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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Development of allosteric and selective CDK2 inhibitors for contraception with negative cooperativity to cyclin binding

Compared to most ATP-site kinase inhibitors, small molecules that target an allosteric pocket have the potential for improved selectivity due to the often observed lower structural similarity at these distal sites. Despite their promise, relatively few examples of structurally confirmed, high-affinity allosteric kinase inhibitors exist. Cyclin-dependent kinase 2 (CDK2) is a target for many therapeutic indications, including non-hormonal contraception. However, an inhibitor against this kinase with exquisite selectivity has not reached the market because of the structural similarity between CDKs. In this paper, we describe the development and mechanism of action of type III inhibitors that bind CDK2 with nanomolar affinity. Notably, these anthranilic acid inhibitors exhibit a strong negative cooperative relationship with cyclin binding, which remains an underexplored mechanism for CDK2 inhibition. Furthermore, the binding profile of these compounds in both biophysical and cellular assays demonstrate the promise of this series for further development into a therapeutic selective for CDK2 over highly similar kinases like CDK1. The potential of these inhibitors as contraceptive agents is seen by incubation with spermatocyte chromosome spreads from mouse testicular explants, where they recapitulate Cdk2 -/- and Spdya -/- phenotypes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Modeling separation of lanthanides via heterogeneous ligand binding

Individual lanthanide elements have physical/electronic/magnetic properties that make each useful for specific applications. Several of the lanthanides cations (Ln 3+ ) naturally occur together in the same ores. They are notoriously difficult to separate from each other due to their chemical similarity. Predicting the Ln 3+ differential binding energies (ΔΔE) or free energies (ΔΔG) at different binding sites, which are key figures of merit for separation applications, will help design of materials with lanthanide selectivity. We apply ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) to calculate ΔΔG for Ln 3+ coordinated to ligands in water and embedded in metal–organic frameworks (MOFs), and ΔΔE for Ln 3+ bonded to functionalized silica surfaces, thus circumventing the need for the computational costly absolute binding (free) energies ΔG and ΔE. Perturbative AIMD simulations of water-inundated simulation cells are applied to examine the selectivity of ligands towards adjacent Ln 3+ in the periodic table. Static DFT calculations with a full Ln 3+ first coordination shell, while less rigorous, show that all ligands examined with net negative charges are more selective towards the heavier lanthanides than a charge-neutral coordination shell made up of water molecules. Amine groups are predicted to be poor ligands for lanthanide-binding. Finally, we also address cooperative ion binding, i.e., using different ligands in concert to enhance lanthanide selectivity.

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

A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance

The elicitation of broadly neutralizing antibodies (bnAbs) is a major goal in the design of vaccines against rapidly-mutating viruses. In the case of influenza, many bnAbs that target conserved epitopes on the stem of the hemagglutinin protein (HA) have been discovered. However, these antibodies are rare, are not boosted well upon reinfection, and often have low neutralization potency, compared to strain-specific antibodies directed to the HA head. Different hypotheses have been proposed to explain this phenomenon. We use a coarse-grained computational model of the germinal center reaction to investigate how B-cell receptor binding valency affects the growth and affinity maturation of competing B-cells. We find that receptors that are unable to bind antigen bivalently, and also those that do not bind antigen cooperatively, have significantly slower rates of growth, memory B-cell production, and, under certain conditions, rates of affinity maturation. The corresponding B-cells are predicted to be outcompeted by B-cells that bind bivalently and cooperatively. We use the model to explore strategies for a universal influenza vaccine, e.g., how to boost the concentrations of the slower growing cross-reactive antibodies directed to the stem. The results suggest that, upon natural reinfections subsequent to vaccination, the protectiveness of such vaccines would erode, possibly requiring regular boosts. Collectively, our results strongly support the importance of bivalent antibody binding in immunodominance, and suggest guidelines for developing a universal influenza vaccine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Site 2 of the Yersinia pestis substrate-binding protein YfeA is a dynamic surface metal-binding site

The substrate-binding protein YfeA (also known as YPO2439 or y1897) is a polyspecific metal-binding protein that is crucial for nutrient acquisition and virulence in Yersinia pestis, the causative microbe of plague. YfeA folds into a monomeric c-clamp like other substrate-binding proteins and has two metal-binding sites (sites 1 and 2). Site 2 is a bidentate surface site capable of binding Zn and Mn atoms and is a unique feature of YfeA. Occasionally, the site 2 residues of two YfeA molecules will cooperate with the histidine tag of a third YfeA molecule in coordinating the same metal and lead to metal-dependent crystallographic packing. Here, three crystal structures of YfeA are presented at 1.85, 2.05 and 2.25 Å resolution. A comparison of the structures reveals that the metal can be displaced at five different locations ranging from ~4 to ~16 Å away from the canonical site 2. These observations reveal different configurations of site 2 that enable cooperative metal binding and demonstrate how site 2 is dynamic and freely available for inter-protein metal coordination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch

T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box to achieve functional conformations remains unclear. Here, by combining SAXS, single-molecule FRET and computational modeling, we elaborate the folding energy landscape of a translational T-box aptamer consisting of stems I, II and IIA/B, which Mg 2+ -induced global folding and tRNA binding are cooperatively coupled. smFRET measurements reveal that high Mg 2+ stabilizes IIA/B and its stacking on II, which drives the pre-docking of I and II into a competent conformation, subsequent tRNA binding promotes docking of I and II to form a high-affinity tRNA binding groove, of which the essentiality of IIA/B and S-turn in II is substantiated with mutational analysis. We highlight a delicate balance among Mg 2+ , the intra- and intermolecular RNA-RNA interactions in modulating RNA folding and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Twisted bilayer graphene. V. Exact analytic many-body excitations in Coulomb Hamiltonians: Charge gap, Goldstone modes, and absence of Cooper pairing

We find exact analytic expressions for the energies and wave functions of the charged and neutral excitations above the exact ground states (at rational filling per unit cell) of projected Coulomb Hamiltonians in twisted bilayer graphene. Our exact expressions are valid for any form of the Coulomb interaction and any form of A A and A B / B A tunneling. The single charge excitation energy is a convolution of the Coulomb potential with a quantum geometric tensor of the TBG bands. The neutral excitations are (high-symmetry group) magnons, and their dispersion is analytically calculated in terms of the form factors of the active bands in TBG. The two-charge excitation energy and wave functions are also obtained, and a sufficient condition on the graphene eigenstates for obtaining a Cooper pair from Coulomb interactions is obtained. For the actual TBG bands at the first magic angle, we can analytically show that the Cooper pair binding energy is zero in all such projected Coulomb models, implying that either phonons and/or nonzero kinetic energy are needed for superconductivity. Since Vafek and Kang [Phys. Rev. Lett. 125, 257602 (2020)] showed that the kinetic energy bounds on the superexchange energy are less 10 -3 in Coulomb units, the phonon mechanism becomes then very likely. If nonetheless the superconductivity is due to kinetic terms which render the bands nonflat, one prediction of our theory is that the highest T c would not occur at the highest DOS.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Characterization of the Superconducting Microwave Properties of Aluminum Manganese

A microwave kinetic inductance detector (MKID) is a superconducting pair breaking detector that offers a number of unique advantages for realizing large-format arrays of ultra-sensitive detectors, such as inherent multiplexibility and relative ease of fabrication. With the detection threshold being set by the Cooper pair binding energy, and correspondingly, the superconducting critical temperature (T c ), typically well-understood MKID materials such as aluminum (Al) present a lower limit on the operating frequency. Aluminum manganese (Al-Mn) is a promising candidate material for MKIDs because it can be fabricated with nearly identical processing as pure Al, but allows for control of the T c , with varying levels of Mn doping or post-deposition heat treatment. In this study, we present initial results from an early characterization of AlMn using a series of lumped-element superconducting microwave resonators, including measurements of T c , internal quality factor, and noise performance over a range of Mn doping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics

A salt bridge, one of the representative structural factors established by non-covalent interactions, plays a crucial role in stabilizing the structure and regulating the protein function, but its role in dynamic processes has been elusive. Here, to scrutinize the structural and functional roles of the salt bridge in the process of performing the protein function, we investigated the effects of salt bridges on the allosteric structural transition of homodimeric hemoglobin (HbI) by applying time-resolved X-ray solution scattering (TRXSS) to the K30D mutant, in which the interfacial salt bridges of the wild type (WT) are abolished. The TRXSS data of K30D are consistent with the kinetic model that requires one monomer intermediate in addition to three structurally distinct dimer intermediates (I 1 , I 2 , and I 3 ) observed in WT and other mutants. The kinetic and structural analyses show that K30D has an accelerated biphasic transition from I 2 to I 3 by more than nine times compared to WT and lacks significant structural changes in the transition from R-like I 2 to T-like I 3 observed in WT, unveiling that the loss of the salt bridges interrupts the R–T allosteric transition of HbI. Besides, the correlation between the bimolecular CO recombination rates in K30D, WT, and other mutants reveals that the bimolecular CO recombination is abnormally decelerated in K30D, indicating that the salt bridges also affect the cooperative ligand binding in HbI. These comparisons of the structural dynamics and kinetics of K30D and WT show that the interfacial salt bridges not only assist the physical connection of two subunits but also play a critical role in the global structural signal transduction of one subunit to the other subunit via a series of well-organized structural transitions.

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

Dark Matter Induced Power in Quantum Devices

We point out that power measurements of single quasiparticle devices open a new avenue to detect dark matter (DM). The threshold of these devices is set by the Cooper pair binding energy, and is therefore so low that they can detect DM as light as about an MeV incoming from the Galactic halo, as well as the low-velocity thermalized DM component potentially present in the Earth. Using existing power measurements with these new devices, as well as power measurements with SuperCDMS-CPD, we set new constraints on the spin-independent DM scattering cross section for DM masses from about 10 MeV to 10 GeV. We outline future directions to improve sensitivity to both halo DM and a thermalized DM population in the Earth using power deposition in quantum devices. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Kinetic Inductance Phonon-Mediated Detectors for Dark Matter: R&D at NEXUS

Superconducting thin films have long been used as phonon sensors, particularly in the field of dark matter (DM) direct detection, due to the meV-scale Cooper-pair binding energy. A novel class of these detectors based on microwave kinetic inductance detectors, dubbed Kinetic Inductance Phonon-Mediated Detectors (KIPMDs), offers an attractive architecture for microcalorimeters to probe DM down to the fermionic thermal relic mass limit of a few keV. Such a device featuring an aluminum resonator patterned onto a silicon substrate was operated at the NEXUS low-background facility at Fermilab for characterization and evaluation of its efficacy for a dark matter search. With this device we have demonstrated a resolution on the energy absorbed by the superconductor of 2.5 eV, a factor of two better than current state-of-the-art. In this talk, I will present our measurement of the energy resolution and phonon collection efficiency performed by exposing the bare substrate to a pulsed source of 470 nm photons. I will also discuss the path forward to obtaining in these devices the sub-eV resolution required to test the “Freeze-in” class of DM models. Finally, I will review other complementary efforts in our group to develop a superconducting qubit-based low-threshold detector.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS2000

Human recombinant soluble guanylyl cyclase: expression, purification, and regulation

The alpha1- and beta1-subunits of human soluble guanylate cyclase (sGC) were coexpressed in the Sf9 cells/baculovirus system. In addition to the native enzyme, constructs with hexahistidine tag at the amino and carboxyl termini of each subunit were coexpressed. This permitted the rapid and efficient purification of active recombinant enzyme on a nickel-affinity column. The enzyme has one heme per heterodimer and was readily activated with the NO donor sodium nitroprusside or 3-(5'-hydroxymethyl-2'furyl)-1-benzyl-indazole (YC-1). Sodium nitroprusside and YC-1 treatment potentiated each other in combination and demonstrated a remarkable 2,200-fold stimulation of the human recombinant sGC. The effects were inhibited with 1H-(1,2, 4)oxadiazole(4,3-a)quinoxalin-1one (ODQ). The kinetics of the recombinant enzyme with respect to GTP was examined. The products of the reaction, cGMP and pyrophosphate, inhibited the enzyme. The extent of inhibition by cGMP depended on the activation state of the enzyme, whereas inhibition by pyrophosphate was not affected by the enzyme state. Both reaction products displayed independent binding and cooperativity with respect to enzyme inhibition. The expression of large quantities of active enzyme will facilitate structural characterization of the protein.

NASA Discipline Cardiopulmonary↗
NASA NTRS2008

Science on the Moon: The Wailing Wall of Space Exploration

Science on and from the Moon has important implications for expanding human knowledge and understanding, a prospect for the 21st Century that has been under discussion for at least the past 25 years. That having been said, however, there remain many issues of international versus national priorities, strategy, economy, and politics that come into play. The result is a very complex form of human behavior where science and exploration take center stage, but many other important human options are sacrificed. To renew this dialogue about the Moon, it seems we are already rushing pell-mell into it as has been done in the past. The U.S., Japan, China, India, and Russia either have sent or plan to send satellites and robotic landers there at this time. What does a return to the Moon mean, why are we doing this now, who should pay for it, and how? The only semblance of such a human enterprise seems to be the LHC currently coming online at CERN. Can it be used as a model of international collaboration rather than a sports or military event focused on national competition? Who decides and what is the human sacrifice? There are compelling arguments for establishing science on the Moon as one of the primary goals for returning to the Moon and venturing beyond. A number of science endeavors will be summarized, beyond lunar and planetary science per se. These include fundamental physics experiments that are background-limited by the Earth's magnetic dipole moment and noise produced by its atmosphere and seismic interior. The Moon is an excellent platform for some forms of astronomy. Other candidate Moon-based experiments vary from neutrino and gravitational wave astronomy, particle astrophysics, and cosmic-ray calorimeters, to space physics and fundamental physics such as proton decay. The list goes on and includes placing humans in a hostile environment to study the long-term effects of space weather. The list is long, and even newer ideas will come from this COSPAR conference. However, whatever the list the issue of cooperation and binding collaboration remains. As observers of Moon and other space enterprises, we all know that a room full of 60 scientists will not agree on much of anything and there will probably be 60! please for more funding. People have special interests and little common sense (e.g., conflict between NSF- and NASA-funding roadmaps). Scientists are no exception. Nevertheless, CERN has done it on Earth! Can we do the same on the Moon? Some of the present generation of proposals for science from and on the Moon, plus new ones, will witness a place in space exploration's future. It is clear, however, that the world has not thought this through adequately, except for talk about an international space federation whatever that is. An outpost on the Moon with humans permanently living there much like Antarctica on Earth may be in our future. However, such planning is our collective international responsibility and not that of special-interest investigators from individual nations unless they intend to pay for it.

Wilson, Thomas↗
NASA NTRS1993

Theoretical Study of the H2-ML(+) Binding Energies

The cooperative ligand effects are studied in MLH2(+) and the results are compared to the recent experiments of Kemper et al. The bonding in these compounds is principally electrostatic in origin; however, ligand to metal and metal to ligand donations are important, especially for H2. We show that differences arise among the vanadium, cobalt, and copper complexes which are due to 3d donation to H2. Electron correlation is required to describe the dative interaction, and we find that second order Moller-Plesset perturbation theory (MP2) yields a good description of these systems compared with higher levels of correlation (such as the modified coupled pair functional and coupled cluster approaches) and experiment. However, obtaining quantitative results requires higher levels of theory than MP2.

Maitre, Philippe↗