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DOE OSTI2024

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Integration of scanning probe microscope with high-performance computing: Fixed-policy and reward-driven workflows implementation

The rapid development of computation power and machine learning algorithms has paved the way for automating scientific discovery with a scanning probe microscope (SPM). The key elements toward operationalization of the automated SPM are the interface to enable SPM control from Python codes, availability of high computing power, and development of workflows for scientific discovery. Here, we build a Python interface library that enables controlling an SPM from either a local computer or a remote high-performance computer, which satisfies the high computation power need of machine learning algorithms in autonomous workflows. We further introduce a general platform to abstract the operations of SPM in scientific discovery into fixed-policy or reward-driven workflows. Furthermore, our work provides a full infrastructure to build automated SPM workflows for both routine operations and autonomous scientific discovery with machine learning.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Delineation of the impact on temporal behaviors of off-axis photoemission in an ultrafast electron microscope

Efforts to push the spatiotemporal imaging-resolution limits of femtosecond laser-driven ultrafast electron microscopes (UEMs) to the combined angstrom–fs range will benefit from stable sources capable of generating high bunch charges. Recent demonstrations of unconventional off-axis photoemitting geometries are promising, but connections to the observed onset of structural dynamics are yet to be established. Here we use the in-situ photoexcitation of coherent phonons to quantify the relative time-of-flight (r-TOF) of photoelectron packets generated from the Ni Wehnelt aperture and from a Ta cathode set-back from the aperture plane. We further support the UEM experiments with particle-tracing simulations of the precise electron-gun architecture and photoemitting geometries. In this way, we measure discernible shifts in electron-packet TOF of tens of picoseconds for the two photoemitting surfaces. Furthermore, these shifts arise from the impact that the Wehnelt-aperture off-axis orientation has on the electron-momentum distribution, which modifies both the collection efficiency and the temporal-packet distribution relative to on-axis emission. Future needs are identified; we expect this and other developments in UEM electron-gun configuration to expand the range of material phenomena that can be directly imaged on scales commensurate with fundamental structural dynamics.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Harnessing quantum light for microscopic biomechanical imaging of cells and tissues

The biomechanical properties of cells and tissues play an important role in our fundamental understanding of the structures and functions of biological systems at both the cellular and subcellular levels. Recently, Brillouin microscopy, which offers a label-free spectroscopic means of assessing viscoelastic properties in vivo, has emerged as a powerful way to interrogate those properties on a microscopic level in living tissues. However, susceptibility to photodamage and photobleaching, particularly when high-intensity laser beams are used to induce Brillouin scattering, poses a significant challenge. This article introduces a transformative approach designed to mitigate photodamage in biological and biomedical studies, enabling nondestructive, label-free assessments of mechanical properties in live biological samples. By leveraging quantum-light-enhanced stimulated Brillouin scattering (SBS) imaging contrast, the signal-to-noise ratio is significantly elevated, thereby increasing sample viability and extending interrogation times without compromising the integrity of living samples. The tangible impact of this methodology is evidenced by a notable three-fold increase in sample viability observed after subjecting the samples to three hours of continuous squeezed-light illumination, surpassing the traditional coherent light-based approaches. The quantum-enhanced SBS imaging holds promise across diverse fields, such as cancer biology and neuroscience where preserving sample vitality is of paramount significance. By mitigating concerns regarding photodamage and photobleaching associated with high-intensity lasers, this technological breakthrough expands our horizons for exploring the mechanical properties of live biological systems, paving the way for an era of research and clinical applications.

Li, Tian↗

DOE OSTI2023

OH density, flux and loss probability measurements in a room temperature atmospheric pressure surface discharge by microscopic laser induced fluorescence

Many applications involving atmospheric pressure plasma-substrate interactions are enabled by the large fluxes of short-lived reactive species such as OH radicals to the substrate, nonetheless, the accurate measurement of radical densities and fluxes at substrates at atmospheric pressure has received little attention to date, particularly for surface ionization waves. We report the measurement of the OH density distribution in a surface discharge on a fused silica (quartz) substrate generated by an impinging atmospheric pressure plasma jet in dry and humid helium. The OH density is measured by microscopic laser induced fluorescence with a spatial resolution of 10 µm in the direction perpendicular to the quartz substrate. The measured OH diffusive flux varied for the investigated experimental conditions by almost three orders of magnitude and had a maximum value of 1.7 × 10 15 cm -2 s -1 . The corresponding surface loss probability of OH on the quartz surface was determined to be ~0.01. The high spatial resolution was required to accurately resolve the near surface gradient of OH radicals.

plasma-surface interactions↗

DOE OSTI2025

The Auger Radioisotope Microscope: an instrument for characterization of Auger electron multiplicities and energy distributions

We describe a new instrument, the Argonne Auger Radioisotope Microscope (ARM), capable of characterizing the Auger electron (AE) emission of radionuclides, including candidates relevant in nuclear medicine. Our approach relies on event-by-event ion–electron coincidence, time-of-flight, and spatial readout measurement to determine correlated electron multiplicity and energy distributions of Auger decays. We present a proof-of-principle measurement with the ARM using x-ray photoionization of stable krypton beyond the K-edge and identify a bifurcation in the electron multiplicity distribution depending on the emission of K-LX electrons. Extension of the ARM to the characterization of radioactive sources of AE emissions is enabled by the combination of two recent developments: (1) cryogenic buffer gas beam technology to introduce Auger emitters into the detection region with well-defined initial conditions, and (2) large-area micro-channel plate detectors with multi-hit detection capabilities to simultaneously detect multiple electrons emitted in a single decay.

Auger emitters↗

DOE OSTI2021

Spin-glass dynamics in the presence of a magnetic field: exploration of microscopic properties

The synergy between experiment, theory, and simulations enables a microscopic analysis of spin-glass dynamics in a magnetic field in the vicinity of and below the spin-glass transition temperature T g . The spin-glass correlation length, ξ(t, t w ; T), is analysed both in experiments and in simulations in terms of the waiting time t w after the spin glass has been cooled down to a stabilised measuring temperature T < T g and of the time t after the magnetic field is changed. This correlation length is extracted experimentally for a CuMn 6 at. % single crystal, as well as for simulations on the Janus II special-purpose supercomputer, the latter with time and length scales comparable to experiment. The non-linear magnetic susceptibility is reported from experiment and simulations, using ξ(t, t w ; T) as the scaling variable. Previous experiments are reanalysed, and disagreements about the nature of the Zeeman energy are resolved. The growth of the spin-glass magnetisation in zero-field magnetisation experiments, M ZFC (t, t w ; T), is measured from simulations, verifying the scaling relationships in the dynamical or non-equilibrium regime. Lastly, our preliminary search for the de Almeida–Thouless line in D = 3 is discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Single Electron Self-coherence and Its Wave/Particle Duality in the Electron Microscope

Intensities in high-resolution phase-contrast images from electron microscopes build up discretely in time by detecting single electrons. A wave description of pulse-like coherent-inelastic interaction of an electron with matter implies a time-dependent coexistence of coherent partial waves. Their superposition forms a wave package by phase decoherence of 0.5 - 1 radian with Heisenbergs energy uncertainty ΔE H = $\hbar$/2 Δt -1 matching the energy loss ΔE of a coherent-inelastic interaction and sets the interaction time Δt. In these circumstances, the product of Planck's constant and the speed of light hc is given by the product of the expression for temporal coherence λ 2 /Δλ and the energy loss ΔE. Experimentally, the self-coherence length was measured by detecting the energy-dependent localization of scattered, plane matter waves in surface proximity exploiting the Goos–Hänchen shift. Chromatic-aberration Cc-corrected electron microscopy on boron nitride (BN) proves that the coherent crystal illumination and phase contrast are lost if the self-coherence length shrinks below the size of the crystal unit cell at ΔE > 200 eV. Finally, in perspective, the interaction time of any matter wave compares with the lifetime of a virtual particle of any elemental interaction, suggesting the present concept of coherent-inelastic interactions of matter waves might be generalizable.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Microscopic changes governing melting anisotropy: Real-time nanosecond x-ray diffraction

To understand the microscopic origins governing melting anisotropy, in-situ x-ray diffraction (XRD) measurements were obtained in aluminum single crystals shocked along $\langle$100$\rangle$ and $\langle$110$\rangle$ to stresses below and above the melting threshold for each orientation. XRD results and analysis for the two orientations showed significant differences in the microstructure prior to the melting threshold stresses, demonstrating the key role of deformation induced microstructure – in addition to temperature and pressure – on the melting transition. As a result, our findings make a strong case for reconsidering theoretical approaches to melting, specifically for dislocation mediated melting, in shock compressed solids.

crystal melting↗

DOE OSTI2025

Efficiently Measuring 𝑑-Wave Pairing and Beyond in Quantum Gas Microscopes

Understanding the mechanism of high-temperature superconductivity is among the most important problems in physics, one for which quantum simulation can provide new insights. However, it remains challenging to characterize superconductivity in existing cold-atom quantum simulation platforms. Here, in this work, we introduce a protocol for measuring a broad class of observables in fermionic quantum gas microscopes, including long-range superconducting pairing correlations (after a repulsive-to-attractive mapping). The protocol only requires global controls followed by site-resolved particle number measurements—capabilities that have been already demonstrated in multiple experiments—and is designed by analyzing the Hilbert space of fermions on two sites. The protocol is sample-efficient and we further optimize our pulses for robustness to experimental imperfections such as lattice inhomogeneity. Our Letter introduces a general tool for manipulating quantum states on optical lattices, enhancing their ability to tackle problems such as high-temperature superconductivity.

Hubbard model↗

DOE OSTI2026

Microscopic constraints for the equation of state and structure of neutron stars: A Bayesian model mixing framework

Bayesian model mixing (BMM) is a statistical technique that can combine constraints from different regions of an input space in a principled way. Here we extend our BMM framework for the equation of state (EOS) of strongly interacting matter from symmetric nuclear matter to asymmetric matter, specifically focusing on zero-temperature, charge-neutral, 𝛽-equilibrated matter. We use Gaussian processes (GPs) to infer constraints on the neutron-star matter EOS at intermediate densities from two different microscopic theories: chiral effective-field theory (𝜒⁢EFT) at baryon densities around nuclear saturation, 𝑛 𝐵 ∼ 𝑛 0 , and perturbative QCD at asymptotically high baryon densities, 𝑛 𝐵 ⩾ 20⁢𝑛 0 . The uncertainties of the 𝜒⁢EFT and pQCD EOSs are obtained using the BUQEYE truncation error model. We demonstrate the flexibility of our framework through the use of two categories of GP kernels: conventional stationary kernels and a nonstationary changepoint kernel. We use the latter to explore potential constraints on the dense matter EOS by including exogenous data representing theory predictions and heavy-ion collision measurements at densities ⩾ 2⁢𝑛 0 . We also use our EOSs to obtain neutron-star mass-radius relations and their uncertainties. Finally, our framework, whose implementation will be available through a GitHub repository, provides a prior distribution for the EOS that can be used in large-scale neutron-star inference frameworks.

Bayesian methods↗

DOE OSTI2021

Quantum Monte Carlo studies of a trimer scaling function with microscopic two- and three-body interactions

Here, we present an energy scaling function to predict, in a specific range, the energy of bosonic trimers with large scattering lengths and finite range interactions, which is validated by quantum Monte Carlo calculations using microscopic Hamiltonians with two- and three-body potentials. The proposed scaling function depends on the scattering length, effective range, and a reference energy, which we chose as the trimer energy at unitarity. We obtained the scaling function as a limit cycle from the solution of the renormalized zero-range model with effective range corrections. We proposed a simple parametrization of the energy scaling function. Besides the intrinsic interest in theoretical and experimental investigations, this scaling function allows one to probe Efimov physics with only the trimer ground states, which may open opportunities to identify Efimov trimers whenever access to excited states is limited.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

3D theory of microscopic instabilities driven by space-charge forces

Microscopic, or short-wavelength, instabilities are known for a drastic reduction of the beam quality and strong amplification of the noise in a beam. Space charge and coherent synchrotron radiation are known to be the leading causes of such instabilities. In this paper, we present a rigorous 3D theory of such instabilities driven by the space-charge forces. We define the condition when our theory is applicable to an arbitrary accelerator system with 3D coupling. Finally, we derive a linear integral equation describing such instability and identify conditions when it can be reduced to an ordinary second-order differential equation.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Measurement and Simulation of the Magnetic Fields from a 555 Timer Integrated Circuit Using a Quantum Diamond Microscope and Finite-Element Analysis

Quantum diamond microscope (QDM) magnetic field imaging is an emerging interrogation and diagnostic technique for integrated circuits (ICs). To date, the ICs measured with a QDM have been either too complex for us to predict the expected magnetic fields and benchmark the QDM performance or too simple to be relevant to the IC community. In this paper, we establish a 555 timer IC as a “model system” to optimize QDM measurement implementation, benchmark performance, and assess IC device functionality. To validate the magnetic field images taken with a QDM, we use a spice electronic circuit simulator and finite-element analysis (FEA) to model the magnetic fields from the 555 die for two functional states. Furthermore, we compare the advantages and the results of three IC-diamond measurement methods, confirm that the measured and simulated magnetic images are consistent, identify the magnetic signatures of current paths within the device, and discuss using this model system to advance QDM magnetic imaging as an IC diagnostic tool.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Microscopic Origin of Polarization Charges at Ga N / ( Al , Ga ) N Interfaces

Ga⁢N/(Al,Ga)⁢N heterojunctions are at the heart of high-electron-mobility transistors that are being adopted for high-power and high-frequency applications. The strong polarization fields present at this interface significantly enhance the density of the two-dimensional electron gas (2DEG) that is confined on the Ga⁢ N side of the junction. The microscopic origin of these electrons has been debated over the years: after excluding that they would be contributed by bulk donors, a model that identifies surface states on the (Al, Ga)⁢N surface as the source of electrons has become widely adopted. Recently, it has become clear, however, that the measured density of surface states is insufficient to account for the high electron density in the 2DEG. Here we demonstrate, based on state-of-the-art first-principles calculations, that the source of electrons is intrinsic to the overall structure and that the negative charge in the 2DEG is balanced by fixed charge on the surface. We perform a rigorous study of polarization, using our recently developed methodology for quantifying polarization fields within the finite-sized systems that can be addressed with density-functional calculations. The results show that the electrons that appear in the 2DEG originate locally at the interface, and that the net charge at the interface is predominantly compensated by fixed charge on the surface, rather than surface states. We elucidate the source of this fixed charge and associate it with surface reconstructions or the presence of heterovalent impurities (such as oxygen). Our results force a reassessment of the impact of surface states on the density of the 2DEG: rather than serving as a supply of electrons, the surface states mainly act to pin the Fermi level. Our conclusions allow a fresh interpretation of experimental observations and allow devising guidelines for optimizing carrier densities in the 2DEG.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Microscopic examination of rf-cavity-quality niobium films through local nonlinear microwave response

The performance of superconducting radio-frequency (SRF) cavities is sometimes limited by local defects. To investigate the rf properties of these local defects, especially those that nucleate rf magnetic vortices, a near-field magnetic microwave microscope is employed. Local third-harmonic response ( P 3 f ) and its temperature dependence and rf power dependence are measured for one Nb / Cu film grown by direct current magnetron sputtering (DCMS) and six Nb / Cu films grown by high-power impulse magnetron sputtering (HiPIMS) with systematic variation of deposition conditions. Five out of the six HiPIMS Nb / Cu films show a strong third-harmonic response that is likely coming from rf vortex nucleation due to a low- T c surface defect with a transition temperature between 6.3 and 6.8 K, suggesting that this defect is a generic feature of air-exposed HiPIMS Nb / Cu films. A phenomenological model of surface-defect grain boundaries hosting a low- T c impurity phase is introduced and studied with time-dependent Ginzburg-Landau (TDGL) simulations of probe-sample interaction to better understand the measured third-harmonic response. The simulation results show that the third-harmonic response of rf vortex nucleation caused by surface defects exhibits the same general features as the data, including peaks in third-harmonic response with temperature, and their shift and broadening with higher microwave amplitude. We find that the parameters of the phenomenological model (the density of surface defects that nucleate rf vortices and the depth an rf vortex travels through these surface defects) vary systematically with film deposition conditions. From the point of view of these two properties, the Nb / Cu film that is most effective at reducing the nucleation of rf vortices associated with surface defects can be identified. Published by the American Physical Society 2024

Wang, Chung-Yang (ORCID:0000000184299633)↗

DOE OSTI2020

Microscopic force driving the photoinduced ultrafast phase transition: Time-dependent density functional theory simulations of IrTe 2

Photoinduced phase transitions can have complex and intriguing behaviors more than material ground-state dynamics. Understanding the underlying mechanism can help us to design new ways to manipulate the materials. A variety of mechanisms has been proposed to explain the photoinduced phase transitions of IrTe 2 , but a consensus has yet to be reached. Here, we study the photo-induced phase transitions of IrTe 2 by performing the real-time time-dependent density functional theory (rt-TDDFT) simulations in combination with the occupation constrained DFT method. We reveal that the microscopic driving force for the photo-induced phase transitions arises from the tendency to lower the energy levels occupied by the excited carriers, through the increase or decrease of the associated atomic pair distances, depending on whether the newly occupied states are antibonding or bonding states, respectively. The geometric constraints between different bonds represented by the Poisson ratio can bring together different tendencies from different atomic pairs, thus forming a complex intriguing dynamic picture depending on the intensity of the excitation. Furthermore, we also find that phonons don't play a primary role, but can assist the phase transition. These findings imply that one can control the structural phase transitions by selectively exciting photocarriers into designated atomic states using appropriate photon sources.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Microscopic diagnosis of universal geometric responses in fractional quantum Hall liquids

Topological quantum liquids contain internal degrees of freedom that are coupled to geometric response. Yet, an explicit and microscopic identification of the geometric response remains difficult. Here, taking notable fractional quantum Hall (FQH) states as typical examples, we systematically investigate a promising protocol—the Dehn-twist deformation on the torus geometry—to probe the geometric response of correlated topological states and establish the relation between such response and universal properties of pertinent states. Based on analytical derivations and numerical simulations, we find that the geometry-induced Berry phase encodes features for a broad class of FQH states at the Laughlin, hierarchy, Halperin and non-Abelian Moore-Read fillings. Our findings conclusively demonstrate that the adiabatic Dehn-twist deformation can faithfully capture rich geometric and topological information, including the Hall viscosity and topological spin of the pertinent FQH state and the chiral central charge of the underlying edge conformal field theory. Our approach provides a powerful way to reveal topological orders of generic FQH states and address previously open questions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗