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Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors"

This model data package is associated with the publication “Thermodynamic control on the decomposition of organic matter across different electron acceptors” submitted to Soil Biology and Biochemistry (Zheng et al., 2023; https://doi.org/10.1016/j.soilbio.2024.109364).In this research, a thermodynamic modeling framework is built to flexibly incorporate both organic matter (OM) molecules and electron acceptors for estimating potential free energy release from various redox reactions and to further predict reaction rates based on Microbial Transition State Theory. The model package includes scripts for thermodynamic modeling and postprocessing. Input Fourier-transform ion cyclotron resonance (FTICR) data are from a previous experimental study (Boye et al., 2018), and model outputs are free energy predictions and stoichiometric coefficients associated with all possible redox reactions.This data package is associated with the project GitHub repository found at MM_bioenergetic_modeling.This data package contains four folders (Input_FTICR, Model, Output, and Output_processing), a file-level metadata (FLMD) csv, and a data dictionary (dd) csv. Please see Zheng_bioenergetic_modeling_flmd.csv for a list of all files contained in this data package and descriptions for each. The Zheng_bioenergetic_modeling_dd.csv file describes the csv column headers. The “Model” folder contains scripts to run energy balance calculations for each electron acceptor. The “Output” folder contains csv files with stoichiometric information from model simulations. And the "Output_processing" folder contains scripts for reaction rate calculations and to generate plots.

54 ENVIRONMENTAL SCIENCES↗

Double diffraction imaging of x-ray induced structural dynamics in single free nanoparticles

Abstract Because of their high photon flux, x-ray free-electron lasers (FEL) allow to resolve the structure of individual nanoparticles via coherent diffractive imaging (CDI) within a single x-ray pulse. Since the inevitable rapid destruction of the sample limits the achievable resolution, a thorough understanding of the spatiotemporal evolution of matter on the nanoscale following the irradiation is crucial. We present a technique to track x-ray induced structural changes in time and space by recording two consecutive diffraction patterns of the same single, free-flying nanoparticle, acquired separately on two large-area detectors opposite to each other, thus examining both the initial and evolved particle structure. We demonstrate the method at the extreme ultraviolet (XUV) and soft x-ray Free-electron LASer in Hamburg (FLASH), investigating xenon clusters as model systems. By splitting a single XUV pulse, two diffraction patterns from the same particle can be obtained. For focus intensities of about 2 × 10 12 W cm −2 we observe still largely intact clusters even at the longest delays of up to 650 picoseconds of the second pulse, indicating that in the highly absorbing systems the damage remains confined to one side of the cluster. Instead, in case of five times higher flux, the diffraction patterns show clear signatures of disintegration, namely increased diameters and density fluctuations in the fragmenting clusters. Future improvements to the accessible range of dynamics and time resolution of the approach are discussed.

Sauppe, M. (ORCID:0000000163123102)↗

Toroidal modeling of plasma flow damping and density pump-out by RMP during ELM mitigation in HL-2A

Reduction of both the plasma density and toroidal flow speed, due to application of the predominantly n = 1 (n is the toroidal mode number) resonant magnetic perturbation (RMP) for controlling the edge localized mode in the HL-2A tokamak, is numerically investigated utilizing the quasi-linear initial-value code MARS-Q (Liu et al 2013 Phys. Plasmas 20 042503). Simulation results reveal that the neoclassical toroidal viscosity (NTV) due to three dimensional fields plays the key role in modifying the plasma momentum and particle transport in the HL-2A discharge. By comparing the modeling results with the measured density pump-out in the experiment, the electron NTV particle flux model, in combination with the free-boundary condition for the axisymmetric change of the density at the plasma edge, is found to yield the best agreement in terms of both the pump-out level and the overall time scale. Further sensitivity studies show that the simulated density pump-out level is reasonably robust against variations in the model assumptions, including the particle diffusion model and the non-ambipolar versus ambipolar NTV particle flux. The latter however affects the time scale for reaching the steady state solution. Finally, it is found that the plasma edge-peeling response, the NTV torque, as well as the plasma momentum and particle transport, all are sensitive to the toroidal phase difference between the upper and lower rows of the RMP coil currents in HL-2A, with the 30 ∘ coil phasing producing the minimal side effects on the plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Compensating slice emittance growth in high brightness photoinjectors using sacrificial charge

Achieving maximum electron beam brightness in photoinjectors requires detailed control of the 3D bunch shape and precise tuning of the beam focusing. Even in state-of-the-art designs, slice emittance growth due to nonlinear space charge forces and partial nonlaminarity often remains non-negligible. In this work, we introduce a new means to linearize the transverse slice phase space: a sacrificial portion of the bunch’s own charge distribution, formed into a wavebroken shock front by highly nonlinear space charge forces within the gun, whose downstream purpose is to dynamically linearize the desired bunch core. We show that linearization of an appropriately prepared bunch can be achieved via strongly nonlaminar focusing of the sacrificial shock front, while the inner core focuses laminarly. This leads to a natural spatial separation of the two distributions: a dense core surrounded by a diffuse halo of sacrificial charge that can be collimated. Multiobjective genetic algorithm optimizations of the ultracompact x-ray free electron laser injector employ this concept, and we interpret it with an analytic model that agrees well with the simulations. In simulation, we demonstrate a final bunch charge of 100 pC, peak current ∼ 30 A, and a sacrificial charge of 150 pC (250 pC total emitted from cathode) with normalized emittance growth of < 20 nm rad due to space charge. This implies a maximum achievable brightness approximately an order of magnitude greater than existing free electron laser injector designs. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

Recovering the phase and amplitude of X-ray FEL pulses using neural networks and differentiable models

Dynamics experiments are an important use-case for X-ray free-electron lasers (XFELs), but time-domain measurements of the X-ray pulses themselves remain a challenge. Shot-by-shot X-ray diagnostics could enable a new class of simpler and potentially higher-resolution pump-probe experiments. Here, we report training neural networks to combine low-resolution measurements in both the time and frequency domains to recover X-ray pulses at high-resolution. Critically, we also recover the phase, opening the door to coherent-control experiments with XFELs. The model-based generative neural-network architecture can be trained directly on unlabeled experimental data and is fast enough for real-time analysis on the new generation of MHz XFELs.

42 ENGINEERING↗

Advanced Modeling of Plasma-based Particle Accelerators

Plasma-based acceleration (PBA) driven by an intense laser (LWFA) or particle beam (PWFA) can produce ultra-high accelerating fields in excess of a GV/cm. PBA could substantially reduce the size and cost of future linear collider facilities if deployed successfully. PBA enables compact tabletop accelerators that can provide lower energy GeV-class beams in a laboratory setting. PBA enables high quality beam generation suitable for x-ray free electron lasers (XFEL) via controllable methods of self-injection. Challenges in modeling and optimization of multi-stage PBA motivate the need for exascale computing and state-of-the-art PIC codes.

43 PARTICLE ACCELERATORS↗

Modeling the energetic tail of a dusty plasma's electron energy distribution and its effect on dust grain charge and behavior

A model for a weakly ionized dusty plasma is proposed in which UV or x-ray radiation continuously creates free electrons at high energy, which then cool through collisions with a cold neutral gas before recombining. The transition of a free electron from high energy at birth to low energy at demise implies that the electron energy distribution is not the simple Maxwellian of an isolated system in thermal equilibrium, but instead has a high-energy tail that depends on the recombination time. This tail can have a major effect on dust grain charging because the flux of tail electrons can be substantial even if the density of tail electrons is small. Detailed analytic and numerical calculations of dust grain charging show that situations exist in which a small high-energy tail dominates charge behavior. This implies that dust grain charge in terrestrial and space dusty plasmas may be significantly underestimated if a Maxwellian distribution is assumed and the non-thermal dynamics are neglected.

Physics↗

Far-infrared absorption of undoped and Br-doped carbon nanofiber powder in stacked-cup cone configuration

In this study, we performed room-temperature far-infrared (40–650cm –1 ) transmission measurements on undoped and bromine-doped powder samples of carbon nanofibers in stacked-cup cone geometry. The transmission spectra show enhanced transmittance after bromine doping and all spectra were fit to a Drude-Lorentz (DL) model. A decreased metallic conductivity along with a redshift of the lowest semiconducting gap was found with doped samples. A significant decrease in the scattering rate upon heavy doping has been qualitatively explained as partial ordering of intercalated dopant ions. Absorption spectra were derived from the transmission spectra under the assumption of nondispersive reflectance and subsequently compared with DL-model-derived spectra. The free-carrier density of the n -type powder and the electronic mean free path were estimated and compared with reported values for single-walled nanotubes and pyrolytic graphite.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Neutron Skin Measurement of 208Pb and 48Ca Using Parity Violating Electron Scattering

Parity-violating electron scattering experiments (PVES) provides a clean probe of neutron densities that is model independent and free from strong interaction uncertainties in interpretation. The PREX-2 and CREX experiments were run in 2019 and 2020 at Jefferson laboratory measured the nucleon skin thickness, the difference between the r.m.s. neutron radius Rn and the r.m.s. proton radius Rp, of 208Pb and 48Ca via parity violating electroweak asymmetry in the elastic scattering of longitudinally polarized electrons. PREX-2 experiment was performed with 950 MeV electrons scattered at a 5¿ angle with Q2 = 0.00616 ± 0.00004 (GeV/c)2, while CREX used 2182 MeV electrons at the same angle with Q2 = 0.0297 ± 0.0002 (GeV/c)2. For PREX-2 the measured asymmetry was AP V = 550 ± 16 (stat.) ± (syst.) ppb, which corresponds to Rskin = 0.278 ± 0.078 (exp.) ± 0.012 (theo.) fm. The CREX asymmetry was AP V = 2668 ± 106 (stat.) ± 40 (syst.) ppb, which corresponds to Rskin = 0.121 ± 0.026 (exp.) ±0.024 (model) fm. One of the crucial systematic uncertainty that PREX-2 and CREX were sensitive to was the non-parity violating asymmetries that resulted from the helicity correlated false asymmetries in the polarized electron beam. There was a lot of work put towards understanding and suppressing the asymmetries arising from these effects. The parity violating asymmetry measurement required a very precise determination of the electron beam polarization. To accurately determine the beam polarization, a Compton polarimeter was used during both PREX-2 and CREX. A careful alignment of the laser to the Fabry-Perot cavity, data analysis and systematic control was employed to get a precise beam polarization result for the experiments. The PREX-2 measurement has broad implications for increasing our knowledge about neutron star structure and the equation of state of nuclear matter. The combined PREX and CREX results will have implications for future energy density functional calculations and the theory of nuclear structure.

Premathilake, Sachinthani↗

Imposing correct jellium response is key to predict the density response by orbital-free DFT

Orbital-free density functional theory constitutes a computationally highly effective tool for modeling electronic structures of systems ranging from room-temperature materials to warm dense matter. Its accuracy critically depends on the employed kinetic energy (KE) density functional, which has to be supplied as an external input. In this work we consider several nonlocal and Laplacian-level KE functionals and use an external harmonic perturbation to compute the static density response at T = 0 K in the linear and beyond-linear response regimes. We test for the satisfaction of exact conditions in the limit of uniform densities and for how approximate KE functionals reproduce the density response of realistic materials (e.g., Al and Si) against the Kohn-Sham DFT reference, which employs the exact KE. The results illustrate that several functionals violate exact conditions in the uniform electron gas (UEG) limit. We find a strong correlation between the accuracy of the KE functionals in the UEG limit and in the strongly inhomogeneous case. This empirically demonstrates the importance of imposing the limit of UEG response for uniform densities and validates the use of the Lindhard function in the formulation of kernels for nonlocal functionals. This conclusion is substantiated by additional calculations for bulk aluminum (Al) with a face-centered cubic (fcc) lattice and silicon (Si) with an fcc lattice, body-centered cubic (bcc) lattice, and semiconducting crystal diamond state. The analysis of fcc Al, and fcc as well as bcc Si data follows closely the conclusions drawn for the UEG, allowing us to extend our conclusions to realistic systems that are subject to density inhomogeneities induced by ions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Excited State Phenomena in Correlated Nanostructures: Transition Metal Oxide Clusters and Nanocrystals

The primary goal of our research program was to apply advanced computational techniques to predict electronic properties of molecular species. These include transition metal monoxide and dioxide clusters and negatively charged copper oxide clusters which are important systems for their utilization in a variety of technological applications. The enhanced electron-electron interactions inherent in these systems make it challenging to model their excited state properties within a parameter-free approach. The excited state properties in question include the interaction of light with these molecules which results in ejection of electrons from the system, or the absorption of light by the molecular system resulting in a molecule in a higher-energy state. Our overall goal was to investigate the impact of various computational and theoretical approaches on such electronic and optical excitations in these systems. Comparing several variants of theoretical approaches with available experimental data, and high-level quantum chemistry computations helped us identify the level of theory and approximations that are needed to achieve a reasonable balance between accuracy and computational demand.

74 ATOMIC AND MOLECULAR PHYSICS↗

Full radiator-perturber interaction in computer simulations of hydrogenic spectral line broadening by plasmas

Spectral line broadening by plasmas can be computed by solving the equation of motion for the dipole of the radiating system perturbed by a fluctuating potential obtained from computer simulations. Such calculations have relied on the multipole expansion of the radiator-plasma interaction often keeping only the dipole term. With increasing density, however, higher multipoles as well as plasma perturbers overlapping the bound electron wave functions are expected to become important. For hydrogenic systems, the atomic matrix elements of the full Coulomb and screened Coulomb interactions are given by analytical formulas. Using these results, a computer simulation approach that accounts for the full radiator-plasma interaction is developed. One benefit is the removal of inherent strong collision divergences in the multipole expansion approximation. Furthermore, it yields the plasma polarization shift produced by perturbers penetrating the wave function of the radiator bound electrons. Here, the model was applied to hydrogenic argon Ly-α , Ly- β , and Ly-$\gamma$ spectral lines in a dense argon plasma at free electron densities of 10 24 or 10 25 cm ⁻3 and temperature of $800$ $eV$ relevant to plasma diagnostic techniques for inertial confinement fusion implosions.

74 ATOMIC AND MOLECULAR PHYSICS↗

Photoinduced Electron-Transfer Distance Is Controlled by the Driving Force in Solid-State Organic Donor-Acceptor Systems

Understanding how short-range electron transfer generates photocurrent in organic solar cells and what photochemical driving force is needed to maximize efficiencies has been an immensely difficult problem. Here we show how these questions are intertwined: the driving force controls the average charge-transfer distance, skipping the shortest-range states in the optimal case. Using photoinduced absorption-detected magnetic resonance, we measure average charge-separation distances in dilute donor–acceptor blends as a function of driving force, and compare these with free charge yields measured by time-resolved microwave conductivity. We find that the largest driving forces show the shortest charge-separation distances, explaining their suppressed free-carrier generation. These results support a long-range electron-transfer model, wherein the driving force controls the initial delocalization of the electron–hole pair. The minimum driving force required for efficient charge separation (and minimal voltage losses) is ultimately set by the dielectric constant of the material.

14 SOLAR ENERGY↗

Particle charge distributions in the effluent of a flow-through atmospheric pressure low temperature plasma

Atmospheric pressure low-temperature plasmas are often utilized to perform particle synthesis, treatment, and removal. It is well-known that dust particles are highly negatively charged in these plasmas; however, little is known about dust particle charging behavior as particles leave the plasma volume and pass through the spatial afterglow region. In this work, monodisperse particles of various sizes and work functions were introduced into an atmospheric pressure radiofrequency capacitively coupled flow-through plasma. Dust particle electrical mobility distributions downstream of the flow-through plasma were measured utilizing a differential mobility analyzer in conjunction with a condensation particle counter at various gas flow velocities. Charge distributions were determined from the measured electrical mobility distributions. Experiments confirm that particles become less negatively charged, and even net-positively charged after leaving the plasma volume, with a distribution that follows a shifted Boltzmann charge distribution. Additionally, particle charge in the effluent of the flow-through plasma is negligibly dependent on work function but highly size and flow velocity dependent. Larger particles were shown to have a higher magnitude of charge under all studied conditions; however, particle polarity was switchable by varying gas flow velocity. The charging dynamics were simulated utilizing a constant number Monte Carlo model that accounts for electron temperature decay and the transition from ambipolar to free diffusion of electrons and ions in the spatial afterglow. Simulation results also suggest that, at the same flow velocity, larger particles obtain a greater magnitude of charge, negative or positive. Furthermore, the decrease in electron mobility and the difference between ion and electron convective loss rates create an ion-rich region in the plasma effluent that promotes ion–particle collisions and drives particle charge removal and even reversal of polarity. Larger particles more favorably collide with energetic species in these environments, which results in higher charge states.

atmospheric pressure low temperature plasma↗

Model-free control for frequency response support in microgrids utilizing wind turbines

Islanded microgrids integrated with renewable energy resources bring additional challenges to the primary frequency control due to their power-electronic interfaced generations. Developing an efficient control strategy for inertia emulation and frequency response support of microgrids is becoming an important issue. Wind turbine dynamics, however, will degrade the emulated inertial and primary responses with most traditional control strategies. On the other hand, compensation methods often require the knowledge of system models at the design stage and state estimation for feedback once deployed online. To overcome these challenges, this paper explores a model-free control (MFC) strategy to emulate the desired inertia and support the frequency response of a diesel-wind microgrid system. Additionally, the proposed MFC strategy utilizes a model reference concept to obtain guaranteed inertial response and improve the frequency response of microgrids. This work considers different control strategies with different operating points. The proposed controller is implemented and verified using the modified 33-bus full nonlinear model of the three-phase diesel-wind system in Simulink. Simulation results demonstrate the improved frequency response by precisely emulating the desired inertia using the MFC strategy.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Polarizability Plays a Decisive Role in Modulating Association between Molecular Cations and Anions

Electrostatic interactions involving proteins depend on not only the ionic charges involved but also their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of different pairs of monovalent molecular ions that are relevant to protein–protein and protein–ligand interactions. Cationic analogues of the basic amino acid side chains are simulated, along with oxyanionic analogues of cation-exchange ligands and acidic amino acids. Experimentally observed association trends with respect to the cations, but not anions, are captured by a nonpolarizable model. An effective continuum correction to account for electronic polarizability can capture both trends better but at the expense of fidelity to the underlying free energy landscape for ion-pair association. Finally, a polarizable model proves decisive in capturing experimentally suggested trends with respect to both cations and anions; critically, the free energy landscape for ion-pair association is itself altered, thus altering configurational sampling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Plasma screening in mid-charged ions observed by K-shell line emission

Dense plasma environment affects the electronic structure of ions via variations of the microscopic electrical fields, also known as plasma screening. This effect can be either estimated by simplified analytical models, or by computationally expensive and to date unverified numerical calculations. We have experimentally quantified plasma screening from the energy shifts of the bound-bound transitions in matter driven by the x-ray free electron laser (XFEL). This was enabled by identification of detailed electronic configurations of the observed Kα, Kβ and Kγ lines. This work paves the way for improving plasma screening models including connected effects like ionization potential depression and continuum lowering, which will advance the understanding of atomic physics in the Warm Dense Matter regime.

Physics - Plasma physics↗

High-Performance Accelerator Modeling: Toward Improving Controls and Diagnostics for High-Brightness Beams in Experiment

One of the main charges of beam physics is to improve the overall beam quality delivered to experiments and applications, which is generally quantified by the beam brightness. High brightness beams have numerous applications, including x-ray free electron lasers and ultrafast electron diffraction (UED). To these ends, this thesis details efforts to use high-performance models --- high-fidelity models that execute quickly --- for controls and diagnostics. To demonstrate the generality of these techniques, this thesis focuses on three of the most successful photoinjector designs currently used worldwide: the UCLA/SLAC/BNL-type high-gradient S-band gun, the continuous-wave high-repetition rate VHF APEX gun and the L-band DESY-PITZ-type gun. Work will be shown from Pegasus (UCLA), HiRES (LBNL) and FAST (FNAL).Specifically, data-driven models for online virtual diagnostics are presented, in this case, in the context of UED at HiRES, leading to a temporal resolution improvement. Methods for improving the fidelity of physics-based models are discussed, with examples at HiRES, Pegasus and FAST. Markov-chain Monte Carlo analysis is applied to match simulations, in the context of photocathode studies at HiRES and Pegasus. Lastly, the augmentation of online model-based predictions with model-independent optimization is explored in a fluctuating environment at Pegasus and HiRES. A central theme of this dissertation is working with parameter fluctuations when modeling an accelerator beamline. Long-term drifts and shot-to-shot jitter exist in every accelerator to a varying degree and therefore play an important role in every chapter of this dissertation. This thesis attempts to address the issues associated with these fluctuations when trying to develop faithful model representations of the system.

43 PARTICLE ACCELERATORS↗