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DOE OSTI2025

Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches.

Biochemistry & Molecular Biology↗

DOE OSTI2022

Applying Crystallography and 19 F NMR to investigate dynamics and partner protein interactions in a long chain Flavodoxin

Flavodoxin (Fld) is a small FMN containing protein that is involved in single electron transfer. The long‐chain flavodoxin in Rhodopseudomonas palustris bacteria replaces ferredoxin as a low‐potential electron carrier when iron is scarce. Thus it is proposed to interact with the bifurcating electron transfer flavoprotein (ETF) that yields low‐potential electrons. A surface loop on Fld interacts with another of Fld's partner proteins, so we hypothesize that it also mediates Fld's interaction with ETF. To monitor interactions with ETF directly and investigate dynamics in this loop, we are using 19 F NMR in solution. 19 F is hyperresponsive to changes in its chemical environment with a chemical shift range of >300 ppm. To provide a static reference point and assess structural heterogeneity, we are also exploiting X‐ray crystallography. In this study we selectively fluorinated the five tyrosine residues in Fld. We obtained resonance assignments from 19 F spectra of Fld variants in which individual tyrosine residues have been replaced. We obtain well resolved signals for each residue, but the resonances' linewidths indicate dynamics that affects some resonances more than others. Y90 residue displays two resonances demonstrating two different conformations that interconvert slowly on an NMR time scale. Meanwhile the crystal structure solved at 2.1Å resolution reveals two molecules per asymmetric unit providing two perspectives on the details of the structure. The crystal symmetry is monoclinic in contrast to most of the other Flds, which are orthorhombic. Interestingly, the long loop bearing Y121 and Y123 is not well resolved in chain B of the crystal structure, and the NMR line of Y123 is exceptionally broad, both indicating that the loop is dynamic and capable of altering its conformation to accomodate binding to a partner protein. Future directions include monitoring the changes in the 19 F NMR of the Fld when titrated with the partner protein, temperature dependence of the NMR spectrum and relaxation studies to evaluate time scales of motions.

Khan, Sharique↗

DOE OSTI2025

Unraveling trace anomaly of supradense matter via neutron star compactness scaling

The trace anomaly Δ ≡ 1/3 −𝑃/𝜖 =1/3 −𝜙 quantifies the possibly broken conformal symmetry in supradense matter under pressure 𝑃 at energy density 𝜖. Perturbative QCD (pQCD) predicts a vanishing Δ at extremely high energy or baryon densities when the conformal symmetry is realized but its behavior at intermediate densities reachable in neutron stars (NSs) is still very uncertain. The extraction of Δ from NS observations strongly depends on the employed model for nuclear equation of state (EOS). Using the IPAD-TOV method based on an intrinsic and perturbative analysis of the dimensionless (IPAD) Tolman-Oppenheimer-Volkoff (TOV) equations that are further verified numerically by using 10 5 EOSs generated randomly with a metamodel in a very broad EOS parameter space constrained by terrestrial nuclear experiments and astrophysical observations, here we first show that the compactness 𝜉 ≡ 𝐺⁡𝑀 NS /𝑅⁢𝑐 2 ≡ 𝑀 NS /𝑅 of a NS with mass 𝑀 NS and radius 𝑅 scales very accurately with $\bar{Π}$ c ≡ $Π$ c · (1 +18⁢X/25) ≡ X/(1 +3⁢X 2 +4⁢X) · (1 +18⁢X/25) where X ≡ 𝜙 c = 𝑃 c /𝜖 c is the ratio of pressure over energy density at NS centers. The scaling of NS compactness thus enables one to readily read off the central trace anomaly Δ c = 1/3 −X directly from the observational data of either the mass-radius or red-shift measurements. Finally, we then demonstrate indeed that the available NS data themselves from recent X-ray and gravitational wave observations can determine model insensitively the trace anomaly as a function of energy density in NS cores, providing a stringent test of existing NS models and a clear guidance in a new direction for further understanding the nature and EOS of supradense matter.

nuclear astrophysics↗

DOE OSTI2026

Rapidity-dependent spin decomposition of the nucleon

We revisit the two-dimensional Fourier transform of generalized parton distributions (GPDs) at nonzero skewness. At 𝜂 = 0 it reduces to the standard impact-parameter density, while at 𝜂 ≠ 0 it is an off-forward amplitude that we interpret as a genuine parton–nucleon correlation. Its overall strength (the transverse-plane integral of the density) is fixed by the GPD at the kinematic point 𝑡 =−𝑐 𝜂 =−4⁢𝜂 2 ⁢𝑚$^{2}_{𝑁}$/(1 − 𝜂 2 ) and decreases monotonically with the rapidity gap Δ⁢𝑦 = ln⁡[(1+𝜂)/(1−𝜂)] = 2 artanh⁡(𝜂). This rapidity dependence implies rapidity-modified Ji identities that connect helicity, orbital, and total angular momenta of the correlation in closed form. To quantify these effects, we construct leading-twist quark and gluon GPDs in a string-based conformal framework: conformal moments are parametrized by linear open- and closed-string Regge trajectories with slopes constrained by parton distribution functions (PDFs), hadron/glueball spectroscopy, and form-factor data, and GPDs are reconstructed over the full (𝑥,𝜂,𝑡) domain by Mellin-Barnes inversion with next-to-leading order evolution. We find qualitative agreement (and fair quantitative agreement within quoted uncertainties) for several moments and selected nonsinglet 𝑥-space channels at 𝜇 = 2 GeV when compared with lattice QCD, while we also identify channels with visible tension and discuss likely sources (PDF priors and 𝑡-slope systematics).

Gauge-gravity dualities↗

DOE OSTI2025

String-based axial and helicity-flip GPDs: A comparison to lattice QCD

We construct an analytic, string-based representation of the nucleon’s axial and helicity-flip conformal moments of generalized parton distributions (GPDs) that holds for skewness and for both the quark and gluon channels. The starting point is the Mellin-Barnes resummation of the conformal partial-wave expansion, where the moments are parametrized by open- (Reggeon) and closed-string (Pomeron) trajectories with slopes determined by experimental form factors and meson/glueball spectroscopy. The forward limits are fixed by the empirical unpolarized and polarized parton distributions. Polynomiality, crossing symmetry, and support are satisfied by construction. After next-to-leading order Dokshitzer-Gribov-Lipatov-Altarelli-Parisi/Efremov-Radyushkin-Brodsky-Lepage evolution to μ = 2 GeV our analytic framework (i) reproduces some of the currently available lattice moments of E and H˜ in the nonsinglet sector, (ii) predicts sea-quark and gluon polarized moments that will be testable by forthcoming simulations and experiments at Jefferson Lab and the future Electron-Ion Collider, and (iii) yields axial and helicity-flip GPDs in x-space in reasonable agreement with lattice QCD.

Gauge-gravity dualities↗

DOE OSTI2020

Measurement-induced criticality in random quantum circuits

We investigate the critical behavior of the entanglement transition induced by projective measurements in (Haar) random unitary quantum circuits. Using a replica approach, we map the calculation of the entanglement entropies in such circuits onto a two-dimensional statistical-mechanics model. In this language, the area- to volume-law entanglement transition can be interpreted as an ordering transition in the statistical-mechanics model. We derive the general scaling properties of the entanglement entropies and mutual information near the transition using conformal invariance. We analyze in detail the limit of infinite on-site Hilbert space dimension in which the statistical-mechanics model maps onto percolation. In particular, we compute the exact value of the universal coefficient of the logarithm of subsystem size in the n th Rényi entropies for n ≥ 1 in this limit using relatively recent results for the conformal field theory describing the critical theory of two-dimensional (2D) percolation, and we discuss how to access the generic transition at finite on-site Hilbert space dimension from this limit, which is in a universality class different from 2D percolation. Here, we also comment on the relation to the entanglement transition in random tensor networks, studied previously in Vasseur et al. [Phys. Rev. B 100, 134203 (2019)].

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Subdimensional criticality: Condensation of lineons and planons in the X-cube model

We study quantum phase transitions out of the fracton ordered phase of the Z N X-cube model. These phase transitions occur when various types of subdimensional excitations and their composites are condensed. The condensed phases are either trivial paramagnets, or are built from stacks of D = 2 or 3 deconfined gauge theories, where D is the spatial dimension. Here, the nature of the phase transitions depends on the excitations being condensed. Upon condensing dipolar bound states of fractons or lineons, for N ≥ 4 we find stable critical points described by decoupled stacks of D = 2 conformal field theories. Upon condensing lineon excitations, when N > 4 we find a gapless phase intermediate between the X-cube and condensed phases, described as an array of D = 1 conformal field theories. In all these cases, effective subsystem symmetries arise from the mobility constraints on the excitations of the X-cube phase and play an important role in the analysis of the phase transitions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Probing quarkyonic matter in neutron stars with the Bayesian nuclear-physics multimessenger astrophysics framework

The interiors of neutron stars contain matter at the highest densities realized in our Universe. Interestingly, theoretical studies of dense matter, in combination with the existence of two-solar-mass neutron stars, indicate that the speed of sound $c_s$ has to increase to values well above the conformal limit ($c_s^2$ = 1/3) before decreasing again at higher densities. Further, the decrease could be explained by either a strong first-order phase transition or a crossover transition from hadronic to quark matter. The latter scenario leads to a pronounced peak in the speed of sound, reaching values above the conformal limit, naturally explaining the inferred behavior. In this work, we use the nuclear-physics multimessenger astrophysics (NMMA) framework to compare predictions of the quarkyonic matter model with astrophysical observations of neutron stars, with the goal of constraining model parameters. Assuming quarkyonic matter to be realized within neutron stars, we find that there can be a significant amount of quarks inside the cores of neutron stars with masses in the two-solar-mass range, amounting to up to ≈0.13$M$ ⊙ , contributing ≈ 5.9% of the total mass. Furthermore, for the quarkyonic matter model investigated here, the radius of a 1.4$M$ ⊙ neutron star would be $13.44_{–1.54}^{+1.69}(13. 54_{–1.04}^{+1.02})$ km, at 95% credibility, without (with) the inclusion of AT2017gfo.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Light scalar meson and decay constant in SU(3) gauge theory with eight dynamical flavors

The SU(3) gauge theory with N f = 8 nearly massless Dirac fermions has long been of theoretical and phenomenological interest due to the near-conformality arising from its proximity to the conformal window. One particularly interesting feature is the emergence of a relatively light, stable flavor-singlet scalar meson σ ( J P C = 0 + + ) in contrast to the N f = 2 theory QCD. In this work, we study the finite-volume dependence of the σ meson correlation function computed in lattice gauge theory and determine the σ meson mass and decay constant extrapolated to the infinite-volume limit. We also determine the infinite-volume mass and decay constant of the flavor-nonsinglet scalar meson a 0 . Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Reviving QFT in ( 2 + 1 )-dimensional de Sitter spacetime

We consider a conformally coupled scalar quantum field theory (QFT) on ( 2 + 1 )-dimensional static Einstein universe R × S 2 and write down the free theory Hilbert space. We explain that this theory is secretly a QFT in ( 2 + 1 )-dimensional de Sitter space because all the quantum observables experience “quantum revivals,” which naturally restricts the timelike R to the appropriate de Sitter time range. Our construction circumvents the causal obstruction to formulating QFT in de Sitter due to event horizons. There are not any in static Einstein. The “unitary gauge” description of the theory is realized by the zonal harmonics P ℓ ( n ^ · n ^ ′ ) . We verify that interactions with conformally invariant external sources are mediated only by these modes. Hence these modes comprise the complete basis of the “bulk” theory. When the theory is cut off in the UV, the basis dimension scales as the Bekenstein-Hawking formula. Published by the American Physical Society 2024

D’Amico, Guido (ORCID:0000000281831214)↗

DOE OSTI2025

Power counting of the pion-dilaton effective field theory

Confining QCD-like theories close to the conformal window have a “walking” coupling. This is believed to lead to a light singlet scalar meson in the low-energy spectrum, a dilaton, which is the pseudo-Nambu-Goldstone boson for the approximate scale symmetry. Extending chiral perturbation theory to include the dilaton requires a new small parameter to control the dilaton mass and its interactions. In our previous work we derived a systematic power counting for the dilaton couplings by matching the effective low-energy theory to the underlying theory using mild assumptions. In this paper we examine two alternative power countings which were proposed in the literature based on a phenomenological picture for the conformal transition. We find that one of these power countings fails, in fact, to generate a systematic expansion; the other coincides with the power counting we derived. We also point out that the so-called Δ -potential coincides with the tree-level potential of the former, invalid, power counting. Published by the American Physical Society 2025

Golterman, Maarten (ORCID:0000000319830672)↗

DOE OSTI2025

Virasoro completeness relation and the inverse Shapovalov form

In this work, we introduce an explicit expression for the inverse of the symmetric bilinear form of Virasoro Verma modules, the so-called Shapovalov form, in terms of singular vector operators and their conformal dimensions. Our proposed expression also determines the resolution of the identity for Verma modules of the Virasoro algebra, and can be thus employed in the computation of Virasoro conformal blocks via the sewing procedure. Published by the American Physical Society 2025

Fortin, Jean-François (ORCID:0000000278135015)↗

DOE OSTI2024

Celestial Dual for Maximal Helicity Violating Amplitudes

It is shown that a 2D conformal field theory consisting of a central charge c Liouville theory, a chiral level one, rank N Kac-Moody algebra, and a weight − 3 / 2 free fermion holographically generate 4D maximal helicity violating tree-level scattering amplitudes. The correlators of this 2D conformal field theory give directly the 4D leaf amplitudes associated to a single hyperbolic slice of flat space. The 4D celestial amplitudes arise in a large- N and semiclassical large- c limit, according to the holographic dictionary, as a translationally invariant combination of leaf amplitudes. A step in the demonstration is showing that the semiclassical limit of Liouville correlators are given by contact 3D anti–de Sitter Witten diagrams. Published by the American Physical Society 2024

Physics↗

DOE OSTI2025

Machine learning inversion from scattering for mechanically driven polymers

A machine learning inversion method is developed for analyzing scattering functions of mechanically driven polymers and extracting the corresponding feature parameters, which include energy parameters and conformation variables. The polymer is modeled as a chain of fixed-length bonds constrained by bending energy, and it is subject to external forces such as stretching and shear. We generate a data set consisting of random combinations of energy parameters, including bending modulus, stretching and shear force, along with Monte Carlo-calculated scattering functions and conformation variables such as end-to-end distance, radius of gyration and off-diagonal component of the gyration tensor. The effects of the energy parameters on the polymer are captured by the scattering function, and principal component analysis ensures the feasibility of the machine learning inversion. Finally, we train a Gaussian process regressor using part of the data set as a training set and validate the trained regressor for inversion using the rest of the data. The regressor successfully extracts the feature parameters.

Gaussian process regressors↗

DOE OSTI2020

Fourfold alkyl wrapping of a copper(II) porphyrin thwarts macrocycle π–π stacking in a compact supramolecular package

Porphyrins are valuable constituents in optoelectronic, catalytic, and other applications, yet control of intermolecular π–π stacking is invariably essential to attain the desired properties. Superstructures built onto the porphyrin, often via meso -aryl groups, can afford facial encumbrance that suppresses π–π stacking, although some molecular designs have provided insufficient facial coverage and many have entailed cumbersome syntheses. In this study, a copper(II) porphyrin bearing four meso substituents, namely, {10,20-bis[2,6-bis(octyloxy)phenyl]-5,15-dibromoporphinato}copper(II), [Cu(C 64 H 82 Br 2 N 4 O 4 )], was prepared by metalation of the corresponding free-base porphyrin and was characterized by single-crystal X-ray diffraction. The crystal structure reveals a dihedral angle of 111.1 (2)° for the plane of the meso -aryl group relative to the plane of the porphyrin, with both aryl groups tilted in the same direction. Each of the four octyloxy groups exhibits a gauche conformation for the –OCH 2 CH 2 – unit but is extended with four or five anti (–CH 2 CH 2 –/H) conformations thereafter, causing each octyl group to span the dimension of the macrocycle. In a global frame of reference where the two Br atoms define the north/south poles and the two aryl groups are at antipodes on the equator, two octyl groups of one aryl unit project over the northern hemisphere (covering pyrroles A and B ), whereas those of the other aryl unit project over the southern hemisphere (covering pyrroles C and D ). Together, the four octyl groups ensheath the two faces of the porphyrin in a self-wrapped assembly. The closest approach of the Cu atom to an octyl methylene C atom (position 6) is 3.5817 (18) Å, the mean separations of neighboring porphyrin planes are 8.059 (4) and 4.693 (8) Å along the a and c axes, respectively, and the center-to-center distances between the Cu atoms of neighboring porphyrins are 10.2725 (4), 12.2540 (6), and 12.7472 (6) Å along the a , b , and c axes, respectively. The Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots provide information concerning contact interactions in the supramolecular assembly of the solid crystal.

Chemistry↗

DOE OSTI2023

Towards a Comparative Assessment of Data-Driven Process Models in Health Information Technology

Process mining for conformance analysis focuses on comparing a reference process model against a data-driven process model that is generated via log files from information technology systems. While this approach is helpful when there is an existing process model in an organization, it leaves the question of what to do in the absence of a complete reference process model unanswered. In this paper, we present a comparative assessment approach that combines process mining, process mapping for dimensionality reduction, and statistical analysis. Our goal is to find similarities and dissimilarities in data-driven process models among U.S. Veterans Health Administration (VHA) facilities to assess process conformance among different healthcare facilities, which can help assess the standardization of care. We illustrate our approach by applying it to two clinical radiology order process models generated by two similar facilities. Our results demonstrate statistical similarities in the standardization of care among those two facilities.

Klasky, Hilda↗

DOE OSTI2022

ECP SOLLVE: Validation and Verification Testsuite Status Update and Compiler Insight for OpenMP

The OpenMP language continues to evolve with every new specification release, as does the need to validate and verify the new features that have been implemented by the different vendors. With the release of OpenMP 5.0 and OpenMP 5.1, new target offload and host-based features have been introduced to the programming model. While OpenMP continues to grow in maturity, there is an observable growth in the number of compiler and hardware vendors that support OpenMP. In this manuscript, the main focus is on evaluating the conformity and OpenMP implementation progress of various compiler vendors such as Cray, IBM, GNU, Clang/LLVM, NVIDIA, and Intel. More specifically, the 4.5, 5.0, and 5.1 versions of the OpenMP specification are analyzed. For our experimental setup, the Crusher and Summit computing systems hosted by Oak Ridge National Lab’s Computing Facilities are utilized. The effort of vendor agnostic analysis of these implementations is especially valuable for application developers who are using new OpenMP features to accelerate their scientific codes. Insights are presented into the current implementation status of various vendors, the progression of specific compiler’s support for OpenMP overtime, the subset of OpenMP 4.5, 5.0, and 5.1 that is supported by all compilers, and examples of how our test suite has influenced discussion regarding the correct interpretation of the OpenMP specification. By evaluating OpenMP conformity of pre-Exascale computing systems, the aim is to detail progress and status of AMD + Cray ecosystem before the system and their OpenMP implementation is used for mission critical applications when the first Exascale Computer Frontier is made available to applications.

Huber, Thomas↗

DOE OSTI2021

Study of the Heater-Coil Electrical Insulation for the HL-LHC Low Beta Quadrupoles

In the framework of the HL-LHC project, the present LHC low-β superconducting quadrupoles will be substituted with higher performance Nb 3 Sn magnets (MQXF) with 11.4 T coil peak field. MQXF coils are impregnated with epoxy resin to reduce risk of stress concentration on the brittle conductor. The magnet quench protection is provided by CLIQ and quench heaters to ensure a redundant system. Quench heaters are impregnated with the coils in order to have suitable thermal contact with them, and to prevent the hot spot temperature from exceeding 350K during normal operation in case of a quench. Quench heaters are insulated from the coil by S-2 Glass and polyimide. Here, the test of the first MQXF prototype (4 m long) MQXFAP1 was stopped by a coil-to-ground short circuit triggered by a heater-to-coil short. This issue triggered a root analysis of the causes of this short. Here we prove that the use of a non-conforming cloth in coil impregnation, further weakened by non-conforming high voltage test, has triggered the shorts. Moreover, we present an analysis of the heater-to-coil insulation strength, showing the role of blistering phenomena and how they are triggered by a combination of magnet powering and heater firing.

43 PARTICLE ACCELERATORS↗