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DOE OSTI2024

Molecular-level architecture of Chlamydomonas reinhardtii’s glycoprotein-rich cell wall

Abstract Microalgae are a renewable and promising biomass for large-scale biofuel, food and nutrient production. However, their efficient exploitation depends on our knowledge of the cell wall composition and organization as it can limit access to high-value molecules. Here we provide an atomic-level model of the non-crystalline and water-insoluble glycoprotein-rich cell wall of Chlamydomonas reinhardtii . Using in situ solid-state and sensitivity-enhanced nuclear magnetic resonance, we reveal unprecedented details on the protein and carbohydrate composition and their nanoscale heterogeneity, as well as the presence of spatially segregated protein- and glycan-rich regions with different dynamics and hydration levels. We show that mannose-rich lower-molecular-weight proteins likely contribute to the cell wall cohesion by binding to high-molecular weight protein components, and that water provides plasticity to the cell-wall architecture. The structural insight exemplifies strategies used by nature to form cell walls devoid of cellulose or other glycan polymers.

09 BIOMASS FUELS↗

DOE OSTI2021

Velocity structure functions in multiphase turbulence: interpreting kinematics of Hα filaments in cool-core clusters

ABSTRACT The central regions of cool-core galaxy clusters harbour multiphase gas, with gas temperatures ranging from $10$ to $10^7\, \mathrm{K}$. Feedback from active galactic nuclei jets prevents the gas from undergoing a catastrophic cooling flow. However, the exact mechanism of this feedback energy input is unknown, mainly due to the lack of velocity measurements of the hot-phase gas. However, recent observations have measured the velocity structure functions (VSFs) of the cooler molecular (${\sim} 10\, \mathrm{K}$) and Hα filaments (${\sim} 10^4\, \mathrm{K}$) and used them to indirectly estimate the motions of the hot phase. In the first part of this study, we conduct high-resolution (3843–15363 resolution elements) simulations of homogeneous isotropic subsonic turbulence, without radiative cooling. We analyse the second-order velocity structure functions (VSF2) in these simulations and study the effects of varying spatial resolution, the introduction of magnetic fields, and the effect of projection along the line of sight (LOS) on it. In the second part of the study, we analyse high-resolution (7683 resolution elements) idealized simulations of multiphase turbulence in the intracluster medium from the companion study Mohapatra et al. We compare the VSF2 for both the hot ($T\sim 10^7\, \mathrm{K}$) and cold ($T\sim 10^4\, \mathrm{K}$) phases and find that their amplitude depends on the density contrast between the phases. They have similar scaling with separation, but introducing magnetic fields steepens the VSF2 of only the cold phase. We also find that projection along the LOS steepens the VSF2 for the hot phase and mostly flattens it for the cold phase.

Mohapatra, Rajsekhar (ORCID:0000000216007552)↗

DOE OSTI2023

Changing temperature profiles and the risk of dengue outbreaks

As temperatures change worldwide, the pattern and competency of disease vectors will change, altering the global distribution of both the burden of infectious disease and the risk of the emergence of those diseases into new regions. To evaluate the risk of potential summer dengue outbreaks triggered by infected travelers under various climate scenarios, we develop an SEIR-type model, run numerical simulations, and conduct sensitivity analyses under a range of temperature profiles. Our model extends existing theoretical frameworks for studying dengue dynamics by introducing temperature dependence of two key parameters: the mosquito extrinsic incubation period and the lifespan of mosquitoes, which empirical data suggests are both highly temperature dependent. We find that changing temperature significantly alters dengue risk in an inverted U-shape, with temperatures in the range 27-31°C producing the highest risk. As temperatures increase beyond 31°C, the determinants of dengue risk begin to shift from mosquito biting rate and carrying capacity to the duration of the human infectious period, suggesting that changing temperatures not only alter dengue risk but also the potential efficacy of control measures. To illustrate the role of spatial and temporal temperature heterogeneity, we select five US cities where the primary dengue vector, the mosquito Aedes aegypti , has been observed, and which have had dengue cases in the past: Los Angeles, Houston, Miami, Brownsville, and Phoenix. Our analysis suggests that an increase of 3°C leads to an approximate doubling of the risk of dengue in Los Angeles and Houston, but a reduction of risk in Miami, Brownsville, and Phoenix due to extreme heat.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Inferring the photolysis rate of NO 2 in the stratosphere based on satellite observations

NO and NO 2 (NO x ) play major roles in both tropospheric and stratospheric chemistry. This paper provides a novel method to obtain a global and accurate photolysis rate for NO 2 based on satellite data. The photolysis rate J(NO 2 ) dominates the daytime diurnal variation of NO x photochemistry. Here the spatial variation of J(NO 2 ) at 50–90°S in December from 20–40km is obtained using data from the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) experiment. Because NO and NO 2 rapidly exchange with one another in the daytime, J(NO 2 ) can be attained assuming steady state, and the results are shown to be consistent with model results. The J(NO 2 ) value decreases as the solar zenith angle increases and has a weak altitude dependence. A key finding is that satellite-derived J(NO 2 ) increases in the polar regions, in good agreement with model predictions, due to the effects of ice and snow on surface albedo. Thus, the method presented here provides an observation-based check on the role of albedo in driving polar photochemistry.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

The Very High n Rydberg Series of Ar^16+ in Alcator C-Mod Tokamak Plasmas

X-ray transitions of the very high-n Rydberg series in Ar^16+ have been observed from Alcator C-Mod tokamak plasmas. Individual emission lines up to 1s16p - 1s^2 have been resolved and the central chord line brightnesses with principal quantum number n between 7 and 16 are generally found to decay as 1/n^alpha, with alpha slightly larger than 3. In the plasma periphery, emission from 1s9p - 1s^2 and 1s10p - 1s^2 are found to be significantly enhanced relative to this decrease, indicative of selected population of these levels through charge exchange between background neutral deuterium in the ground state and Ar^17+. An unresolved feature between the wavelengths of 1s27p - 1s^2 and 1s30p - 1s^2 is also present, which arises through charge exchange with neutral deuterium in the n^* = 3 excited state. The brightnesses of transitions populated by charge exchange are spatially up/down asymmetric, with an excess on the side of the magnetic surface X-point. The relative brightness of the unresolved very high-n feature compared to 1s7p - 1s^2 is found to increase with electron temperature and decrease with electron density. Simulations of line emission just on the long wavelength side of the Ar^16$ ionization limit indicate that the principal quantum number decay exponent is closer to alpha = 4 at very high n. The brightness dependence on n below 16 is in excellent agreement with calculations from the Flexible Atomic Code package.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

A Study on Computational Cost Reduction of Simulations of Phase-Change Material (PCM) Embedded Heat Exchangers

Thermal storage can be implemented using Phase-Change Materials (PCM), which absorb significant latent heat with a relatively small temperature change. PCM phase-change processes are transient and are driven by thermal diffusion and natural convection – the latter, especially for melting process. Modeling and simulation of PCM heat exchangers (HX’s) is typically computationally intensive due to the relatively complex time-dependent physics. Most of the PCM modeling work in the literature uses high-order modeling tools such as Computational Fluid Dynamics (CFD) and Lattice-Boltzmann Method (LBM). For design purposes, the existing PCM modeling approaches are not practical, limiting researchers in their ability to investigate new ideas and different PCM’s with faster turnarounds. This paper presents a study investigating the reduction of computational cost of PCM embedded HX’s CFD models by evaluating the feasibility of spatial reduction without losing accuracy. The analysis consists of comparing full and partial domain under full melting conditions. The subject of this study is a single straight tube with circular transverse fins in the vertical orientation, using PCM’s with 35oC nominal melting temperature. Different tube and fin dimensions are investigated. Results indicate that the reduced domain reproduces - in half the run time - the same behavior as the full domain since the buoyancy effects are localized and patterned. The outputs from the partial domain simulation were used to build a non-general correlation for the PCM heat transfer characteristics and demonstrated how it can be implemented in a Finite Control Volume Reduced Order Model (ROM). The ROM can accurately reproduce the CFD simulations at 4 to 5 orders of magnitude faster.

25 ENERGY STORAGE↗

DOE OSTI2021

The very high n Rydberg series of Ar 16+ in Alcator C-Mod tokamak plasmas

We report x-ray transitions of the very high-n Rydberg series in Ar 16+ have been observed from Alcator C-Mod tokamak plasmas. Individual emission lines up to 1s16p-1s 2 have been resolved and the central chord line brightnesses with principal quantum number n between 7 and 16 are generally found to decay as 1/n α , with α slightly larger than 3. In the plasma periphery, emission from 1s9p-1s 2 and 1s10p-1s 2 are found to be significantly enhanced relative to this decrease, indicative of selected population of these levels through charge exchange between background neutral deuterium in the ground state and Ar 17+ . An unresolved feature between the wavelengths of 1s27p-1s 2 and 1s30p-1s 2 is also present, which arises through charge exchange with neutral deuterium in the n* = 3 excited state. The brightnesses of transitions populated by charge exchange are spatially up/down asymmetric, with an excess on the side of the magnetic surface X-point. The relative brightness of the unresolved very high-n feature compared to 1s7p-1s 2 is found to increase with electron temperature and decrease with electron density. Simulations of line emission just on the long wavelength side of the Ar 16+ ionization limit indicate that the principal quantum number decay exponent is closer to α = 4 at very high n. The brightness dependence on n below 16 is in excellent agreement with calculations from the flexible atomic code package.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

An Integrated Multiscale Modeling Framework for Unconventional Stimulation and Production (Final Report)

The production of oil and gas from unconventional reservoirs largely depends upon two main features operating at different scales: (1) the establishment of a reservoir scale stimulated fracture network that effectively communicates with the rock volume, enhancing permeability and transport to the wellbore and (2) the coupled multi-phase flow, chemical and mechanical processes affecting the migration of hydrocarbons from the low permeability country rock adjacent to the stimulated fracture network. To date, there has been no simulation framework that allows seamless and integrated prediction of these features across spatial scales extending from the pore structure of the reservoir rock to the volume of the reservoir. In addition, there has been a lack of suitable field measurements to test such models, as stimulation and production data are often proprietary and not freely available to national laboratories and academic institutions. New multi-scale simulation capabilities are needed that are validated against suitable field-based research experiments on hydraulic fracturing and shale production.

02 PETROLEUM↗

DOE OSTI2025

Building partnerships for development of sustainable energy systems with atmospheric measurements

Atmospheric dynamics often play a critical role in the sustainability and reliability of diverse forms of energy production. This is especially true for the growing number of renewable energy deployments that harness aspects of the environment for power production. While the University of Memphis has a strong research background in energy systems, we have little experience working with the Earth and Environmental Systems Science Division (EESSD) and their associated User Facilities. Of particular interest to us is the Atmospheric Science Research and the Atmospheric Radiation Measurement (ARM) user facility to address surface-boundary layer interactions and physical phenomena. One of the major challenges for understanding and developing energy systems and management platforms is accurate modeling/forecasting of atmospheric conditions across disparate spatial and temporal scales. These conditions are often required to understand the lowest levels of the atmospheric boundary layer, but are also important to understand higher atmospheric conditions where aerosols affect cloud development. The objective of this work was to develop partnerships with national laboratories for collaboration on environmental science and its intersection with sustainable energy systems, as well as to leverage the ARM user facility data repositories to enhance our research capabilities in energy systems and their inter-dependence on environmental systems for future engagement with EESSD. Specifically, we accomplished these objectives by (1) developing collaborations with Oakridge National Laboratory ARM Data Science and Integration Group which resulted in student internships, (2) employed ARM data to develope modeling of the atmospheric boundary layer optical turbulence, and (3) optimally-sized large-scale renewable energy systems and their associated energy storage systems with ARM repository data.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2022

A finite-volume scheme for modeling compressible magnetohydrodynamic flows at low Mach numbers in stellar interiors

Fully compressible magnetohydrodynamic (MHD) simulations are a fundamental tool for investigating the role of dynamo amplification in the generation of magnetic fields in deep convective layers of stars. The flows that arise in such environments are characterized by low (sonic) Mach numbers ($\mathscr{M}$ son ≲ 10 –2 ). In these regimes, conventional MHD codes typically show excessive dissipation and tend to be inefficient as the Courant–Friedrichs–Lewy (CFL) constraint on the time step becomes too strict. In this work we present a new method for efficiently simulating MHD flows at low Mach numbers in a space-dependent gravitational potential while still retaining all effects of compressibility. The proposed scheme is implemented in the finite-volume SEVEN-LEAGUE HYDRO (SLH) code, and it makes use of a low-Mach version of the five-wave Harten–Lax–van Leer discontinuities (HLLD) solver to reduce numerical dissipation, an implicit–explicit time discretization technique based on Strang splitting to overcome the overly strict CFL constraint, and a well-balancing method that dramatically reduces the magnitude of spatial discretization errors in strongly stratified setups. The solenoidal constraint on the magnetic field is enforced by using a constrained transport method on a staggered grid. We carry out five verification tests, including the simulation of a small-scale dynamo in a star-like environment at $\mathscr{M}$ son ~ 10 –3 . We demonstrate that the proposed scheme can be used to accurately simulate compressible MHD flows in regimes of low Mach numbers and strongly stratified setups even with moderately coarse grids.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Growth Phenomena and Bandgap Shift in Melt-Grown β-(In x Ga 1- x ) 2 O 3 Alloys

β-Ga 2 O 3 is an emerging ultra-wide bandgap semiconductor with great promise for power electronics and optoelectronics. Alloys in the In 2 O 3 -Ga 2 O 3 system are interesting for optoelectronic applications, particularly where bandgap tuning is desirable. Herein, β-(In x Ga 1- x ) 2 O 3 alloys with target compositions x = 0.025 or 0.10 are grown from the melt using the Czochralski and vertical gradient freeze techniques. Growth with 10 mol% In yields only small, needle-like crystals, while 2.5 mol% In allows growth of centimeter-sized single crystals. A substantial degree of indium segregation is unveiled by spatial measurements of lattice parameters and the bandgap. The bandgap decreases by a maximum of 0.28 eV in the case of the highest In content crystals. Z-contrast transmission electron microscopy confirms a solely octahedral coordination of In in the β-Ga 2 O 3 lattice. With indium concentrations higher than 2.5 mol%, samples contain micron-scale voids that impart a dark coloration. All measured crystals are electrically conductive, with carrier concentrations varying 10 16 –10 17 cm -3 depending upon the location of the sample in the growth. Lastly, a unique luminescence with unknown origin centered around 2.0 eV is revealed by photoluminescence spectroscopy.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Using 3D position sensitivity to reveal response non-uniformities in CdZnTe, TlBr, and CsPbBr 3 detectors

Position sensitivity enables the correction of response non-uniformities in room-temperature semiconductor detectors caused by crystal defects and other factors. It can also be used to pinpoint the exact location of crystal defects responsible for the response variations. This work describes a technique for revealing and visualizing the detector regions affecting the charge collection efficiency in CdZnTe (CZT), TlBr, and CsPbBr 3 detectors configured as position-sensitive virtual Frisch-grid (VFG) devices. The technique correlates the photopeak events in energy spectra with their spatial distributions inside the detectors using the position information. By selecting the events from narrow energy intervals within a photopeak, we can visualize the detector volumes with particular charge collection efficiencies, which, in turn, correlate with the locations of electrode and crystal defects. Here, we demonstrate this technique in several examples. Columnar structures in the volume plots (position distribution maps) are consistent with signal losses near or at the anode in selected samples of CZT and TlBr. Structures exhibiting a distinct depth dependence are consistent with grain boundaries or other crystal defects.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2022

Faster network disruption from layered oscillatory dynamics

Nonlinear complex network-coupled systems typically have multiple stable equilibrium states. Following perturbations or due to ambient noise, the system is pushed away from its initial equilibrium, and, depending on the direction and the amplitude of the excursion, it might undergo a transition to another equilibrium. It was recently demonstrated [M. Tyloo, J. Phys. Complex. 3 03LT01 (2022)] that layered complex networks may exhibit amplified fluctuations. Here, I investigate how noise with system-specific correlations impacts the first escape time of nonlinearly coupled oscillators. Interestingly, I show that, not only the strong amplification of the fluctuations is a threat to the good functioning of the network but also the spatial and temporal correlations of the noise along the lowest-lying eigenmodes of the Laplacian matrix. Finally, I analyze first escape times on synthetic networks and compare noise originating from layered dynamics to uncorrelated noise.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Entanglement properties of disordered quantum spin chains with long-range antiferromagnetic interactions

Entanglement measures are useful tools in characterizing otherwise unknown quantum phases and indicating transitions between them. Here we examine the concurrence and entanglement entropy in quantum spin chains with random long-range couplings, spatially decaying with a power-law exponent $\textit{α}$. Using the strong disorder renormalization group (SDRG) technique, we find by analytical solution of the master equation a strong disorder fixed point, characterized by a fixed point distribution of the couplings with a finite dynamical exponent, which describes the system consistently in the regime $α > \frac{1}{2}$ . A numerical implementation of the SDRG method yields a power-law spatial decay of the average concurrence, which is also confirmed by exact numerical diagonalization. However, we find that the lowest-order SDRG approach is not sufficient to obtain the typical value of the concurrence. We therefore implement a correction scheme which allows us to obtain the leading-order corrections to the random singlet state. This approach yields a power-law spatial decay of the typical value of the concurrence, which we derive both by a numerical implementation of the corrections and by analytics. Next, using numerical SDRG, the entanglement entropy (EE) is found to be logarithmically enhanced for all $\textit{α}$, corresponding to a critical behavior with an effective central charge $\textit{c}$ = ln(2), independent of $\textit{α}$. This is confirmed by an analytical derivation. Using numerical exact diagonalization (ED), we confirm the logarithmic enhancement of the EE and a weak dependence on $\textit{α}$. For a wide range of partition size $\textit{l}$, the EE fits a critical behavior with a central charge close to $\textit{c}$ = 1, which is the same as for the clean Haldane-Shastry model with a power-law-decaying interaction with $\textit{α}$ = 2. Only for small $l \ll L$, in a range which increases with the number of spins N, we find deviations which are rather consistent with the strong disorder fixed point central charge $\textit{c}$ = ln(2). Furthermore, we find using ED that the concurrence shows power-law decay, albeit with smaller power exponents than obtained by SDRG. Finally, we also present results obtained with DMRG and find agreement with ED for sufficiently small $\textit{α}$ < 2, whereas for larger $\textit{α}$ DMRG tends to underestimate the entanglement entropy and finds a faster decaying concurrence.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Nanoscale dynamics during self-organized ion beam patterning of Si. II. Kr + bombardment

Understanding the self-organized ion beam nanopatterning of elemental semiconductors, particularly silicon, is of intrinsic scientific and technological interest. This is the second component of a two-part coherent x-ray scattering and x-ray photon correlation spectroscopy (XPCS) investigation of the kinetics and fluctuation dynamics of nanoscale ripple development on silicon during 1 keV Ar + (part I) and Kr + bombardment at 65° polar angle. Here it is found that the ion-enhanced viscous flow relaxation is essentially equal for Kr + -induced patterning as previously found for Ar + patterning despite the difference in ion masses. However, the magnitude of the surface curvature-dependent roughening rate in the early-stage kinetics is larger for Kr + than for Ar + , consistent with expectations that the heavier ion gives an increased mass redistributive contribution to the initial surface instability. As with the Ar + case, fluctuation dynamics in the late stage show a peak in correlation times at the length scale corresponding to the dominant structural feature on the surface—the ripples. Finally, it is shown that speckle motion during the surface evolution can be analyzed to determine spatial inhomogeneities in erosion rate and ripple velocity. This allows the direction and speed of ripple motion to be measured in a real time experiment. In the present case, ripple motion is found to be into the projected direction of the ion source, in contrast to expectations from an existing sputter erosion driven model with parameters derived from binary collision approximation simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Grain boundary segregation and chemical ordering in CoCrFeMnNi multi-principal element alloy

Owing to their far-from-dilute compositions, multi-principal element alloys (MPEAs) can exhibit unique combinations of engineering properties. As nearly all MPEAs are polycrystalline aggregates, it is necessary to understand the interactions of various elemental species with grain boundaries (GBs). This is of particular importance in extreme environments, such as radiation and elevated temperatures, where such interactions have implications on the properties of MPEAs. Herein, we employ atomistic simulations to generate a series of [001] asymmetric tilt GBs in a model CoCrFeMnNi MPEA and quantify solute interactions and segregation to these boundaries. We employ the Warren-Cowley order parameters to investigate the interplay between GB segregation and chemical short-range order (SRO). At temperatures above 800 K, simulation results reveal the segregation of Cr and Mn to CoCrFeMnNi GBs and show weak dependence of boundary solute excess on GB geometry, at least for the boundaries explored in this work. At temperatures in the range of 673–800 K, formation of domains rich in Cr is observed at GBs in agreement with experimental observations. Quantitative analysis shows that solute excess of various alloying elements decreases rapidly with the increase in temperature in the range of 1000–1200 K. Furthermore, we show that GB regions exhibit SRO characteristics that are distinct from the bulk crystals, leading to spatial variations in SRO. In broad terms, our study highlights the need to account for GB interactions with alloying elements when designing advanced MPEAs with novel chemistries.

Wang, Yitao [Lehigh University, Bethlehem, PA (Uni↗

DOE OSTI2020

Neutron scattering in photosynthesis research: recent advances and perspectives for testing crop plants

The photosynthetic performance of crop plants under a variety of environmental factors and stress conditions, at the fundamental level, depends largely on the organization and structural flexibility of thylakoid membranes. These highly organized membranes accommodate virtually all protein complexes and additional compounds carrying out the light reactions of photosynthesis. Most regulatory mechanisms fine-tuning the photosynthetic functions affect the organization of thylakoid membranes at different levels of the structural complexity. In order to monitor these reorganizations, non-invasive techniques are of special value. On the mesoscopic scale, small-angle neutron scattering (SANS) has been shown to deliver statistically and spatially averaged information on the periodic organization of the thylakoid membranes in vivo and/or, in isolated thylakoids, under physiologically relevant conditions, without fixation or staining. More importantly, SANS investigations have revealed rapid reversible reorganizations on the timescale of several seconds and minutes. In this paper, we give a short introduction into the basics of SANS technique, advantages and limitations, and briefly overview recent advances and potential applications of this technique in the physiology and biotechnology of crop plants. We also discuss future perspectives of neutron crystallography and different neutron scattering techniques, which are anticipated to become more accessible and of more use in photosynthesis research at new facilities with higher fluxes and innovative instrumentation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Kink-antikink collisions and multi-bounce resonance windows in higher-order field theories

In this work, we study collisions of coherent structures in higher-order field-theoretic models, such as the Φ 8 , Φ 10 and Φ 12 ones. The main distinguishing feature, of the example models considered herein, is that the collision arises due to the long-range interacting algebraic tails of these solitary waves. We extend the approach to suitably initialize the relevant kinks, in the additional presence of finite initial velocity, in order to minimize the dispersive wave radiation potentially created by their slow spatial decay. We find that, when suitably initialized, these models still feature the multi-bounce resonance windows earlier found in models in which the kinks bear exponential tails, such as the Φ 4 and Φ 6 field theories among others. Also present is the self-similar structure of the associated windows with three- and more-bounce windows at the edges of two- and lower-bounce ones. Moreover, phenomenological but highly accurate (and predictive), scaling relations are derived for the dependence of the time between consecutive collisions and, e.g., the difference in kinetic energy between the incoming one and the critical one for one-bounces. Such scalings are traced extensively over two-bounce collision windows throughout the three models, hinting at the possibility of an analytical theory in this direction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗