nearly linear relationship.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

A nitrogen- and carbonyl-rich conjugated small-molecule organic cathode for high-performance sodium-ion batteries

Organic-based cathode materials have attracted considerable attention for sustainable Na-ion batteries due to their great promise to overcome the issues arising from the insertion of large Na + into the rigid structures of conventional transition-metal-containing inorganic electrodes. The structural flexibility as a result of weak intermolecular interactions and simple electron- and ion-storage mechanisms found in organic compounds ensure facile and reversible transport of Na ions. In order to address the general drawbacks of small-molecule organic electrodes such as material dissolution in commonly used organic electrolytes and poor electronic conductivity, we report the use of a nitrogen- and carbonyl-rich highly extended π-conjugated small molecule, hexaazatrianthranylene (HATA) embedded quinone (HATAQ), as a cathode for sodium-ion batteries. The unique hydrogen bonds between highly functionalized conjugated HATAQ molecules allow supramolecular graphite-like 2D layered arrangements in the solid state which help facilitate the structural stability during long-term cycling and promote charge transfer. The compound delivers a capacity as high as 460 mA h g -1 at 500 mA g -1 and an excellent capacity retention of 99% (~138 mA h g -1 ) after 5000 cycles at an extremely high rate of 60 A g -1 . The reaction kinetics and redox mechanism of the material have been elucidated by several characterization techniques together with density functional theory (DFT) studies. The insights gained in this work could pave the way for ultra-high-performance small-molecule organic cathodes for sustainable energy storage.

25 ENERGY STORAGE↗

NASA NTRS1993

A nonlinear control design for energy sink simulation in the Euler-Poinsot problem

A nonlinear control design is presented for the purpose of quantitatively simulating the effects of internal damping mechanisms modeled as energy sinks on the attitude dynamics of rigid body spacecraft. Damping is important because it is often the driving mechanism behind passive attitude acquisition maneuvers. Introduction of the controller into the Euler attitude equations of motion allows for the explicit representation of damping without the introduction of additional degrees of freedom required for a physical damping mechanism. This result is significant because perturbation techniques which rely on the closed form solution of the unperturbed problem can then be used to analyze the effects of perturbations upon a damped system. The controller is designed to dissipate kinetic energy while maintaining the magnitude of the angular momentum vector. Control torques are nonlinear functions of the angular momentum components expressed in a body-fixed frame. A numerical simulation of an actual damping mechanism during a decay from minor axis spin into a flat spin is presented showing that the nonlinear controller gives a good qualitative representation and, in many instances, a good quantitative approximation of the attitude motion of a representative spacecraft containing a damping mechanism.

Kammer, Daniel C.↗

NASA NTRS2003

Transonic Unsteady Aerodynamics of the F/A-18E at Conditions Promoting Abrupt Wing Stall

A transonic wind tunnel test of an 8% F/A-18E model was conducted in the NASA Langley Research Center (LaRC) 16-Foot Transonic Tunnel (16-Ft TT) to investigate the Abrupt Wing Stall (AWS) characteristics of this aircraft. During this test, both steady and unsteady measurements of balance loads, wing surface pressures, wing root bending moments, and outer wing accelerations were performed. The test was conducted with a wide range of model configurations and test conditions in an attempt to reproduce behavior indicative of the AWS phenomenon experienced on full-scale aircraft during flight tests. This paper focuses on the analysis of the unsteady data acquired during this test. Though the test apparatus was designed to be effectively rigid. model motions due to sting and balance flexibility were observed during the testing, particularly when the model was operating in the AWS flight regime. Correlation between observed aerodynamic frequencies and model structural frequencies are analyzed and presented. Significant shock motion and separated flow is observed as the aircraft pitches through the AWS region. A shock tracking strategy has been formulated to observe this phenomenon. Using this technique, the range of shock motion is readily determined as the aircraft encounters AWS conditions. Spectral analysis of the shock motion shows the frequencies at which the shock oscillates in the AWS region, and probability density function analysis of the shock location shows the propensity of the shock to take on a bi-stable and even tri-stable character in the AWS flight regime.

Schuster, David M.↗

NASA NTRSDate not supplied

Free-Flight CFD Simulations and Dynamic StabilityAnalysis of the Orion Crew Module

Dynamic stability analysis of the Multi-Purpose Crew Vehicle (MPCV) is performed us-ing the US3D flow solver and a plugin library to solve rigid-body dynamics, Free-Flight CFD(FF-CFD). Previous efforts investigated the free-flight behavior of higher speed, open-backaeroshell shapes. Three primary experimental sources are used to evaluate the predictivecapability of the FF-CFD solver in the low supersonic range (Mach≈1). First, the ballisticrange results obtained at the HFFAF facility at NASA Ames is used to verify the six degree-of-freedom (6-DoF) dynamic capability of the FF-CFD solver. Next, FF-CFD simulationsare preformed using restricted motion and the resultant trajectories are post-processed toobtain pitch damping coefficient as a function of angle-of-attack. The comparison of thepitch damping results obtained with one degree-of-freedom (1-DoF) FF-CFD compare wellwith experimental fits derived from ballistic range data. Finally, the atmospheric flight ca-pability of FF-CFD is compared to data from the Ascent Abort-2 (AA-2) flight experiment.Two simulations were performed using forced and forced-free flight to investigate surfacepressure predictive capability and free-flight aerodynamic performance through a varyingatmosphere at low speed (Mach 0.6-0.2). Surface pressure predicted with FF-CFD agreeswell with experimental trends, with slight over-prediction near the end of the trajectory.The total angle-of-attack for the free-flight portion agrees well with experimental data.

FFCFD↗

NASA NTRS1975

Modal equations for cellular convection

We expand the fluctuating flow variables of Boussinesq convection in the planform functions of linear theory. Our proposal is to consider a drastic truncation of this expansion as a possible useful approximation scheme for studying cellular convection. With just one term included, we obtain a fairly simple set of equations which reproduces some of the qualitative properties of cellular convection and whose steady-state form has already been derived by Roberts (1966). This set of 'modal equations' is analyzed at slightly supercritical and at very high Rayleigh numbers. In the latter regime the Nusselt number varies with Rayleigh number just as in the mean-field approximation with one horizontal scale when the boundaries are rigid. However, the Nusselt number now depends also on the Prandtl number in a way that seems compatible with experiment. The chief difficulty with the approach is the absence of a deductive scheme for deciding which planforms should be retained in the truncated expansion.

Gough, D. O.↗

DOE OSTI2021

Small Molecule Activation with Intramolecular “Inverse” Frustrated Lewis Pairs

The intramolecular “inverse” frustrated Lewis pairs (FLPs) of general formula 1-BR 2 -2-[(Me 2 N) 2 C=N]-C 6 H 4 (3-6) [BR 2 = BMes 2 (3), BC 12 H 8 , (4), BBN (5), BBNO (6)] were synthesized and structurally characterized by multinuclear NMR spectroscopy and X-ray analysis. Furthermore, these novel types of pre-organized FLPs, featuring strongly basic guanidino units rigidly linked to weakly Lewis acidic boryl moieties via an ortho-phenylene linker, are capable of activating H-H, C-H, N-H, O-H, Si-H, B-H and C=O bonds. 4 and 5 deprotonated terminal alkynes to form the zwitterionic borates 1-(RC≡C-BR 2 )-2-[(Me 2 N) 2 C=NH]-C 6 H 4 (R = Ph, H) and reacted with ammonia, BnNH 2 and pyrrolidine, to generate the adducts 1-(R 2 HN→BR 2 )-2-[(Me 2 N) 2 C=NH]-C 6 H 4 , where the N-H functionality is activated by intramolecular H-bond interactions. In addition, 5 was found to rapidly add across the double bond of H 2 CO, PhCHO and PhNCO to form cyclic zwitterionic guanidinium borates in excellent yields. Likewise, 5 is capable of cleaving H 2 , HBPin and PhSiH 3 to form various amino boranes. Collectively, the results demonstrate that these new types of intramolecular FLPs featuring weakly Lewis acidic boryl and strongly basic guanidino moieties are as potent as conventional intramolecular FLPs with strongly Lewis acidic units in activating small molecules.

08 HYDROGEN↗

DOE OSTI2022

Reviewing clinical considerations and guideline recommendations of C1 inhibitor prophylaxis for hereditary angioedema

Abstract Background Hereditary angioedema (HAE), a rare disease that is characterized by painful and recurring non‐allergic swelling episodes, is caused by the deficiency or dysfunction of C1 inhibitor (C1INH) protein. A comprehensive HAE management plan may require long‐term prophylaxis (LTP) in addition to on‐demand treatment to help “normalize” patients' lives so that they may fully engage in work, school, family, and leisure activities. Aim The main objective of this narrative review is to provide an overview of updated guideline recommendations specific to LTP of HAE and discuss clinical considerations and pharmacologic management options, with a focus on C1INH. Materials and Methods The authors reviewed relevant HAE literature for current recommendations regarding LTP and the role of C1NH. Results Acute HAE attacks are treated with on‐demand medication; however, there is a consensus that LTP should routinely be considered for risk reduction and prevention of future episodes. The 2017 World Allergy Organization/European Academy of Allergy and Clinical Immunology guidelines recommend that all patients with HAE be evaluated for LTP routinely and the 2020 HAE Association (HAEA) guidelines emphasize that the decision to use LTP should not be based on rigid criteria, but rather should be based on individual patient needs. Both guidelines recommend C1INH as first‐line/preferred therapy for LTP in a range of patient types including adults, children/adolescents, and pregnant/lactating patients. The HAEA also recommends the kallikrein inhibitor, lanadelumab, as a first‐line option for LTP. HAE pathway‐specific agents for LTP have not been associated with notable safety concerns. Discussion Plasma‐derived C1INH has been available for 40+ years in Europe and impacts multiple targets within the HAE pathway. C1INH has been used for on‐demand treatment and LTP. A subcutaneous formulation of plasma‐derived C1INH is approved for LTP and produces functional C1INH activity levels consistently above the threshold needed for protection from HAE attacks. Other pathway‐specific options for LTP include the plasma kallikrein inhibitors, lanadelumab‐flyo and berotralstat, approved for adults and pediatric patients aged ≥12 years. C1INH is approved for adults and pediatric patients aged ≥6 years. Conclusion Assessing the need for LTP is vital in the ongoing dialogue between clinicians and patients, as both disease‐related factors and patient preferences may change over time. Among available options for LTP, plasma‐derived C1INH is the broadly recommended first‐line option for LTP in patients with HAE, including pregnant/lactating women and pediatric patients (≥6 years).

Anderson, John↗

DOE OSTI2017

Exchange interactions and the state of iron atoms in Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ}

On the basis of the results of magnetic susceptibility and ESR studies of the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions iron atoms in the solid solutions of cubic modification of bismuth niobate were found to exist as Fe(III) monomers and exchange bound Fe(III)-O-Fe(III) dimers with antiferro- and ferromagnetic type of superexchange. The exchange parameters and the distribution of monomers and dimers in the solid solutions were calculated as a function of paramagnetic atom content. - Graphical abstract: The study of the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions showed that the introduction of iron atoms into the structure of Bi{sub 3}NbO{sub 7} stabilizes the cubic structure of bismuth niobate making the phase transition tetragonal ↔ cubic structure irreversible. In the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions we observe the formation of dimers with antiferro- and ferromagnetic exchange. Such clusters are partially retained even at the infinite dilution of the solid solution, which testifies for their rigidity. A sufficiently high parameter of ferromagnetic exchange in a dimer (+53 cm{sup −1}) seems to result from iron atoms being located in the vicinity of oxygen vacancy. - Highlights: • The reversible transition cubic – tetragonal modifications in Bi{sub 3}NbO{sub 7} becomes irreversible. • Only cubic modification of Bi{sub 3}Nb{sub 1-x}Fe{sub x}O{sub 7-δ} is stable due to clusters of Fe atoms. • These clusters are sufficiently strong and retained even at the infinite dilution. • The calculations of magnetic susceptibility give the distribution of the clusters and single atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Mechanistic insights into allosteric regulation of the A 2A adenosine G protein-coupled receptor by physiological cations

Cations play key roles in regulating G-protein-coupled receptors (GPCRs), although their mechanisms are poorly understood. Here, 19 F NMR is used to delineate the effects of cations on functional states of the adenosine A 2A GPCR. While Na + reinforces an inactive ensemble and a partial-agonist stabilized state, Ca 2+ and Mg 2+ shift the equilibrium toward active states. Positive allosteric effects of divalent cations are more pronounced with agonist and a G-protein-derived peptide. In cell membranes, divalent cations enhance both the affinity and fraction of the high affinity agonist-bound state. Molecular dynamics simulations suggest high concentrations of divalent cations bridge specific extracellular acidic residues, bringing TM5 and TM6 together at the extracellular surface and allosterically driving open the G-protein-binding cleft as shown by rigidity-transmission allostery theory. Lastly, an understanding of cation allostery should enable the design of allosteric agents and enhance our understanding of GPCR regulation in the cellular milieu.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

One-dimensional twisted and tubular structures of zinc oxide by semiconductor-catalyzed vapor–liquid–solid synthesis

The exploration of unconventional catalysts for the vapor-liquid-solid synthesis of one-dimensional materials promises to yield new morphologies and functionality. Here, we show, for the model ZnO system, that unusual nanostructures can be produced via a semiconductor (Ge) catalyst. As well as the usual straight nanowires, we describe two other distinct morphologies: twisted nanowires and twisted nanotubes. The twisted nanotubes show large hollow cores and surprisingly high twisting rates, up to 9°/μm, that cannot be easily explained through the Eshelby twist model. A combination of ex situ and in situ transmission electron microscopy measurements suggest that the hollow core results from a competition between growth and etching at the Ge-ZnO interface during synthesis. The twisting rate is consistent with a softening of elastic rigidity. Finally, these results indicate that the use of unconventional, nonmetallic catalysts provides opportunities to synthesize unusual oxide nanostructures with potentially useful properties.

36 MATERIALS SCIENCE↗

NASA NTRS1979

Theory of flux anisotropies in a guiding center plasma

Assuming time stationarity of the one-particle distribution function f on the scale of the bounce motion of particles in a magnetic field, the paper expands the Vlasov equation through O(epsilon) in the adiabatic parameter epsilon, which is the ratio of particle gyroradius to scale length of the magnetic field. Since f is directly proportional to particle flux differential in kinetic energy and solid angle, f is in principle measurable in space experiments, and the present analysis is tailored to be explicitly applicable to space problems. It is shown that the usual expression for the electric field which produces plasma corotation in an axisymmetric system such as a dipole also holds for any nonaxisymmetric but rigidly rotating magnetic field pattern, provided the observed magnetic field is used in place of the dipole field. The analysis is applied to the electric field in a rigidly corotating magnetosphere.

Birmingham, T. J.↗

NASA NTRS1980

The dynamics and control of large flexible space structures, 3. Part A: Shape and orientation control of a platform in orbit using point actuators

The dynamics, attitude, and shape control of a large thin flexible square platform in orbit are studied. Attitude and shape control are assumed to result from actuators placed perpendicular to the main surface and one edge and their effect on the rigid body and elastic modes is modelled to first order. The equations of motion are linearized about three different nominal orientations: (1) the platform following the local vertical with its major surface perpendicular to the orbital plane; (2) the platform following the local horizontal with its major surface normal to the local vertical; and (3) the platform following the local vertical with its major surface perpendicular to the orbit normal. The stability of the uncontrolled system is investigated analytically. Once controllability is established for a set of actuator locations, control law development is based on decoupling, pole placement, and linear optimal control theory. Frequencies and elastic modal shape functions are obtained using a finite element computer algorithm, two different approximate analytical methods, and the results of the three methods compared.

Bainum, P. M.↗

NASA NTRS1986

The isotopes of hydrogen and helium in the Galactic cosmic radiation - Their source abundances and interstellar propagation

A self-consistent model describing the interstellar propagation of Galactic cosmic radiation is developed using low-energy measurements and calculations of the effects of interstellar propagation and solar modulation. The source ratio H-1/He-4 at constant energy per nucleon is determined to be 12.2 + or - 1.5, and the mean path length for an exponential path length weighting function required to account for the data is 7.2 + or - 1.0 g/sq cm. The measured H-2/He-4 and He-3/He-4 ratios do not vary by more than about 30 percent over the solar cycle. The behavior of the ratios during the solar cycle reflects the energy dependence of the local interstellar ratios, and leads to an energy dependence of the mean path length below 1 GeV per nucleon weaker than that inferred from boron/carbon. The source ratio H-1/He-4 inferred from the low-energy data is consistent both with the value inferred from high-energy cosmic ray data using a model of rigidity-dependent confinement and with the solar system abundance ratio.

Beatty, James J.↗