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Overview of the Graphical User Interface for the GERMcode (GCR Event-Based Risk Model)

The descriptions of biophysical events from heavy ions are of interest in radiobiology, cancer therapy, and space exploration. The biophysical description of the passage of heavy ions in tissue and shielding materials is best described by a stochastic approach that includes both ion track structure and nuclear interactions. A new computer model called the GCR Event-based Risk Model (GERM) code was developed for the description of biophysical events from heavy ion beams at the NASA Space Radiation Laboratory (NSRL). The GERMcode calculates basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at NSRL for the purpose of simulating space radiobiological effects. For mono-energetic beams, the code evaluates the linear-energy transfer (LET), range (R), and absorption in tissue equivalent material for a given Charge (Z), Mass Number (A) and kinetic energy (E) of an ion. In addition, a set of biophysical properties are evaluated such as the Poisson distribution of ion or delta-ray hits for a specified cellular area, cell survival curves, and mutation and tumor probabilities. The GERMcode also calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle. The contributions from primary ion and nuclear secondaries are evaluated. The GERMcode accounts for the major nuclear interaction processes of importance for describing heavy ion beams, including nuclear fragmentation, elastic scattering, and knockout-cascade processes by using the quantum multiple scattering fragmentation (QMSFRG) model. The QMSFRG model has been shown to be in excellent agreement with available experimental data for nuclear fragmentation cross sections, and has been used by the GERMcode for application to thick target experiments. The GERMcode provides scientists participating in NSRL experiments with the data needed for the interpretation of their experiments, including the ability to model the beam line, the shielding of samples and sample holders, and the estimates of basic physical and biological outputs of the designed experiments. We present an overview of the GERMcode GUI, as well as providing training applications.

Kim, Myung-Hee Y.

Overview of the Graphical User Interface for the GERM Code (GCR Event-Based Risk Model

The descriptions of biophysical events from heavy ions are of interest in radiobiology, cancer therapy, and space exploration. The biophysical description of the passage of heavy ions in tissue and shielding materials is best described by a stochastic approach that includes both ion track structure and nuclear interactions. A new computer model called the GCR Event-based Risk Model (GERM) code was developed for the description of biophysical events from heavy ion beams at the NASA Space Radiation Laboratory (NSRL). The GERM code calculates basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at NSRL for the purpose of simulating space radiobiological effects. For mono-energetic beams, the code evaluates the linear-energy transfer (LET), range (R), and absorption in tissue equivalent material for a given Charge (Z), Mass Number (A) and kinetic energy (E) of an ion. In addition, a set of biophysical properties are evaluated such as the Poisson distribution of ion or delta-ray hits for a specified cellular area, cell survival curves, and mutation and tumor probabilities. The GERM code also calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle. The contributions from primary ion and nuclear secondaries are evaluated. The GERM code accounts for the major nuclear interaction processes of importance for describing heavy ion beams, including nuclear fragmentation, elastic scattering, and knockout-cascade processes by using the quantum multiple scattering fragmentation (QMSFRG) model. The QMSFRG model has been shown to be in excellent agreement with available experimental data for nuclear fragmentation cross sections, and has been used by the GERM code for application to thick target experiments. The GERM code provides scientists participating in NSRL experiments with the data needed for the interpretation of their experiments, including the ability to model the beam line, the shielding of samples and sample holders, and the estimates of basic physical and biological outputs of the designed experiments. We present an overview of the GERM code GUI, as well as providing training applications.

Kim, Myung-Hee

Distribution of centrality measures on undirected random networks via the cavity method

The Katz centrality of a node in a complex network is a measure of the node’s importance as far as the flow of information across the network is concerned. For ensembles of locally tree-like undirected random graphs, this observable is a random variable. Its full probability distribution is of interest but difficult to handle analytically because of its “global” character and its definition in terms of a matrix inverse. Leveraging a fast Gaussian Belief Propagation-Cavity algorithm to solve linear systems on tree-like structures, we show that i) the Katz centrality of a single instance can be computed recursively in a very fast way, and ii) the probability P ( K ) that a random node in the ensemble of undirected random graphs has centrality K satisfies a set of recursive distributional equations, which can be analytically characterized and efficiently solved using a population dynamics algorithm. We test our solution on ensembles of Erdős-Rényi and Scale Free networks in the locally tree-like regime, with excellent agreement. The analytical distribution of centrality for the configuration model conditioned on the degree of each node can be employed as a benchmark to identify nodes of empirical networks with over- and underexpressed centrality relative to a null baseline. We also provide an approximate formula based on a rank- 1 projection that works well if the network is not too sparse, and we argue that an extension of our method could be efficiently extended to tackle analytical distributions of other centrality measures such as PageRank for directed networks in a transparent and user-friendly way.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

SQuaD: Smart Quantum Detection for Photon Recognition and Dark Count Elimination

Quantum detectors of single photons are an essential component for quantum information processing across computing, communication and networking. Today's quantum detection system, which consists of single photon detectors, timing electronics, control and data processing software, is primarily used for counting the number of single photon detection events. However, it is largely incapable of extracting other rich physical characteristics of the detected photons, such as their wavelengths, polarization states, photon numbers, or temporal waveforms. This work, for the first time, demonstrates a smart quantum detection system, SQuaD, which integrates a field programmable gate array (FPGA) with a neural network model, and is designed to recognize the features of photons and to eliminate detector dark-count. The SQuaD is a fully integrated quantum system with high timing-resolution data acquisition, onboard multi-scale data analysis, intelligent feature recognition and extraction, and feedback-driven system control. Our \name experimentally demonstrates 1) reliable photon counting on par with the state-of-the art commercial systems; 2) high-throughput data processing for each individual detection events; 3) efficient dark count recognition and elimination; 4) up to 100% accurate feature recognition of photon wavelength and polarization. Additionally, we deploy the SQuaD to an atomic (erbium ion) photon emitter source to realize noise-free control and readout of a spin qubit in the telecom band, enabling critical advances in quantum networks and distributed quantum information processing.

Linne, Karl C. [U. Chicago (main)] (ORCID:00090009

A Tutorial on Bayesian analysis of linear shock compression data

Gas gun and other shock compression experiments often produce shock wave velocity measurements that are linearly associated with particle velocity. Traditionally, this empirical relationship is quantified with a single Hugoniot curve that is estimated using least squares regression. However, for downstream modeling and simulation tasks, it is often more useful to have multiple Hugoniot curves in the pressure–volume plane that are consistent with the data. We employ Bayesian uncertainty quantification methods as a framework for propagating measurement uncertainty through to model parameters and predictions. Specifically, this Tutorial shows how to sample multiple Hugoniot curves in the pressure–volume plane that are consistent with the shock wave-particle velocity measurements in a two-step Bayesian approach. First, we obtain an analytical expression for the posterior distribution of the linear model parameters using Bayesian linear regression. Second, we propagate samples from the posterior distribution through the Rankine–Hugoniot equations to yield Hugoniot curves in the pressure–volume plane. The procedure is demonstrated with publicly available data on argon, copper, and nickel, and compared against bootstrapping and linear regression. The Bayesian procedure is shown to be interpretable, computationally inexpensive, and less sensitive than an alternative bootstrapping approach to the removal of the point in the copper dataset that has the largest particle velocity. As a Tutorial on Bayesian methodology for the shock compression community, we provide several derivations and explanations that make this paper self-contained, and make all code and data available at github.com/llnl/BALSCD.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Magneto-optical study of Nb thin films for superconducting qubits

Among the recognized sources of decoherence in superconducting qubits, the spatial inhomogeneity of the superconducting state and the possible presence of magnetic-flux vortices remain comparatively underexplored. Niobium is commonly used as a structural material in transmon qubits that host Josephson junctions, and excess dissipation anywhere in the transmon can become a bottleneck that limits overall quantum performance. The metal/substrate interfacial layer may simultaneously host pair-breaking loss channels (e.g., two-level systems, TLS) and control thermal transport, thereby affecting dissipation and temperature stability. Here, we use quantitative magneto-optical imaging of the magnetic-flux distribution to characterize the homogeneity of the superconducting state and the critical current density, $j_{c}$, in niobium films fabricated under different sputtering conditions. The imaging reveals distinct flux-penetration regimes, ranging from a nearly ideal Bean critical state to strongly nonuniform thermo-magnetic dendritic avalanches. By fitting the measured magnetic-induction profiles, we extract $j_{c}$ and correlate it with film physical properties and with measured qubit internal quality factors. Our results indicate that the Nb/Si interlayer can be a significant contributor to decoherence and should be considered an important factor that must be optimized.

Datta, Amlan [Ames Lab; Iowa State U.]

Universal energy-speed-accuracy trade-offs in driven nonequilibrium systems

The connection between measure theoretic optimal transport and dissipative nonequilibrium dynamics provides a language for quantifying nonequilibrium control costs, leading to a collection of thermodynamic speed limits, which rely on the assumption that the target probability distribution is perfectly realized. This is almost never the case in experiments or numerical simulations, so here we address the situation in which the external controller is imperfect. We obtain a lower bound for the dissipated work in generic nonequilibrium control problems that (1) is asymptotically tight and (2) matches the thermodynamic speed limit in the case of optimal driving. Along with analytically solvable examples, we refine this imperfect driving notion to systems in which the controlled degrees of freedom are slow relative to the nonequilibrium relaxation rate, and identify independent energy contributions from fast and slow degrees of freedom. Furthermore, we develop a strategy for optimizing minimally dissipative protocols based on optimal transport flow matching, a generative machine learning technique. Furthermore, this latter approach ensures the scalability of both the theoretical and computational framework we put forth. Crucially, we demonstrate that we can compute the terms in our bound numerically using efficient algorithms from the computational optimal transport literature and that the protocols we learn saturate the bound.

59 BASIC BIOLOGICAL SCIENCES

Carbon Nanotubes in Water: MD Simulations of Internal and External Flow, Self Organization

We have developed computational tools, based on particle codes, for molecular dynamics (MD) simulation of carbon nanotubes (CNT) in aqueous environments. The interaction of CNTs with water is envisioned as a prototype for the design of engineering nano-devices, such as artificial sterocillia and molecular biosensors. Large scale simulations involving thousands of water molecules are possible due to our efficient parallel MD code that takes long range electrostatic interactions into account. Since CNTs can be considered as rolled up sheets of graphite, we expect the CNT-water interaction to be similar to the interaction of graphite with water. However, there are fundamental differences between considering graphite and CNTs, since the curvature of CNTs affects their chemical activity and also since capillary effects play an important role for both dynamic and static behaviour of materials inside CNTs. In recent studies Gordillo and Marti described the hydrogen bond structure as well as time dependent properties of water confined in CNTs. We are presenting results from the development of force fields describing the interaction of CNTs and water based on ab-initio quantum mechanical calculations. Furthermore, our results include both water flows external to CNTs and the behaviour of water nanodroplets inside heated CNTs. In the first case (external flows) the hydrophobic behaviour of CNTs is quantified and we analyze structural properties of water in the vicinity of CNTs with diagnostics such as hydrogen bond distribution, water dipole orientation and radial distribution functions. The presence of water leads to attractive forces between CNTs as a result of their hydrophobicity. Through extensive simulations we quantify these attractive forces in terms of the number and separation of the CNT. Results of our simulations involving arrays of CNTs indicate that these exhibit a hydrophobic behaviour that leads to self-organising structures capable of trapping water clusters. In the second case (internal flows) we study the behaviour of water droplets confined inside CNTs. Constant temperature simulations allow us to capture structural properties such as the contact angles and density profiles of the equilibrated drops. By heating and subsequently cooling of the CNT, we are able to measure the evaporation and the condensation rate of the entrapped water.

Jaffe, Richard L.

Design and Optimization of a Hybrid Design for Quantum Transduction

This study presents the mechanical design and analysis of a quantum electro-optical transducer engineered to operate at millikelvin temperatures within a dilution refrigerator. The transducer enables bidirectional microwave-optical frequency conversion through a hybrid architecture that integrates a superconducting radiofrequency (SRF) cavity with an electro-optic optical cavity. Among several design options investigated, the configuration offering the best thermal and mechanical performance was selected, yielding a robust solution with reduced sensitivity to fabrication tolerances, improved heat dissipation, as well as alignment precision. The design ensures uniform temperature distribution, enabling higher laser pump powers and, thus, increased conversion efficiency, while maintaining mechanical stresses safely below the material yield strength. Electromagnetic simulations further validate the design, demonstrating enhanced coupling between the optical and microwave modes, as well as a broader tuning range achieved with smaller tuner displacements.

quantum computing

A simple three-component mixing problem for the evaluation of a new reaction rate model

A simple computational mixing problem is presented which can be utilized to assess the behavior of Reynolds-averaged reaction rate models in a problem with temporally varying mixedness. In this problem, three mixing components are homogeneously distributed but initially separated in a triply periodic domain. Further, these components are initialized within a Taylor–Green-like velocity field, which creates a mixing history evolving from the so-called “no-mix limit” to a well-mixed state. Large-eddy simulation results from this problem in configurations involving both premixed and nonpremixed reactants are then compared with zero-dimensional Reynolds-averaged Navier–Stokes results utilizing a new model for multicomponent reacting mixtures. The new model is shown to appropriately respect the no-mix limit and outperforms an earlier model (Morgan, 2022), particularly at early times when components are near the no-mix limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Dual-unitary shadow tomography

We introduce a classical shadow tomography scheme based on dual-unitary brick-wall circuits termed "dual-unitary shadow tomography" (DUST). For this we study operator spreading and Pauli weight dynamics in one-dimensional qubit systems, evolved by random two-local dual-unitary gates arranged in a brick-wall structure, ending with a final measurement layer. We do this by deriving general constraints on the Pauli weight transfer matrix and specializing to the case of dual-unitarity. We first show that dual-unitaries must have a minimal amount of entropy production. Remarkably, we find that operator spreading in these circuits have a rich structure resembling that of relativistic quantum field theories, with massless chiral excitations that can decay or fuse into each other, which we call left- or right-movers. We develop a mean-field description of the Pauli weight in terms of $\rho(x,t)$, which represents the probability of having nontrivial support at site $x$ and depth $t$ starting from a fixed weight distribution. We develop an equation of state for $\rho(x,t)$, and simulate it numerically using Monte Carlo simulations. Lastly, we demonstrate that the fast-thermalizing properties of dual-unitary circuits make them better at predicting large operators than shallow brick-wall Clifford circuits. Our results are robust to finite-size effects due to the chirality of dual-unitary brick-wall circuits.

97 MATHEMATICS AND COMPUTING

Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Furthermore, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Mixed stochastic-deterministic density functional theoretic decomposition of Kubo–Greenwood conductivities in the projector augmented wave formalism

Pairing the accuracy of the Kohn–Sham density-functional framework with the efficiency of a stochastic algorithmic approach, mixed stochastic-deterministic density functional theory (mDFT) achieves a favorable computational scaling with system sizes and electronic temperatures. We employ the recently developed mDFT formalism to investigate the dynamic charge-transport properties of systems in the warm dense matter regime. The optical conductivity spectra are computed for single- and multi- component mixtures of carbon, hydrogen, and beryllium using two complementary approaches: Kubo–Greenwood in the mDFT picture and real-time time-dependent mDFT. We further devise a decomposition of the Onsager coefficients leading up to the Kubo–Greenwood spectra to exhibit contributions from the deterministic, stochastic, and mixed electronic state transitions at different incident photon energies.

36 MATERIALS SCIENCE

Magneto-optical study of Nb thin films for superconducting qubits

Abstract Among the recognized sources of decoherence in superconducting qubits, the spatial inhomogeneity of the superconducting state and the possible presence of magnetic-flux vortices remain comparatively underexplored. Niobium is commonly used as a structural material in transmon qubits that host Josephson junctions, and excess dissipation anywhere in the transmon can become a bottleneck that limits overall quantum performance. The metal/substrate interfacial layer may simultaneously host pair-breaking loss channels (e.g. two-level systems) and control thermal transport, thereby affecting dissipation and temperature stability. Here, we use quantitative magneto-optical imaging of the magnetic-flux distribution to characterize the homogeneity of the superconducting state and the critical current density, j c , in niobium films fabricated under different sputtering conditions. The imaging reveals distinct flux-penetration regimes, ranging from a nearly ideal Bean critical state to strongly nonuniform thermo-magnetic dendritic avalanches. By fitting the measured magnetic-induction profiles, we extract j c and try to correlate it with film physical properties and with measured qubit internal quality factors. Our results indicate that the Nb/Si interlayer can be a significant contributor to decoherence and should be considered an important factor that must be optimized.

Datta, Amlan [Ames National Laboratory; Iowa State

NASA Tech Briefs, January 2003

Topics covered include: Optoelectronic Tool Adds Scale Marks to Photographic Images; Compact Interconnection Networks Based on Quantum Dots; Laterally Coupled Quantum-Dot Distributed-Feedback Lasers; Bit-Serial Adder Based on Quantum Dots; Stabilized Fiber-Optic Distribution of Reference Frequency; Delay/Doppler-Mapping GPS-Reflection Remote-Sensing System; Ladar System Identifies Obstacles Partly Hidden by Grass; Survivable Failure Data Recorders for Spacecraft; Fiber-Optic Ammonia Sensors; Silicon Membrane Mirrors with Electrostatic Shape Actuators; Nanoscale Hot-Wire Probes for Boundary-Layer Flows; Theodolite with CCD Camera for Safe Measurement of Laser-Beam Pointing; Efficient Coupling of Lasers to Telescopes with Obscuration; Aligning Three Off-Axis Mirrors with Help of a DOE; Calibrating Laser Gas Measurements by Use of Natural CO2; Laser Ranging Simulation Program; Micro-Ball-Lens Optical Switch Driven by SMA Actuator; Evaluation of Charge Storage and Decay in Spacecraft Insulators; Alkaline Capacitors Based on Nitride Nanoparticles; Low-EC-Content Electrolytes for Low-Temperature Li-Ion Cells; Software for a GPS-Reflection Remote-Sensing System; Software for Building Models of 3D Objects via the Internet; "Virtual Cockpit Window" for a Windowless Aerospacecraft; CLARAty Functional-Layer Software; Java Library for Input and Output of Image Data and Metadata; Software for Estimating Costs of Testing Rocket Engines; Energy-Absorbing, Lightweight Wheels; Viscoelastic Vibration Dampers for Turbomachine Blades; Soft Landing of Spacecraft on Energy-Absorbing Self-Deployable Cushions; Pneumatically Actuated Miniature Peristaltic Vacuum Pumps; Miniature Gas-Turbine Power Generator; Pressure-Sensor Assembly Technique; Wafer-Level Membrane-Transfer Process for Fabricating MEMS; A Reactive-Ion Etch for Patterning Piezoelectric Thin Film; Wavelet-Based Real-Time Diagnosis of Complex Systems; Quantum Search in Hilbert Space; Analytic Method for Computing Instrument Pointing Jitter; and Semiselective Optoelectronic Sensors for Monitoring Microbes.

Source record

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron–oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

59 BASIC BIOLOGICAL SCIENCES

Improved energies and local energies with weighted variational Monte Carlo

Neural network parametrizations have increasingly been used to represent the ground and excited states in variational Monte Carlo (VMC) with promising results. However, traditional VMC methods only optimize the wave function in regions of peak probability. The wave function is uncontrolled in the tails of the probability distribution, which can limit the accuracy of the trained wave function. To improve the approximation accuracy in the probability tails, this paper interprets VMC as a gradient flow in the space of wave functions, followed by a projection step. From this perspective, arbitrary probability distributions can be used in the projection step, allowing the user to prioritize accuracy in different regions of state space. Motivated by this theoretical perspective, the paper tests a weighted VMC method on the antiferromagnetic Heisenberg model for a periodic spin chain. Compared to traditional VMC, weighted VMC reduces the error in the ground state energy by a factor of 2, and it reduces the errors in the local energies away from the mode by large factors of 10 2 –10 4 .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Temporal Coarse Graining for Classical Stochastic Noise in Quantum Systems

Simulations of quantum systems with Hamiltonian classical stochastic noise can be challenging when the noise exhibits temporal correlations over a multitude of time scales, such as for 1/f noise in solid-state quantum information processors. Here we present an approach for simulating Hamiltonian classical stochastic noise that performs temporal coarse-graining by effectively integrating out the high-frequency components of the noise. We focus on the case where the stochastic noise can be expressed as a sum of Ornstein-Uhlenbeck processes. Temporal coarse-graining is then achieved by conditioning the stochastic process on a coarse realization of the noise, expressing the conditioned stochastic process in terms of a sum of smooth, deterministic functions and bridge processes with boundaries fixed at zero, and performing the ensemble average over the bridge processes. For Ornstein-Uhlenbeck processes, the deterministic components capture all dependence on the coarse realization, and the stochastic bridge processes are not only independent but taken from the same distribution with correlators that can be expressed analytically, allowing the associated noise propagators to be precomputed once for all simulations. This combination of noise trajectories on a coarse time grid and ensemble averaging over bridge processes has practical advantages, such as a simple concatenation rule, that we highlight with numerical examples.

Albash, Tameem [Sandia National Lab. (SNL-NM), Alb