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At least 235 records · Page 13

A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides

In multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here, we combine ideas from cell signalling and electronic circuitry to propose a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide could be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction–diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental waveguide implementation, we propose a sink reaction and spatially inhomogeneous DNA concentrations that could mitigate the spurious amplification of an autocatalyst within the waveguide, allowing for controlled waveguide triggering. Chemical waveguides could facilitate the design of synthetic biomaterials with distributed sensing machinery integrated throughout their structure and enable coordinated self-regulating programmes triggered by changing environmental conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A NUMERICAL STUDY OF DIFFUSIVE COSMIC-RAY TRANSPORT WITH ADIABATIC FOCUSING

Focused particle transport in a nonuniform large-scale magnetic field is investigated numerically in the case of isotropic pitch-angle scattering. Evolving particle density profiles and distribution moments are computed from solutions of a system of stochastic differential equations, equivalent to the original Fokker-Planck equation for the particle distribution. Conflicting analytical predictions for the transport coefficients in the diffusion limit, independently calculated by Beeck and Wibberenz and Shalchi, are compared with the numerical results. The reasons for the discrepancies among the analytical and numerical treatments, as well as the general limitations of the diffusion model, are discussed. The telegraph equation, derived in a higher-order expansion of the particle distribution function, is shown to describe the particle transport much more accurately than the diffusion model, especially ahead of a moving density pulse.

79 ASTRONOMY AND ASTROPHYSICS↗

Mass Transport Limitations and Kinetic Consequences of Corn Stover Deacetylation

Alkaline pretreatment of herbaceous feedstocks such as corn stover prior to mechanical refining and enzymatic saccharification improves downstream sugar yields by removing acetyl moieties from hemicellulose. However, the relationship between transport phenomena and deacetylation kinetics is virtually unknown for such feedstocks and this pretreatment process. Here, we report the development of an experimentally validated reaction–diffusion model for the deacetylation of corn stover. A tissue-specific transport model is used to estimate transport-independent kinetic rate constants for the reactive extraction of acetate, hemicellulose and lignin from corn stover under representative alkaline conditions (5–7 g L -1 NaOH, 10 wt% solids loadings) and at low to mild temperatures (4–70°C) selected to attenuate individual component extraction rates under differential kinetic regimes. The underlying transport model is based on microstructural characteristics of corn stover derived from statistically meaningful geometric particle and pore measurements. These physical descriptors are incorporated into distinct particle models of the three major anatomical fractions (cobs, husks and stalks) alongside an unsorted, aggregate corn stover particle, capturing average Feret lengths of 917–1239 μm and length-to-width aspect ratios of 1.8–2.9 for this highly heterogeneous feedstock. Individual reaction–diffusion models and their resulting particle model ensembles are used to validate and predict anatomically-specific and bulk feedstock performance under kinetic-controlled vs. diffusion-controlled regimes. In general, deacetylation kinetics and mass transfer processes are predicted to compete on similar time and length scales, emphasizing the significance of intraparticle transport phenomena. Critically, we predict that typical corn stover particles as small as ~2.3 mm in length are entirely diffusion-limited for acetate extraction, with experimental effectiveness factors calculated to be 0.50 for such processes. Debilitatingly low effectiveness factors of 0.021–0.054 are uncovered for cobs—implying that intraparticle mass transfer resistances may impair observable kinetic measurements of this anatomical fraction by up to 98%. These first-reported quantitative maps of reaction vs. diffusion control link fundamental insights into corn stover anatomy, biopolymer composition, practical size reduction thresholds and their kinetic consequences. These results offer a guidepost for industrial deacetylation reactor design, scale-up and feedstock selection, further establishing deacetylation as a viable biorefinery pretreatment for the conversion of lignocellulosics into value-added fuels and chemicals.

09 BIOMASS FUELS↗

Modeling precursor diffusion and reaction of atomic layer deposition in porous structures

Atomic layer deposition (ALD) is a technique for depositing thin films of materials with a precise thickness control and uniformity using the self-limitation of the underlying reactions. Usually, it is difficult to predict the result of the ALD process for given external parameters, e.g., the precursor exposure time or the size of the precursor molecules. Therefore, a deeper insight into ALD by modeling the process is needed to improve process control and to achieve more economical coatings. In this paper, a detailed, microscopic approach based on the model developed by Yanguas-Gil and Elam is presented and additionally compared with the experiment. Precursor diffusion and second-order reaction kinetics are combined to identify the influence of the porous substrate's microstructural parameters and the influence of precursor properties on the coating. The thickness of the deposited film is calculated for different depths inside the porous structure in relation to the precursor exposure time, the precursor vapor pressure, and other parameters. Good agreement with experimental results was obtained for ALD zirconiumdioxide (ZrO{sub 2}) films using the precursors tetrakis(ethylmethylamido)zirconium and O{sub 2}. The derivation can be adjusted to describe other features of ALD processes, e.g., precursor and reactive site losses, different growth modes, pore size reduction, and surface diffusion.

36 MATERIALS SCIENCE↗

Swelling and Diffusion during Methanol Sorption into Hydrated Nafion

Diffusion within polymer electrolyte membranes is often coincident with time-dependent processes such as swelling and polymer relaxation, which are factors that limit their ability to block molecular crossover during use. The solution-diffusion model of membrane permeation, which is the accepted theory for dense polymers, applies only to steady-state processes and does not address dynamic internal structural changes that can accompany permeation. To begin discovery of how such changes can be coupled to the permeation process, we have constructed here a stochastic multiscale reaction-diffusion model that examines time-dependent methanol uptake into and swelling of hydrated Nafion. Several potential mechanisms of diffusion and polymer response are tested. The simulation predictions are compared to real-time Fourier transform infrared attenuated total reflectance spectroscopy (FTIR-ATR) absorbance reported in the literature [ Hallinan , D. T. , Jr. ; Elabd , Y. A. J. Phys. Chem. B 2007 , 111 , 13221 - 13230 ]. Of the proposed polymer response mechanisms, only one, a reaction-limited, local response to increasing methanol concentration that takes the entire experimental time frame of 600 s, produces simulated FTIR-ATR data consistent with experiment. The simulations show that water diffusion out of the membrane is minimal during methanol sorption and that changes in the measured infrared absorbances are due primarily to the increase in methanol concentration accompanied by dilution of water during swelling. Swelling involves densification of the polymer structure even as there is an overall volume expansion of the film. Potential connections between the polymer densification and molecular-level structural changes of Nafion in methanol are discussed. These results indicate that the interaction between methanol and Nafion serves to increase Nafion's capacity to accommodate large volumes of methanol-water solutions, facilitating increased permeation across the membrane relative to pure water.

36 MATERIALS SCIENCE↗

Determination of krypton diffusion coefficients in uranium dioxide using atomic scale calculations

We present a study of the diffusion of krypton in UO 2 using atomic scale calculations combined with diffusion models adapted to the system studied. The migration barriers of the elementary mechanisms for interstitial or vacancy assisted migration are calculated in the DFT + U framework using the nudged elastic band method. The attempt frequencies are obtained from the phonon modes of the defect at the initial and saddle points using empirical potential methods. The diffusion coefficients of Kr in UO 2 are then calculated by combining this data with diffusion models accounting for the concentration of vacancies and the interaction of vacancies with Kr atoms. We determined the preferred mechanism for Kr migration and the corresponding diffusion coefficient as a function of the oxygen chemical potential μ O or nonstoichiometry. For very hypostoichiometric (or U-rich) conditions, the most favorable mechanism is interstitial migration. For hypostoichiometric UO 2 , migration is assisted by the bound Schottky defect and the charged uranium vacancy, V U 4– . Around stoichiometry, migration assisted by the charged uranium–oxygen divacancy (V UO 2– ) and V U 4– is the favored mechanism. Finally, for hyperstoichiometric or O-rich conditions, the migration assisted by two V U 4– dominates. Kr migration is enhanced at higher μ O , and in this regime, the activation energy will be between 4.09 and 0.73 eV depending on nonstoichiometry. The experimental values available are in the latter interval. Since it is very probable that these values were obtained for at least slightly hyperstoichiometric samples, our activation energies are consistent with the experimental data, even if further experiments with precisely controlled stoichiometry are needed to confirm these results. Finally, the mechanisms and trends with nonstoichiometry established for Kr are similar to those found in previous studies of Xe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Self-consistent drift-diffusion-reaction model for the electron beam interaction with dielectric samples

The charging of insulating samples degrades the quality and complicates the interpretation of images in scanning electron microscopy and is important in other applications, such as particle detectors. In this paper, we analyze this nontrivial phenomenon on different time scales employing the drift-diffusion-reaction approach augmented with the trapping rate equations and a realistic semi-empirical source function describing the pulsed nature of the electron beam. We consider both the fast processes following the impact of a single primary electron, the slower dynamics resulting from the continuous bombardment of a sample, and the eventual approach to the steady-state regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analytical model of diffuse reflectance spectrum of skin tissue

We have derived simple analytical expressions that enable highly accurate calculation of diffusely reflected light signals of skin in the spectral range from 450 to 800 nm at a distance from the region of delivery of exciting radiation. The expressions, taking into account the dependence of the detected signals on the refractive index, transport scattering coefficient, absorption coefficient and anisotropy factor of the medium, have been obtained in the approximation of a two-layer medium model (epidermis and dermis) for the same parameters of light scattering but different absorption coefficients of layers. Numerical experiments on the retrieval of the skin biophysical parameters from the diffuse reflectance spectra simulated by the Monte Carlo method show that commercially available fibre-optic spectrophotometers with a fixed distance between the radiation source and detector can reliably determine the concentration of bilirubin, oxy- and deoxyhaemoglobin in the dermis tissues and the tissue structure parameter characterising the size of its effective scatterers. We present the examples of quantitative analysis of the experimental data, confirming the correctness of estimates of biophysical parameters of skin using the obtained analytical expressions. (biophotonics)

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tunable Atomic Layer Deposition into Ultra-High-Aspect-Ratio (>60000:1) Aerogel Monoliths Enabled by Transport Modeling

Atomic layer deposition (ALD) modification of ultra-high-aspect-ratio structures (>10,000:1) is a powerful platform with applications in catalysis, filtration, and energy conversion. However, the deposition of conformal and tunable ALD coatings at these aspect ratios remains challenging, resulting in empirical tradeoffs between precursor utilization and reaction time. Here, we demonstrate tunable control of the ALD infiltration depth into an aerogel monolith (AM) and develop a reaction-diffusion model to accurately describe the coating process. Specifically, we investigate the ALD exposure time and precursor dose needed to conformally coat a silica AM with pore sizes of ~20 nm, a monolith thickness of ~2.5 mm, and aspect ratios exceeding 60,000:1. We demonstrate complete infiltration into the AM, which is quantified by elemental mapping. A reaction-diffusion model is developed, which accounts for multiple doses and precursor depletion in the ALD chamber during an exposure step. The experimentally validated model enables the prediction and tuning of infiltration depth into a tortuous, high-aspect-ratio structure such as an AM, allowing for the synthesis of rationally designed material architectures. Additionally, the model allows for co-optimization of the total deposition time and percentage of unreacted precursor, which are important for the manufacturability and sustainability of ALD processing. Lastly, we demonstrate that ultra-thin ALD Al 2 O 3 coatings can be used to stabilize silica AMs against structural degradation under high-temperature annealing conditions (700-800 °C), by limiting changes in surface area and monolith volume. As a result, this improved high-temperature stability has implications for numerous aerogel applications, including catalysis and thermal insulation.

14 SOLAR ENERGY↗

Timescales of mafic magmatic fractionation documented by paleosecular variation in basaltic drill core, Snake River Plain volcanic province, Idaho, USA

Abstract The timescales over which fractional crystallization and recharge work in mafic volcano-plutonic provinces is subject to great uncertainty. Currently modeled processes are subject to the scale of measurement: monogenetic basaltic fields accumulate over hundreds of thousands of years, consistent with U-Th-Ra isotopic variations that imply 50% crystallization of basic magmas on timescales of 100,000 years or more, whereas crystal diffusion modeling implies phenocryst residence times of ~1–1000 years. Monogenetic basalts of the Snake River Plain in southern Idaho, USA, are up to 2 km thick and postdate passage over the Yellowstone–Snake River Plain hotspot. Detailed lithologic and geophysical logging of core from deep drill holes, along with chemical stratigraphy and high-resolution paleomagnetic inclination measurements, document individual eruptive units, compound lava flows, and basaltic flow groups that accumulated over 1–6 m.y. Hiatuses are commonly marked by loess or fluvial interbeds that vary from ~0.1 m thick to 20 m thick. Radiometric (40Ar-39Ar, detrital zircon U-Pb) and paleomagnetic timescale ages show that the deepest hole (Kimama drill hole, 1912 m total depth) accumulated over ~6 m.y. Cycles of fractional crystallization and recharge are recognized in the chemical stratigraphy as up-section shifts in major and trace elements; these fractionation cycles commonly represent 40%–50% fractionation. Individual fractionation cycles may comprise 20–40 eruptive units (8–17 lava flows) with little to no change in paleomagnetic inclination (0°–1°), whereas adjacent cycles may differ by several degrees from one another or reflect changes in polarity. Rates of paleosecular variation in Holocene lavas and sediments dated using 14C document significant shifts in magnetic inclination over short timescales, ranging from ~0.05° to 2°/decade, with an average of ~0.5°/decade and a minimum rate of 0.05°/decade. This implies that fractionation cycles with ≤1° variation in magnetic inclination formed on timescales of a few decades up to a few centuries (20–200 years). Thus, the lavas collectively represent only a few thousand years of eruptive activity, with major flow groups separated in time by tens to hundreds of thousands of years. We suggest that the rates defined by paleosecular variation capture the timescales of magmatic chamber evolution (fractionation/recharge) in the seismically imaged mid-crustal sill complex; in contrast, we suggest that crystal diffusion modeling captures the residence times in shallow subvolcanic magmatic chambers that underlie individual monogenetic volcanoes.

Geology↗

A computational study of turbulent kinetic energy transport in barotropic turbulence on the f-plane

Energy transport by eddies is diagnosed from a series of simulations of stochastically forced, inhomogeneous two-dimensional turbulence—barotropic dynamics on the f-plane. The divergence of the energy flux is compared to diffusive models, both fractional and harmonic, and the inferred diffusivity κ is compared to a mixing-length model κ ∝ Vℓ where V and ℓ are eddy velocity and length scales, respectively. The flux-divergence is found to be well approximated by Laplacian diffusion with a mixing-length approximation. This study provides some support for diffusive modeling of mesoscale eddy energy transport in ocean model parameterizations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Simulations of the churning mode: Toroidally symmetric plasma convection and turbulence around the X-points in a snowflake divertor

Using a reduced MHD model, extended to include field-aligned thermal conduction, we present numerical simulations of the churning mode (CM): a toroidally symmetric, non-linear plasma vortex in the vicinity of the null points in a snowflake (SF) divertor [D. D. Ryutov et al., Phys. Scr. 89, 088002 (2014)]. Simulations are carried out across a range of inter-null separations, d xx ⁠, and inter-null orientations, θ⁠, primarily in conditions relevant to the MAST-U tokamak. We find that, when d xx is small, the CM induces additional transport across the X-points when β pm ≳8%, where β pm is the ratio of the plasma pressure in the null region to poloidal magnetic pressure at the midplane. This transport also increases approximately linearly as d xx is reduced. A diffusive model of this transport is shown to predict the total transport across the null points, where diffusion coefficients of up to ∼ 10 2 m 2 s −1 centered on a small region around the X-points are used. However, the CM also results in significant changes to the flux surfaces in the null region, which is not captured by this diffusive model. The changes in magnetic geometry mean the fractional exhaust power delivered to each divertor leg is highly sensitive to β pm ⁠, d xx ⁠, and θ⁠. For small values of θ⁠, the CM can induce a change in topology, redirecting exhaust power from a secondary divertor leg on the high field side to one on the low field side. Similar behavior is found in the fraction of exhaust power going to the inner and outer divertor. Such changes in the flux surfaces may not be captured by Grad–Shafranov solvers and so may be a source of error in the magnetic reconstruction of SF experiments. We consistently find that the fractional exhaust power going to a secondary divertor leg on the high field side is small, consistent with SF experiments.

Computer simulation↗

Resolving turbulent magnetohydrodynamics: a hybrid operator-diffusion framework

We present a hybrid machine learning framework that combines physics-informed neural operators (PINOs) with score-based generative diffusion models to simulate the full spatio-temporal evolution of two-dimensional, incompressible, resistive magnetohydrodynamic turbulence across a broad range of Reynolds numbers (Re). The framework leverages the equation-constrained generalization capabilities of PINOs to predict coherent, low-frequency dynamics, while a conditional diffusion model stochastically corrects high-frequency residuals, enabling accurate modeling of fully developed turbulence. Trained on a comprehensive ensemble of high-fidelity simulations with Re ϵ {100, 250, 500, 750, 1000, 3000, 10000}, the approach achieves state-of-the-art accuracy in regimes previously inaccessible to deterministic surrogates. At Re = 1000 and 3000, the model faithfully reconstructs the full spectral energy distributions of both velocity and magnetic fields late into the simulation, capturing non-Gaussian statistics, intermittent structures, and cross-field correlations with high fidelity. At extreme turbulence levels (Re = 10 000), it remains the first surrogate capable of recovering the high-wavenumber evolution of the magnetic field, preserving large-scale morphology and enabling statistically meaningful predictions.

Diffusion-Integrated Neural Operators↗

Phase space effects on fast ion distribution function modeling in tokamaks

Integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities, ad-hoc models can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. The kick model implemented in the tokamak transport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Observation of kinetic mix enhancement in thin-shell OMEGA implosions

Recent separated reactant experiments for thin-shell (6 µ⁢m) shock-driven implosions on OMEGA have demonstrated significant mix from a buried deuterated layer of the shell into the hot spot. Time resolved D 3 He-p reaction history data demonstrate a (50 ± 20)⁢ ps shift earlier in peak nuclear emission for separated reactant experiments relative to control, in contrast to past experimental data for thicker, 20 µ⁢m shells with no laser burn through that show a 75 ps delay due to the time required for hydrodynamic instabilities to develop. This contrast suggests that the mix mechanism was not hydrodynamic. Ion kinetic simulations utilizing fall line analyses show much closer agreement with mix yield and temperature than diffusion models, predicting a D 3 He-p mix yield of 1.7 × 10 9 as compared to the experimental value of 9.3⁢ (±2.1) × 10 8 . This is three orders of magnitude closer than the fall line analysis from a hydrodynamic simulation with an inline diffusive mix model, which suggests minimal mix and D 3 He-p yields of 5×10 5 . This makes kinetic mechanisms the only feasible explanation for the mix seen, demonstrating impact of a non-standard mix mechanism. An analytical model of this kinetic mix mechanism suggests that it can remain significant in situations when the shell expands significantly to low densities, and diffusive models predict negligible mix. Finally, kinetic mix will impact multiple types of high energy density, laser-driven fusion experiments including high-adiabat direct drive cryoexperiments, nuclear cross section experiments, and thin-shell polar direct drive experiments used to tune heat conduction models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An Ensemble Score Filter for Tracking High-Dimensional Nonlinear Dynamical Systems

We propose an ensemble score filter (EnSF) for solving high-dimensional nonlinear filtering problems with superior accuracy. A major drawback of existing filtering methods, e.g., particle filters or ensemble Kalman filters, is the low accuracy in handling high-dimensional and highly nonlinear problems. EnSF attacks this challenge by exploiting the score-based diffusion model, defined in a pseudo-temporal domain, to characterizing the evolution of the filtering density. EnSF stores the information of the recursively updated filtering density function in the score function, in stead of storing the information in a set of finite Monte Carlo samples (used in particle filters and ensemble Kalman filters). Unlike existing diffusion models that train neural networks to approximate the score function, we develop a training-free score estimation that uses mini-batch-based Monte Carlo estimator to directly approximate the score function at any pseudo-spatial-temporal location, which provides sufficient accuracy in solving high-dimensional nonlinear problems as well as saves tremendous amount of time spent on training neural networks. Another essential aspect of EnSF is its analytical update step, gradually incorporating data information into the score function, which is crucial in mitigating the degeneracy issue faced when dealing with very high-dimensional nonlinear filtering problems. High-dimensional Lorenz systems are used to demonstrate the performance of our method. EnSF provides surprisingly impressive performance in reliably tracking extremely high-dimensional Lorenz systems (up to 1,000,000 dimension) with highly nonlinear observation processes, which is a well-known challenging problem for existing filtering methods.

97 MATHEMATICS AND COMPUTING↗

Water transport in reverse osmosis membranes is governed by pore flow, not a solution-diffusion mechanism

We performed nonequilibrium molecular dynamics (NEMD) simulations and solvent permeation experiments to unravel the mechanism of water transport in reverse osmosis (RO) membranes. The NEMD simulations reveal that water transport is driven by a pressure gradient within the membranes, not by a water concentration gradient, in marked contrast to the classic solution-diffusion model. We further show that water molecules travel as clusters through a network of pores that are transiently connected. Permeation experiments with water and organic solvents using polyamide and cellulose triacetate RO membranes showed that solvent permeance depends on the membrane pore size, kinetic diameter of solvent molecules, and solvent viscosity. This observation is not consistent with the solution-diffusion model, where permeance depends on the solvent solubility. Motivated by these observations, we demonstrate that the solution-friction model, in which transport is driven by a pressure gradient, can describe water and solvent transport in RO membranes.

42 ENGINEERING↗

Spatial profiles of photon chemical potential in near-field thermophotovoltaic cells

Emitted photons stemming from the radiative recombination of electron–hole pairs carry chemical potential in radiative energy converters. This luminescent effect can substantially alter the local net photogeneration in near-field thermophotovoltaic cells. Several assumptions involving the luminescent effect are commonly made in modeling photovoltaic devices; in particular, the photon chemical potential is assumed to be zero or a constant prescribed by the bias voltage. The significance of photon chemical potential depends upon the emitter temperature, the semiconductor properties, and the injection level. Hence, these assumptions are questionable in near-field thermophotovoltaic devices with nanoscale separation distances between the emitter and the cell. In the present work, an iterative solver that combines fluctuational electrodynamics with the drift-diffusion model is developed to tackle the coupled photon and charge transport problem, enabling the determination of the spatial profile of photon chemical potential beyond the detailed balance approach. Here, the difference between the results obtained by allowing the photon chemical potential to vary spatially and by assuming a constant value demonstrates the limitations of the conventional approaches. This study is critically important for performance evaluation of near-field thermophotovoltaic systems with nanoscale vacuum gaps.

30 DIRECT ENERGY CONVERSION↗