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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

The accurate and reliable prediction of protein–ligand binding affinities can play a central role in the drug discovery process as well as in personalized medicine. Of considerable importance during lead optimization are the alchemical free energy methods that furnish an estimation of relative binding free energies (RBFE) of similar molecules. Recent advances in these methods have increased their speed, accuracy, and precision. This is evident from the increasing number of retrospective as well as prospective studies employing them. However, such methods still have limited applicability in real-world scenarios due to a number of important yet unresolved issues. Here, we report the findings from a large data set comprising over 500 ligand transformations spanning over 300 ligands binding to a diverse set of 14 different protein targets which furnish statistically robust results on the accuracy, precision, and reproducibility of RBFE calculations. We use ensemble-based methods which are the only way to provide reliable uncertainty quantification given that the underlying molecular dynamics is chaotic. These are implemented using TIES (Thermodynamic Integration with Enhanced Sampling). Results achieve chemical accuracy in all cases. Ensemble simulations also furnish information on the statistical distributions of the free energy calculations which exhibit non-normal behavior. We find that the “enhanced sampling” method known as replica exchange with solute tempering degrades RBFE predictions. We also report definitively on numerous associated alchemical factors including the choice of ligand charge method, flexibility in ligand structure, and the size of the alchemical region including the number of atoms involved in transforming one ligand into another. Our findings provide a key set of recommendations that should be adopted for the reliable application of RBFE methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Unusual electrical conductivity driven by localized stoichiometry modification at vertical epitaxial interfaces

Precise control of lattice mismatch accommodation and interfacial cation diffusion is critical to modulate correlated functionalities in epitaxial heterostructures, particularly when the interface composition is positioned near a compositional phase transition boundary. Here we select La 1-x Sr x MnO 3 (LSMO) as a prototype phase transition oxide and establish vertical epitaxial interfaces with NiO for exploring the strong interplay between strain accommodation, stoichiometry modification, and localized electron transport across the interface. It is found that localized stoichiometry modification overcomes the dead layer problem plaguing LSMO and leads to strongly directional conductivity, as manifested by a more than three orders of magnitude difference between out-of-plane and in-plane conductivity. Comprehensive atomic scale structural characterization and transport measurements reveal that this emerging behavior is created by a compositional change produced by preferential cation diffusion that pushes the LSMO phase transition from insulating into metallic within an ultrathin interface region. This study explores the nature of unusual electrical conductivity at vertical epitaxial interfaces and highlights the beneficial role of controllable cation diffusion that enables emerging functionalities for a broad range of potential applications such as memristors, spintronic devices, and novel nanoelectronic devices using strongly correlated materials.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Probing fundamental constant oscillation in the Galactic Center with S-Star Spectroscopy

Astrophysical spectroscopy provides a powerful probe of spacetime variations of fundamental constants, as atomic and ionic emission and absorption lines depend sensitively on the fine-structure constant. In particular, coherent temporal oscillations induced by an ultralight scalar background produce characteristic, time-resolved signatures that can be robustly disentangled from intrinsic variability. In the Galactic Center, such scalar backgrounds can be substantially enhanced, either through the formation of dense scalar clouds powered by black hole rotational energy extraction or as ultralight scalar dark matter forming a soliton-like core. These scalar configurations generically induce oscillations of the fine-structure constant, with periods set by the scalar mass and spatial profiles determined by the scalar wavefunction and its coupling to the electromagnetic sector. We show that precise, time-resolved spectroscopy of S-stars orbiting the supermassive black hole Sgr A^* provides a sensitive test of these effects, enabling constraints on quadratic scalar-photon couplings in the exceptionally high boson-density environment of the Galactic Center.

Bai, Zhaoyu [Weizmann Inst.] (ORCID:00000002075815↗
DOE OSTI2025

Seedless nonresonant gas-flow velocimetry with single-shot coherent Rayleigh-Brillouin scattering

We demonstrate neutral gas-flow velocimetry by exploiting the optical dipole forces exerted by precisely tailored high-intensity laser fields on polarizable particles, in the form of single-shot coherent Rayleigh-Brillouin scattering (CRBS). This enables mapping of the velocity distribution function of the particles in a single laser shot of approximately 200 ns duration, allowing us to perform spectroscopic measurements in the time, rather than the frequency, domain. Importantly, CRBS results in a coherent signal beam, which renders the technique ideal for measurements in optically noisy environments. By correlating the time shift of the resulting spectrum to the Doppler shift caused by the bulk motion of particles, we perform neutral gas-flow velocimetry without the need to seed the flow, nondestructively, for a variety of gases, atomic or molecular. We demonstrate gas-flow velocimetry at flow velocities as low as 1 m ⁢s −1 , with similar velocity resolution, while temperature and gas density can also be estimated from the same single-shot spectra. To prove the effectiveness of the measurement technique, we benchmark it against Pitot tube measurements, which show excellent agreement.

Gerakis, Alexandros [Luxembourg Institute of Scien↗
DOE OSTI2020

A Proposed Forward Silicon Tracker for the Future Electron-Ion Collider and Associated Physics Studies

The future Electron-Ion Collider (EIC) will explore several fundamental questions in a broad Bjorken-x (x BJ ) and Q 2 phase space. Heavy flavor and jet products are ideal probes to precisely study the tomography of nucleon/nuclei structure, help solve the proton spin puzzle and understand the hadronizaton processes in vacuum or in the QCD medium. Due to the asymmetric collisions at the EIC, most of the final state hadrons are produced in the nucleon/nuclei beam going (forward) direction. A silicon vertex/tracking is critical to precisely measure these forward hadrons at the EIC. Details of different conceptual designs of the proposed Forward Silicon Tracker (FST) and the relevant detector performance are presented in this technical note. The associated heavy flavor and jet studies with the evaluated FST performance are discussed as well.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

First Measurement of the Isospin-Dependence of Nuclear Structure Functions at 12 GeV Jefferson Lab

The structure functions of protons and neutrons provide crucial insight into how the strong nuclear force, as described by Quantum Chromodynamics (QCD), manifests at everyday energies, allowing us to better understand precisely how quarks and gluons interact to form the basic building blocks of almost all visible mass in our universe. Despite more than 40 years of experimental and theoretical effort, the EMC effect – the observation that nuclear structure functions appear to be modified from those of free nucleons – is still not fully understood. One open question that remains is whether or not the modification of quark distributions is the same for all quark flavors. Determining the flavor (isospin) dependence of the EMC effect, which is predicted by several models, is essential for coming to a complete understanding of how QCD manifests in nuclei. To this end, inclusive electron Deep Inelastic Scattering (DIS) from nuclei with approximately constant atomic mass number A and variable proton-to-neutron ratio N/Z was measured in Jefferson Lab experiment E12-10-008 to look for isospin-dependent modification of nuclear structure functions. The preliminary EMC ratios presented here cover a kinematic range of 2.8 < Q2 < 8.1 GeV2 and 0.18 < xBj < 1.0. The size of the EMC effect in these nuclei is extracted by calculating the slope of the EMC ratio as a function of Bjorken x (xBj ) over the ranges 0.3 < xBj < 0.6 and 0.3 < xBj < 0.7; these slopes then are compared with existing world data. Our preliminary results do not appear to indicate significant isospin-dependence of the EMC effect, though a more careful study is needed once all results are confirmed.

Cotton, Cameron William [Univ. of Virginia, Charlo↗
DOE OSTI2026

Orientation-tunable local crystallization of Si films enabled by atomic imprint crystallization

Here, in this paper, we demonstrate area-selective crystallization of amorphous Si into tunable crystal orientations enabled by atomic imprint crystallization (AIC), where an amorphous Si layer is crystallized by solid phase epitaxy (SPE) from an externally impressed single-crystalline Si template. Using micro-patterned single-crystalline Si templates, a limited area of an amorphous Si film, where the film surface and patterned template surface are in contact, is crystallized via SPE to create an array of crystallographically aligned dots embedded in amorphous matrix. Combining AIC from the top surface and conventional SPE from the substrate, we demonstrate the fabrication of an array of crystalline dots embedded in single-crystalline matrix with tunable in-plane rotation angle. The results indicate the high tunability of the crystallization process enabled by AIC, allowing precise control of crystallographic properties of thin films with area-selectivity; such capability opens opportunities for the design of new materials for a wide range of applications in materials science.

Amorphous↗
DOE OSTI2020

Sampling and Analysis Plan for Investigation of Undeclared Nuclear Activities - 20104

The nuclear-centered energy policy in South Korea is moving towards a nuclear-free era. It also facilitates an action or progress on the denuclearization of the Korean peninsula. The Nuclear Safety and Security Commission (NSSC) launched a new R and D project which attempts to verify nuclear activities via analyzing environmental samples. Environmental samples possibly contain significant radiological information relevant to past undeclared activities. In order to precisely verify them, it is essential to provide 1) the concrete information of target facilities, 2) appropriate methodologies and procedures, and 3) well-suited instrumentation and equipment corresponding to sample signatures. It is also important to provide scientific reliability or validity in any process such as sample collection, handling, transportation and laboratory analysis. Therefore, the information of nuclear facilities (fuel fabrication plant, graphite moderated reactor, reprocessing plant) in North Korea are reviewed in order to determine parameters for appropriate sampling methods representing a facility's characteristics. Secondly, a sampling procedure for radioactive elements is being developed based on international and domestic standards such as ASTM (American Society for Testing and Materials), KS (Korean industrial Standards), and International Atomic Energy Agency (IAEA) manuals. The procedure contains some specific information including sampling process, sampling tools, amount of sample, sample identification, and other related information. Developing the qualified national guidelines is most important since sampling and analyzing results can be used as evidences of nuclear activities. The guideline developed through this work will clearly define various methodologies such as document verification, sampling procedures, collection methods, sample storage criteria, chain of custody, and transportation conditions. The final objective of this work is to establish the infrastructure and regulatory framework for assessment of nuclear activities, and provide a national guideline for sampling and analysis. This will bring confidence in the results and play a critical role in complete denuclearization progress in South Korea. (authors)

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2025

Heavy boron doping effects on biaxially tensile strained germanium (>1.5%) investigated via structural characterization, effective lifetime assessment and atomistic modeling

Highly tensile strained germanium (ε-Ge) represents an essential material system for emerging electronic and photonics applications. Moreover, adjusting the doping levels to moderate or high concentrations can effectively tailor the properties of ε-Ge for specific applications. This article combines experimental characterization with a theoretical framework to examine the effects of heavy elemental boron (B) doping on pseudomorphic sub-50 nm ε-Ge. High resolution X-ray diffractometry is used to validate tensile strain levels of 1.53% and 1.68% in Ge epilayers, surpassing the indirect-to-direct band gap crossover point at ∼1.5% biaxial tensile strain. Cross-sectional transmission electron microscopy revealed visual evidence of stacking faults and surface roughening in 1.68% ε-Ge, although a coherent and abrupt Ge/III–V heterointerface is observed, devoid of interfacial misfit dislocations. Effective lifetime measurements demonstrated approximately twofold enhancement in 1.53% B-doped ε-Ge (N B ∼7 × 10 19 cm −3 ) compared to its unstrained B-doped counterpart, while no such improvement was observed in 1.68% B-doped ε-Ge. This lack of enhancement is attributed to the presence of stacking faults and surface roughness within the ε-Ge epilayer. Through density functional theory calculations, we independently demonstrate that substitutional B atoms induce local deformation of Ge–Ge bonds in both unstrained Ge and ε-Ge epilayers, resulting in an additive tensile strain. This phenomenon could potentially lead to dynamic reduction and overcoming of the critical layer thickness for the system, facilitating the nucleation and subsequent glide of 90° leading Shockley partial dislocations, thereby generating stacking faults. In essence, these findings establish an upper limit on the B-doping concentration that can be achieved in highly ε-Ge epilayers, and collectively, offer valuable insights into the significance of heavy doping in Ge-based heterostructures. As such, this study delineates a fundamental constraint for integrating heavily doped ε-Ge in high-performance optoelectronic systems, necessitating precise strain-doping co-optimization to avoid performance degradation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Optimizing qubit control pulses for state preparation

In the burgeoning field of quantum computing, the precise design and optimization of quantum pulses are essential for enhancing qubit operation fidelity. This study focuses on refining the pulse engineering techniques for superconducting qubits, employing a detailed analysis of square and Gaussian pulse envelopes under various approximation schemes. We evaluated the effects of coherent errors induced by naive pulse designs. Furthermore, we identified the sources of these errors in the Hamiltonian model’s approximation level. We mitigated these errors through adjustments to the external driving frequency and pulse durations, thus implementing a pulse scheme with stroboscopic error reduction. Our results demonstrate that these refined pulse strategies improve performance and reduce coherent errors. Moreover, the techniques developed herein are applicable across different quantum architectures, such as ion-trap, atomic, and photonic systems.

Chirp modulation↗
DOE OSTI2025

Rippled metamaterials with scale-dependent tailorable elasticity

Thermally induced ripples are intrinsic features of nanometer-thick films, atomically thin materials, and cell membranes, significantly affecting their elastic properties. Despite decades of theoretical studies on the mechanics of suspended thermalized sheets, controversy still exists over the impact of these ripples, with conflicting predictions about whether elasticity is scale-dependent or scale-independent. Experimental progress has been hindered so far by the inability to have a platform capable of fully isolating and characterizing the effects of ripples. This knowledge gap limits the fundamental understanding of thin materials and their practical applications. Here, we show that thermal-like static ripples shape thin films into a class of metamaterials with scale-dependent, customizable elasticity. Utilizing a scalable semiconductor manufacturing process, we engineered nanometer-thick films with precisely controlled frozen random ripples, resembling snapshots of thermally fluctuating membranes. Resonant frequency measurements of rippled cantilevers reveal that random ripples effectively renormalize and enhance the average bending rigidity and sample-to-sample variations in a scale-dependent manner, consistent with recent theoretical estimations. The predictive power of the theoretical model, combined with the scalability of the fabrication process, was further exploited to create kirigami architectures with tailored bending rigidity and mechanical metamaterials with delayed buckling instability.

Applied Physical Sciences↗
DOE OSTI2024

Ultrafast Optically Induced Perturbation of Oxygen Octahedral Rotations in Multiferroic BiFeO 3 Thin Films

The functional properties of complex oxides, including magnetism and ferroelectricity, are closely linked to subtle structural distortions. Ultrafast optical excitations provide the means to manipulate structural features and ultimately to affect the functional properties of complex oxides with picosecond-scale precision. Here, we report that the lattice expansion of multiferroic BiFeO 3 following above-bandgap optical excitation leads to distortion of the oxygen octahedral rotation (OOR) pattern. The continuous coupling between OOR and strain was probed using time-resolved X-ray free-electron laser diffraction with femtosecond time resolution. Density functional theory calculations predict a relationship between the OOR and the elastic strain consistent with the experiment, demonstrating a route to employing this approach in a wider range of systems. Ultrafast control of the functional properties of BiFeO 3 thin films is enabled by this approach because the OOR phenomena are related to ferroelectricity, and via the Fe-O-Fe bond angles, the superexchange interaction between Fe atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Insights into the mechanisms of NH3 inhibition on Cu-CHA SCR catalysts

This work elucidates the atomic-scale mechanism behind ammonia (NH3) inhibition during the selective catalytic reduction (SCR) of NO? on Cu-CHA catalysts, a key issue limiting low-temperature emission control. Using SCR kinetic analysis, operando electron paramagnetic resonance (EPR) spectroscopy, and density functional theory (DFT), we demonstrate that NH3 inhibition primarily slows the oxidation half-cycle (OHC), while the reduction half-cycle (RHC) remains unaffected. DFT simulations reveal that excess NH3 substantially increases the diffusion barrier for CuI ions, hindering formation of essential CuII-oxo dimer intermediates and thus suppressing OHC kinetics. Operando EPR studies confirm that this inhibition strongly depends on operating temperature and catalyst Cu loading. Our findings highlight strategies to counteract NH3 inhibition, including optimizing Cu loading, precisely managing NH3:NO feed ratios, and enhancing CuI ion mobility through tailored catalyst design and operational adjustments, thereby advancing the efficiency of emission control technologies in automotive applications.

Deka, Dhruba Jyoti↗
DOE OSTI2020

Systematic error analysis in the absolute hydrogen gas jet polarimeter at RHIC

The Polarized Atomic Hydrogen Gas Jet Target polarimeter (HJET) is operated at the Relativistic Heavy Ion Collider (RHIC) since 2004 to measure the absolute polarization of each colliding proton beam. Polarimeter detectors and data acquisition were upgraded in 2015 to increase the solid angle, energy range, and to improve the energy and time resolution. These upgrades along with an improved beam intensity and polarization allowed us to greatly reduce the statistical and systematic errors for the proton polarization measurements in RHIC Runs 15 (E beam = 100 GeV) and 17 (255 GeV). For a typical 8 hour RHIC store, the measured proton beam average polarization was about P beam ~ 55 ± 2.0 stat ± 0.3 syst %. The elastic pp analyzing power, AN(t)~0.04, was determined with a precision of about |δA N (t)|~0.0002 in the momentum transfer squared range 0.001<-t<0.020 GeV 2 . In this paper we present a detailed systematic error analysis of the polarization measurements at HJET. Perspectives of using the HJET based absolute polarimeters in the future Electron Ion Collider (EIC) will be also discussed.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Exploiting 20 Ne Isotopes for Precision Characterizations of Collectivity in Small Systems

Whether or not femto-scale droplets of quark-gluon plasma (QGP) are formed in so-called small systems at high-energy colliders is a pressing question in the phenomenology of the strong interaction. For proton-proton or proton-nucleus collisions the answer is inconclusive due to the large theoretical uncertainties plaguing the description of these processes. While upcoming data on collisions of 16 O nuclei may mitigate these uncertainties in the near future, here we demonstrate the unique possibilities offered by complementing 16 O + 16 O data with collisions of 20 Ne ions. We couple both nuclear lattice effective field theory (NLEFT) and projected generator coordinate method (PGCM) ab initio descriptions of the structure of 20 Ne and 16 O to hydrodynamic simulations of 16 O + 16 O and 20 Ne + 20 Ne collisions at high energy. We isolate the imprints of the bowling-pin shape of 20 Ne on the collective flow of hadrons, which can be used to perform quantitative tests of the hydrodynamic QGP paradigm. In particular, we predict that the elliptic flow of 20 Ne + 20 Ne collisions is enhanced by as much as 1.174⁢(8) stat ⁢(31) syst for NLEFT and 1.139⁢(6) stat ⁢(39) syst for PGCM relative to 16 O + 16 O collisions for the 1% most central events. At the same time, theoretical uncertainties largely cancel when studying relative variations of observables between two systems. This demonstrates a method based on experiments with two light-ion species for precision characterizations of the collective dynamics and its emergence in a small system.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Copper Clusters Containing Hydrides in Trigonal Pyramidal Geometry

Structurally precise copper hydrides [Cu 11 H 2 {S 2 P(O i Pr) 2 } 6 (C≡CR) 3 ], R = Ph (1), C 6 H 4 F (2), and C 6 H 4 OMe (3), were first synthesized from the polyhydrido copper cluster [Cu 20 H 11 {S 2 P(O i Pr) 2 } 9 ] with nine equivalents of terminal alkynes. Later, their isolated yields were significantly improved by direct synthesis from [Cu(CH 3 CN) 4 ](PF 6 ), [NH 4 ][S 2 P(O i Pr) 2 ], NaBH 4 , and alkynes along with NEt 3 in THF. 1, 2, and 3 were fully characterized by single-crystal X-ray diffraction, ESI-MS, and multinuclear NMR spectroscopy. All three clustershave 11 copper atoms, adopting 3,3,4,4,4-pentacapped trigonal prismatic geometry, with two hydrides inside the Cu 11 cage, the position of which was ascertained by a single-crystal neutron diffraction structure of cluster 1 co-crystallized with a [Cu 7 (H){S 2 P(O i Pr) 2 } 6 ] (4) cluster. Six dithiophosphate and three alkynyl ligands stabilize the Cu 11 H 2 core in which the two hydrides adopt a trigonal pyramidal coordination mode. This coordination mode is so far unprecedented for hydride. The 1 H NMR resonance frequency of the two hydrides appears at 4.8 ppm, a value further confirmed by 2 H NMR spectroscopy for their deuteride derivatives [Cu 11 (D) 2 {S 2 P(O i Pr) 2 } 6 (C≡CR) 3 ]. A DFT investigation allows understanding the bonding within this new type of copper(I) hydrides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Hybrid interatomic potential for Sn

To design materials for extreme applications, it is important to understand and predict phase transitions and their influence on material properties under high pressures and temperatures. Atomistic modeling can be a useful tool to assess these behaviors. However, this can be difficult due to the lack of fidelity of the interatomic potentials in reproducing this high pressure and temperature extreme behavior. Here, in this work, a hybrid EAM-R—which is the combination of embedded atom method (EAM) and rapid artificial neural network potential—for Tin (Sn) is described which is capable of accurately modeling the complex sequence of phase transitions between different metallic polymorphs as a function of pressure. This hybrid approach ensures that a basic empirical potential like EAM is used as a lower energy bound. By using the final activation function, the neural network contribution to energy must be positive, assuring stability over the whole configuration space. This implementation has the capacity to reproduce density functional theory results at 6 orders of magnitude slower than a pair potential for molecular dynamics simulation, including elastic and plastic characteristics and relative energies of each phase. Using calculations of the Gibbs free energy, it is demonstrated that the potential precisely predicts the experimentally observed phase changes at temperatures and pressures across the whole phase diagram. At 10.2 GPa, the present potential predicts a first-order phase transition between body-centered tetragonal (BCT) β-Sn and another polymorph of BCT-Sn. This structure transforms into body-centered cubic near the experimentally reported value at 33 GPa. Thus, the Sn potential developed in this paper can be used to study complex deformation mechanisms under extreme conditions of high pressure and strain rates unlike existing potentials. Moreover, the framework developed in this paper can be extended for different material systems with complex phase diagrams.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Coarse-grained simulation of colloidal self-assembly, cation exchange, and rheology in Na/Ca smectite clay gels

Knowledge Gap: The aggregation of clay minerals—layered silicate nanoparticles—strongly impacts fluid flow, solute migration, and solid mechanics in soils, sediments, and sedimentary rocks. Experimental and computational characterization of clay aggregation is inhibited by the delicate water-mediated nature of clay colloidal interactions and by the range of spatial scales involved, from 1 nm thick platelets to flocs with dimensions up to micrometers or more. Simulations: Using a new coarse-grained molecular dynamics (CGMD) approach, we predicted the microstructure, dynamics, and rheology of hydrated smectite (more precisely, montmorillonite) clay gels containing up to 2,000 clay platelets on length scales up to 0.1 μm. Further, simulations investigated the impact of simulation time, platelet diameters (6 to 25nm), and the ratio of Na to Ca exchangeable cations on the assembly of tactoids (i.e., stacks of parallel clay platelets) and larger aggregates (i.e., assemblages of tactoids). We analyzed structural features including tactoid size and size distribution, basal spacing, counterion distribution in the electrical double layer, clay association modes, and the rheological properties of smectite gels. Findings: Our results demonstrate new potential to characterize and understand clay aggregation in dilute suspensions and gels on a scale of thousands of particles with explicit representation of counterion clouds and with accuracy approaching that of all-atom molecular dynamics (MD) simulations. For example, our simulations predict the strong impact of Na/Ca ratio on clay tactoid formation and the shear-thinning rheology of clay gels.

42 ENGINEERING↗