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DOE OSTI2021

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Signatures of Kramers-Weyl fermions in the charge density wave material (TaSe 4 ) 2 I

The quasi-one-dimensional charge density wave (CDW) material (TaSe 4 ) 2 I has been recently predicted to host Kramers-Weyl (KW) fermions which should exist in the vicinity of high symmetry points in the Brillouin zone in chiral materials with strong spin-orbit coupling. However, direct spectroscopic evidence of KW fermions is limited. Here we use helicity-dependent laser-based angle-resolved photoemission spectroscopy (ARPES) in conjunction with tight-binding and first-principles calculations to identify KW fermions in (TaSe 4 ) 2 I. We find that topological and symmetry considerations place distinct constraints on the (pseudo-) spin texture and the observed spectra around a KW node. Our findings highlight the unique topological nature of (TaSe 4 ) 2 I and provide a pathway for identifying KW fermions in other chiral materials.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Rigorous constraints on three-nucleon forces in chiral effective field theory from fast and accurate calculations of few-body observables

We explore the constraints on the three-nucleon force (3NF) of chiral effective field theory (χ EFT) that are provided by bound-state observables in the A = 3 and A = 4 sectors. Our statistically rigorous analysis incorporates experimental error, computational method uncertainty, and the uncertainty due to truncation of the χ EFT expansion at next-to-next-to-leading order. A consistent solution for the 3 H binding energy, the 4 He binding energy and radius, and the 3 H β-decay rate can only be obtained if χ EFT truncation errors are included in the analysis. Here, the β-decay rate is the only one of these that yields a nondegenerate constraint on the 3NF low-energy constants, which makes it crucial for the parameter estimation. We use eigenvector continuation for fast and accurate emulation of no-core shell model calculations of the few-nucleon observables. This facilitates sampling of the posterior probability distribution, allowing us to also determine the distributions of the parameters that quantify the truncation error. We find a χ EFT expansion parameter of Q = 0.33 ± 0.06 for these observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Density matrix renormalization group description of the island of inversion isotopes F 28 – 33

Recent experiments have confirmed that the neutron-rich isotopes 28,29 F belong to the so-called island of inversion (IOI), a region of the nuclear chart around Z = 10 and N = 20 where nuclear structure deviates from the standard shell model predictions due to deformation and continuum effects. However, while the general principles leading to the IOI are relatively well understood, the details of the low-lying structure of the exotic fluorine isotopes 28–33 F are basically unknown. In this study, we perform large-scale shell model calculations including continuum states to investigate the properties of the neutron-rich isotopes 25–33 F, from a core of 24 O and using an effective two-body interaction with a small number of adjustable parameters in the central and tensor channels. We develop two models adjusted on experimentally confirmed states in 25,26 O and 25–27 F based on different assumptions concerning the positions of the neutron 0d 3/2 and 1p 3/2 shells, and solve the many-body problem using the density matrix renormalization group (DMRG) method for open quantum systems in an sd–fp model space. We obtain the first detailed spectroscopy of 25–33F in the continuum and show how the interplay between continuum effects and deformation explains the recent data on 28,29 F. Several deformed one- and two-neutron halo states are predicted in 29,31 F, and we provide some information about the possible structure of the heaviest fluorine isotopes. We also suggest several experimental studies of interest to constraint models and test the present predictions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2013

Multi-User Space Link Extension (SLE) System

The Multi-User Space (MUS) Link Extension system, a software and data system, provides Space Link Extension (SLE) users with three space data transfer services in timely, complete, and offline modes as applicable according to standards defined by the Consultative Committee for Space Data Systems (CCSDS). MUS radically reduces the schedule, cost, and risk of implementing a new SLE user system, minimizes operating costs with a lights-out approach to SLE, and is designed to require no sustaining engineering expense during its lifetime unless changes in the CCSDS SLE standards, combined with new provider implementations, force changes. No software modification to MUS needs to be made to support a new mission. Any systems engineer with Linux experience can begin testing SLE user service instances with MUS starting from a personal computer (PC) within five days. For flight operators, MUS provides a familiar-looking Web page for entering SLE configuration data received from SLE. Operators can also use the Web page to back up a space mission's entire set of up to approximately 500 SLE service instances in less than five seconds, or to restore or transfer from another system the same amount of data from a MUS backup file in about the same amount of time. Missions operate each MUS SLE service instance independently by sending it MUS directives, which are legible, plain ASCII strings. MUS directives are usually (but not necessarily) sent through a TCP-IP (Transmission Control Protocol Internet Protocol) socket from a MOC (Mission Operations Center) or POCC (Payload Operations Control Center) system, under scripted control, during "lights-out" spacecraft operation. MUS permits the flight operations team to configure independently each of its data interfaces; not only commands and telemetry, but also MUS status messages to the MOC. Interfaces can use single- or multiple-client TCP/IP server sockets, TCP/IP client sockets, temporary disk files, the system log, or standard in, standard out, or standard error as applicable. By defining MUS templates in ASCII, the flight operations team can include any MUS system variable in telemetry or command headers or footers, and/or in status messages. Data fields can be arranged within messages in different sequences, according to the mission s needs. The only constraints imposed are on the format of MUS directive strings, and some bare minimum logical requirements that must be met in order for MUS to read the mission control center's spacecraft command inputs. The MUS system imposes no limits or constraints on the numbers and combinations of missions and SLE service instances that it will support simultaneously. At any time, flight operators may add, change, delete, bind, connect, or disconnect.

Perkins, Toby↗

DOE OSTI2023

Towards the understanding of the genuine three-body interaction for p–p–p and p–p–Λ

Three-body nuclear forces play an important role in the structure of nuclei and hypernuclei and are also incorporated in models to describe the dynamics of dense baryonic matter, such as in neutron stars. So far, only indirect measurements anchored to the binding energies of nuclei can be used to constrain the three-nucleon force, and if hyperons are considered, the scarce data on hypernuclei impose only weak constraints on the three-body forces. In this work, we present the first direct measurement of the p–p–p and p–p–Λ systems in terms of three-particle correlation functions carried out for pp collisions at $\sqrt{s}$=13 TeV. Three-particle cumulants are extracted from the correlation functions by applying the Kubo formalism, where the three-particle interaction contribution to these correlations can be isolated after subtracting the known two-body interaction terms. A negative cumulant is found for the p–p–p system, hinting to the presence of a residual three-body effect while for p–p–Λ the cumulant is consistent with zero. This measurement demonstrates the accessibility of three-baryon correlations at the LHC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

Abstract The sequence‐specific hybridization of DNA facilitates its use as a building block for designer nanoscale structures and reaction networks that perform computations. However, the strong binding energy of Watson–Crick base pairing that underlies this specificity also causes the DNA dehybridization rate to depend sensitively on sequence length and temperature. This strong dependency imposes stringent constraints on the design of multi‐step DNA reactions. Here we show how an ATP‐dependent helicase, Rep‐X, can drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. To illustrate how this new capacity can speed up designed DNA reaction networks, we show that Rep‐X extends the range of conditions where the primer exchange reaction, which catalytically adds a domain provided by a hairpin template to a DNA substrate, proceeds rapidly.

Moerman, Pepijn G.↗

DOE OSTI2022

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2000

Intramolecular activation of a Ca(2+)-dependent protein kinase is disrupted by insertions in the tether that connects the calmodulin-like domain to the kinase

Ca(2+)-dependent protein kinases (CDPK) have a calmodulin-like domain (CaM-LD) tethered to the C-terminal end of the kinase. Activation is proposed to involve intramolecular binding of the CaM-LD to a junction sequence that connects the CaM-LD to the kinase domain. Consistent with this model, a truncated CDPK (DeltaNC) in which the CaM-LD has been deleted can be activated in a bimolecular interaction with an isolated CaM-LD or calmodulin, similar to the activation of a calmodulin-dependent protein kinase (CaMK) by calmodulin. Here we provide genetic evidence that this bimolecular activation requires a nine-residue binding segment from F436 to I444 (numbers correspond to CPK-1 accession number L14771). Two mutations at either end of this core segment (F436/A and VI444/AA) severely disrupted bimolecular activation, whereas flanking mutations had only minor effects. Intramolecular activation of a full-length kinase was also disrupted by a VI444/AA mutation, but surprisingly not by a F436/A mutation (at the N-terminal end of the binding site). Interestingly, intramolecular but not bimolecular activation was disrupted by insertion mutations placed immediately downstream of I444. To show that mutant enzymes were not misfolded, latent kinase activity was stimulated through binding of an antijunction antibody. Results here support a model of intramolecular activation in which the tether (A445 to G455) that connects the CaM-LD to the kinase provides an important structural constraint and is not just a simple flexible connection.

NASA Discipline Plant Biology↗

DOE OSTI2020

Measurement of the mass difference and the binding energy of the hypertriton and antihypertriton

According to the CPT theorem, which states that the combined operation of charge conjugation, parity transformation and time reversal must be conserved, particles and their antiparticles should have the same mass and lifetime but opposite charge and magnetic moment. In this work, we test CPT symmetry in a nucleus containing a strange quark, more specifically in the hypertriton. This hypernucleus is the lightest one yet discovered and consists of a proton, a neutron and a Λ hyperon. With data recorded by the STAR detector at the Relativistic Heavy Ion Collider, we measure the Λ hyperon binding energy B Λ for the hypertriton, and find that it differs from the widely used value and from predictions, where the hypertriton is treated as a weakly bound system. Our results place stringent constraints on the hyperon–nucleon interaction and have implications for understanding neutron star interiors, where strange matter may be present. A precise comparison of the masses of the hypertriton and the antihypertriton allows us to test CPT symmetry in a nucleus with strangeness, and we observe no deviation from the expected exact symmetry.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Project 18-15263 X-ray Studies of Interfacial Molecular Complexes in ALSEP Back-Extraction (Research Performance Final Report)

The objective of the project was to use synchrotron X-rays to measure the molecular-scale organization of extractants, complexants, buffers, and metal ions at the organic-aqueous (liquid-liquid) interface during solvent back-extraction under conditions relevant to ALSEP (Actinide-Lanthanide Separation Process). The capability of X-ray fluorescence near total reflection (XFNTR) was extended to explore the distribution of Eu(III) between the liquid-liquid interface and bulk organic and aqueous phases which contained extractants HDEHP (bis(2-ethylhexyl) phosphoric acid) and HEHEHP (2-ethylhexyl phosphonic acid mono-2-ethylhexyl ester), the complexant DTPA (diethylene triamine pentaacetic acid), and citric and nitric acids. Although an Am-compatible sample cell was developed, extending x-ray measurements of flat liquid-liquid interfaces to the actinide Am(III) did not prove to be possible within constraints imposed by the Advanced Photon Source. However, preliminary measurements with a drop cell may eventually provide a path forward to investigate Am(III) at a liquid interface. It was also demonstrated that competitive binding that occurs during back-extraction of lanthanide ions to either a phosphoric acid extractant (DHDP, di-hexadecyl phosphate) at the liquid interface or to complexant DTPA in the bulk aqueous phase could be reversibly tuned by X-ray exposure. Separately, X-ray measurements from the liquid-vapor interface explored the role of the aqueous solubility of HDEHP and HEHEHP and their interactions with a range of lanthanides and transition metal ions. Finally, the capability of X-ray absorption spectroscopy (EXAFS) was extended to probe metal ion coordination in lanthanide ion-extractant complexes at the liquid-vapor interface. Complementary to the specific interfacial systems studied during this project, the development of x-ray techniques expands our ability to understand ion ordering at liquid interfaces.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

NASA NTRS1985

Spectral constraints on models of gas in clusters of galaxies

The HEAO 1A2 spectra of clusters of galaxies are used to determine the temperature profile which characterizes the X-ray emitting gas. Strong evidence of nonisothermality is found for the Coma, A85, and A1795 clusters. Properties of the cluster potential which binds the gas are calculated for a range of model parameters. The typical binding mass, if the gas is adiabatic, is 2-4E14 solar masses and is quite centrally concentrated. In addition, the Fe abundance in Coma is .26 + or - .06 solar, less than the typical value (.5) found for rich clusters. The results for the gas in Coma may imply a physical description of the cluster which is quite different from what was previously believed.

Henriksen, M. J.↗

NASA NTRS1985

Spectral constraints on models of gas in clusters of galaxies

Henriksen, M. J.↗

DOE OSTI2022

Contrasting Trivalent Lanthanide and Actinide Complexation by Polyoxometalates via Solution-State NMR

Deciphering the solution chemistry and speciation of actinides is inherently difficult due to radioactivity, rarity, and cost constraints, especially for transplutonium elements. In this context, the development of new chelating platforms for actinides and associated spectroscopic techniques is particularly important. In this study, we investigate a relatively overlooked class of chelators for actinide binding, namely, polyoxometalates (POMs). We provide the first NMR measurements on americium–POM and curium–POM complexes, using one-dimensional (1D) 31 P NMR, variable-temperature NMR, and spin-lattice relaxation time (T 1 ) experiments. The proposed POM–NMR approach allows for the study of trivalent f-elements even when only microgram amounts are available and in phosphate-containing solutions where f-elements are typically insoluble. The solution-state speciation of trivalent americium, curium, plus multiple lanthanide ions (La 3+ , Nd 3+ , Sm 3+ , Eu 3+ , Yb 3+ , and Lu 3+ ), in the presence of the model POM ligand PW 11 O 39 7– was elucidated and revealed the concurrent formation of two stable complexes, [M III (PW 11 O 39 )(H 2 O) x ] 4– and [M III (PW 11 O 39 ) 2 ] 11– . Interconversion reaction constants, reaction enthalpies, and reaction entropies were derived from the NMR data. The NMR results also provide experimental evidence of the weakly paramagnetic nature of the Am 3+ and Cm 3+ ions in solution. Furthermore, the study reveals a previously unnoticed periodicity break along the f-element series with the reversal of T 1 relaxation times of the 1:1 and 1:2 complexes and the preferential formation of the long T 1 species for the early lanthanides versus the short T 1 species for the late lanthanides, americium, and curium. Furthermore, given the broad variety of POM ligands that exist, with many of them containing NMR-active nuclei, the combined POM–NMR approach reported here opens a new avenue to investigate difficult-to-study elements such as heavy actinides and other radionuclides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Rational Design of Lanmodulin Variants for Size-Based Selectivity of Individual Rare Earth Elements

Rare earth elements (REEs) are essential to modern technologies, yet their high physical and chemical similarity makes separation of individual REEs difficult and environmentally taxing. Metalloproteins offer a promising alternative for selective REE binding, as they tend to have high metal ion affinity and specificity. Lanmodulin (LanM), in particular, has arisen as a potential candidate for REE separation as it exhibits picomolar affinity for elements in the REE family. Prior work has shown that the single point mutation D9N can shift LanM’s preference away from lanthanides toward actinides, motivating efforts to tune selectivity of LanM through targeted mutagenesis. Here, we tested the hypothesis that introducing selective aspartic acid to glutamic acid substitutions in the metal coordinating EF hands of LanM would impose steric constraints that would drive LanM affinity away from larger ions, such as La3+, to smaller ions, such as Y3+. To test this hypothesis, a combination of computational and experimental approaches were employed to evaluate the signal mutations LanM D5E and LanM D3E and the double mutants LanM D1ED5E and LanM D3ED9E. Surprisingly, increasing the number of mutations within the metal center did not enhance affinity for smaller REEs, or decrease affinity for larger ions. Only the single point mutation LanM D5E weakened La3+ binding by one order of magnitude relative to LanM wild type (WT), and pairing it with a second mutation to produce LanM D1ED5E drove La3+ affinity to be stronger than that seen for LanM WT. The D3E mutation alone prevented proper expression and folding, but paring it with D9E to produce LanM D3ED9E rescued expression and yielded La3+ affinities comparable to LanM WT. All variants that expressed (LanM D5E, LanM D1ED5E, LanM D3ED9E) displayed Y3+ affinities comparable to LanM WT. Overall, these results highlight the tunability of LanM’s metal-binding environment but also expose current limitations in predicting structural responses to point mutations within a protein sequence. This work establishes a foundation that can be used for refining computational and experimental strategies to engineer metalloproteins with tailored REE selectivity.

Close, Emily [Pacific Northwest National Laborator↗

DOE OSTI2025

Embedded random phase approximation for magnetic systems: H 2 dissociative adsorption on Fe(110)

The random phase approximation (RPA), a method for treating electron correlation, has been shown to be superior to standard density functional theory (DFT) approximations in numerous cases. However, the RPA’s computational cost is substantially higher than that of DFT, particularly restricting its application to extended surfaces. The recently introduced embedded RPA (emb-RPA) approach [Wei et al., J. Chem. Phys. 159(19), 194108 (2023)] reduces this computational cost by approximately two orders of magnitude. While previous applications of emb-RPA focused on non-spin-polarized systems, here we extend the approach to ferromagnetic ones. Unlike other embedded correlated wavefunction methods, such as embedded complete active space self-consistent field theory, emb-RPA is advantageous for spin-polarized systems because the RPA is compatible with unrestricted DFT solutions, which are eigenfunctions of the spin angular momentum operator S z but not the total spin-squared operator S 2 . By applying emb-RPA with specific magnetization constraints, we achieved a speedup of two to three orders of magnitude (one order when accounting for the one-time embedding potential optimization cost) with only small errors (∼50 meV) compared to full periodic RPA. Moreover, emb-RPA significantly reduces the over-binding errors of DFT approximations. In conclusion, we anticipate that the acceleration enabled by the spin-polarized emb-RPA approach will broaden the applicability of RPA to magnetic materials.

Density functional theory↗

NASA NTRS2004

cWINNOWER algorithm for finding fuzzy dna motifs

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in protein-binding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if a clique consisting of a sufficiently large number of mutated copies of the motif (i.e., the signals) is present in the DNA sequence. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum detectable clique size qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting three-member sub-cliques. Imposing consensus constraints reduces qc by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N = 12,000 for (l, d) = (15, 4). Copyright Imperial College Press.

Evaluation Studies↗

DOE OSTI2023

Promotion of adsorptive and catalytic properties of zeolitic Brønsted acid sites by proximal extra-framework Si(OH) x groups

Steric confinement in zeolites influences the catalytic conversion of alkanes. For zeolitic Brønsted acid sites, proximate extra-framework species introduce additional confinement to the pore constraints, enhancing the catalytic activity of alkane cracking. Although extra-framework alumina has been the most studied, here we report the element-specific impact of silica species. Further, by grafting extra-framework silica species close to Brønsted acid sites in H-ZSM-5 zeolite, the binding of bases like pyridine and amines is strengthened via van der Waals interactions with their aryl or alkyl chains. Brønsted acid sites close to extra-framework silica achieve a higher reaction rate of protolytic cracking of n-pentane via enthalpic (unlike entropic, as with extra-framework alumina) stabilization of the transition state by 24–51 kJ mol −1 . The lower activation energy points to an earlier transition state than in the presence of extra-framework alumina, with a better stabilization of the carbonium ions in the transition state compared to the parent zeolite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗