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At least 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Cryogenic electron tomography reveals novel structures in the apical complex of Plasmodium falciparum

Intracellular infectious agents, like the malaria parasite, Plasmodium falciparum, face the daunting challenge of how to invade a host cell. This problem may be even harder when the host cell in question is the enucleated red blood cell, which lacks the host machinery co-opted by many pathogens for internalization. Evolution has provided P. falciparum and related single-celled parasites within the phylum Apicomplexa with a collection of organelles at their apical end that mediate invasion. This apical complex includes at least two sets of secretory organelles, micronemes and rhoptries, and several structural features like apical rings and a putative pore through which proteins may be introduced into the host cell during invasion. We perform cryogenic electron tomography (cryo-ET) equipped with Volta Phase Plate on isolated and vitrified merozoites to visualize the apical machinery. Through tomographic reconstruction of cellular compartments, we see new details of known structures like the rhoptry tip interacting directly with a rosette resembling the recently described rhoptry secretory apparatus (RSA), or with an apical vesicle docked beneath the RSA. Subtomogram averaging reveals that the apical rings have a fixed number of repeating units, each of which is similar in overall size and shape to the units in the apical rings of tachyzoites of Toxoplasma gondii. Comparison of these polar rings in Plasmodium and Toxoplasma parasites also reveals them to have a structurally conserved assembly pattern. These results provide new insight into the essential and structurally conserved features of this remarkable machinery used by apicomplexan parasites to invade their respective host cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Enhancing trap and fault seal analyses by integrating observations from HR3D seismic data with well logs and conventional 3D seismic data, Texas inner shelf

An understanding of trap and fault seal quality is critical for assessing hydrocarbon prospectivity. To achieve this, modern analytical techniques leverage well data and conventional industry-standard 3D seismic data to evaluate the trap, and any faults displacing the reservoir and top seal intervals. Above all, geological interpretation provides the framework of trap and fault seal analyses, but can be hindered by the data resolution, quality and acquisition style of the conventional seismic data. Furthermore, limiting the analysis to only the petroleum system at depth may lead to erroneous perceptions because interpreting overburden features, such as shallow faults or gas chimneys, can provide valuable observations with respect to container performance, and can to help validate trap and fault seal predictions. Here, a supplement to conventional 3D data are high-resolution 3D seismic (HR3D) data, which provide detailed images of the overburden geology. This study utilizes an HR3D seismic volume in the San Luis Pass area of the Texas inner shelf, where shallow fault tips and a sizeable gas chimney are interpreted over an unsuccessful hydrocarbon prospect. Static post-drill fault seal and trap analyses suggest that the primary fault displacing the structural closure could have withheld columns of gas c. 100 m high, but disagree with our HR3D seismic interpretations and dry-well analyses. From our results, we hypothesize that tertiary gas migration through fault conduits reduced the hydrocarbon column in the prospective Early Miocene reservoir, and may have resulted from continued movement along the intersecting faults. Overall, this study reinforces the importance of understanding the overburden geology and geohistory of faulted prospects, and demonstrates the utility of pre-drill HR3D acquisition when conducting trap and fault seal analyses.

3D seismic↗
DOE OSTI2020

Understanding Li-Ion Cell Internal Short Circuit and Thermal Runaway through Small, Slow and In Situ Sensing Nail Penetration

Here we report a small, slow and in situ sensing (3S) nail penetration test method to understand Li-ion cell internal short circuit (ISC) and thermal runaway. The method not only keeps conventional nail penetration's advantage of simple implementation, but also enhances its relevance to field failures and enables detailed in situ diagnosis. It was applied to 3-Ah pouch cells and revealed insights that could not be captured by conventional methods. Most interestingly, multiple in situ temperature peaks were observed during a period of over 100 s before thermal runaway. These initial peaks exceeded safety limit but the temperature rapidly decreased after each peak instead of causing immediate thermal runaway. Further investigation suggested that the initial temperature peaks occurred when nail tip reached aluminum foil current collector to form a low resistance ISC between anode and aluminum foil. The rapid temperature decrease after each peak can be attributed to sudden drop of ISC current, which can be further attributed to rupture of aluminum foil and increase of contact resistance. The findings show that 3S nail penetration test can separate processes of ISC from thermal runaway and provide details of ISC at the level of individual electrode and current collector.

25 ENERGY STORAGE↗
DOE OSTI2024

Unraveling Morphology and Chemistry Dynamics in Fluoroethylene Carbonate Generated Silicon Anode Solid Electrolyte Interphase Across Delithiated and Lithiated States: Relative Cycling Stability Enabled by an Elastomeric Polymer Matrix

The silicon solid electrolyte interphase (SEI) faces cyclical cracking and reconstruction due to the ∼350% volume expansion. Understanding the SEI dynamic morphology and chemistry evolution from delithiated to lithiated states is thereby paramount to engineering a stable Si anode. Fluoroethylene carbonate (FEC) is a preferred additive with widely demonstrated enhancement of the Si cycling. Thus, insights into the dynamics of the FEC-SEI may provide hints toward engineering the Si interface. Herein, complementary ATR-FTIR, AFM, tip IR, and XPS probing reveal the presence of an elastomeric polycarbonate-like matrix in the FEC-generated SEI which is absent from the FEC-free SEI. Adding FEC to the baseline 1 M LiPF 6 in EC:EMC (1:1) electrolyte promotes formation of a thinner and more conformal SEI, and subdues morphology and chemistry changes between consecutive half-cycles. From AFM, morphological stabilization of the FEC-SEI occurs earlier. Furthermore, conventional SEI biproducts such as Li 2 CO 3 and LiEDC appear in reduced quantities in the FEC-SEI implying a reduced quantity of Li-consuming species. The thin polymeric FEC-SEI enables deeper (de)lithiation of silicon. In conclusion, the enhanced mechanical compliance, chemical invariance, and reduced Li inventory consumption of the FEC-SEI are logically the key features underlying the Si cycling enhancement by FEC.

25 ENERGY STORAGE↗
DOE OSTI2024

Correlation Between Microscopic Current Fluctuations Observed at Ultra-Microelectrodes and Macroscopic Bulk Electrolysis Performance in Redox-Active Microemulsions

Microemulsions (μEs) have been proposed as redox flow battery (RFB) electrolytes that maximize ionic conductivity and charge capacity by synergizing two immiscible phases. However, charge transfer during electrolysis in μEs is poorly understood. Here, we show that ultramicroelectrode electrolysis of ferrocene-loaded μEs –20%, 60%, and 90% water - reveals stochastic current fluctuations. These are differentiated in the scanning electrochemical microscopy (SECM) geometry, where power spectral density analysis showed distinct changes in the frequency contributions. SECM in the substrate generation-tip collection mode showed that fluctuations arise under mass-transfer control. Significant differences in the diffusion coefficient of ferrocene species were deducted from SECM approach curves, suggesting phase transfer behavior. Using bulk electrolysis, we calculated the charge accessibility and cycling behavior in the μEs. A decrease in the stochastic behavior of the μEs seems to correlate to a higher accessibility and cycling performance, with the 90% water μE displaying the best reversibility and the 60% the lowest. Altogether, these results suggest that Marangoni-type convection driven by concentration gradients and/or μE restructuring during charge transfer play a role in the electrochemical performance of μEs. This presents opportunities for screening and diagnosing the performance of these emerging RFB electrolytes.

25 ENERGY STORAGE↗
DOE OSTI2021

Getting Hydrogen to the Gigaton Scale

Due to its ability to perform clean, efficient processes, hydrogen has long been promoted as the energy carrier of the future, but recent activity and advances suggest a tipping point has been reached as hydrogen is now being recognized by much of the world for its unique capabilities to strongly support global efforts in achieving climate neutrality. The coming decades will require a massive increase in the amount of hydrogen used in the energy system as well as a transition from largely thermochemical to predominantly electrochemical processes involving hydrogen. For this to happen, hydrogen will need to globally approach the gigaton-scale on an annual basis. Thus, before hydrogen can fully achieve its potential, challenges that need to be addressed include achieving scale and further research and development (R&D) advances.

climate neutrality↗
DOE OSTI2024

Conditional multi-step attribution for climate forcings

SAND2025-11608O Conditional multi-step attribution for climate forcings and its associated dataset present a framework for attributing a climate impacts, such as stratospheric warming or surface cooling, to a specific magnitude of climate forcing, such as stratospheric aerosol injection. The objective is to improve on existing methods that struggle to attribute highly noisy climate signals. This has potential broader use in climate security applications to identify and understand geoengineering and climate tipping point effects. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Swiler, Laura↗
DOE OSTI2024

General Applications for Hamilton Vantage (GenApps for Vantage) v0.6.1

General applications for Hamilton Vantage is a flexible liquid handling method used to automate the most widely applicable types of automated liquid transfers. General applications can also be used as a tool to onboard new fully-automated workflows by breaking them down step by step into single transfers. The goal of General Applications is to make using the Hamilton Vantage liquid handler as easy & practical as using a handheld pipette for the end user. The software supports plate-to-plate transfers for a variety of method types including: Stamp: One-to-One, Stamp: One-To-Many, Split, Combine, Hitpick, and Qtray plating. General Applications eliminates the need for automation engineers to customize individual methods for each new workflow that gets onboarded. Steps can be customized within GenApps according to the needs of the researcher. The software utilizes a GUI to prompt the users to input variables – Allowing for flexible control over plate types, transfer volumes, number of replicates, tip types, liquid classes, mixing steps, aspiration/dispense heights and more. General Applications also generates a deck image and setup instructions to guide the researcher on how to load the deck and start the instrument.

Yoder, Sam↗
DOE OSTI2021

Description of Paraxiopsis kensleyi n. sp., a new axiid lobster from the Gulf of Mexico (Crustacea: Decapoda: Axiidea)

A new species of axiid was discovered during sampling offshore deep banks on the middle continental shelf off Louisiana. Paraxiopsis kensleyi n. sp. appears to inhabit interstices and cavities of coralline algal rubble, rhodoliths, coral rubble, and other eroded calcareous substrates. Weakly separated from Eutrichocheles Wood-Mason, 1876 on the basis of morphology, present assignments of western Atlantic species to Paraxiopsis de Man, 1905 are regarded as provisional. The new species is described morphologically, and the coloration of freshly captured specimens is documented and compared to related species where possible. Coloration readily distinguishes mature specimens of the new species from Paraxiopsis spinipleura Kensley, 1996, with which it was initially confused. The diagnosis includes GenBank accession numbers for COI sequences to allow future molecular phylogenetic comparisons. Compared to regional species that share a similar dentation or spination on the submedian carina, the pleon of the new species is distinctive in the truncate ventral margin on pleura 2–4, as opposed to being broadly rounded or directed ventrally in an acutely triangular tip. The new species is the eighteenth species of Paraxiopsis worldwide and the ninth from western Atlantic waters, seven of which are now known to range into the Gulf of Mexico. An updated key to western Atlantic members of the genus is provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Simplified Ab Initio Molecular Dynamics-Based Raman Spectral Simulations

We describe a simplified approach to simulating Raman spectra from ab initio molecular dynamics (AIMD) calculations. The protocol relies on on-the-fly calculations of approximate molecular polarizabilities using the well-known sum over orbitals (as opposed to states) method. This approach bypasses the more accurate but computationally expensive approach to calculating molecular polarizabilities along AIMD trajectories, i.e., solving the coupled perturbed Hartree–Fock/Kohn–Sham equations. We demonstrate the advantages and limitations of our method through a few case studies targeting molecular systems of interest to surface- and/or tip-enhanced Raman spectroscopy practitioners.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Coupling of the Liquid Sampling–Atmospheric Pressure Glow Discharge to Orbitrap Mass Analyzers for Uranium Isotope Ratio Analysis: Evolution of the Methodology and Implications to the Field

Just over a decade ago, a truly outside-of-the-box approach to isotope ratio mass spectrometry (IRMS) was undertaken between research groups at Clemson University and the Pacific Northwest National Laboratory. The original motivation dealt with projections as to whether or not microplasmas could be developed into practical elemental ionization sources, perhaps for transportable analysis applications. In particular, the use of the liquid sampling–atmospheric pressure glow discharge (LS-APGD) was pursued. Its interfacing to an ultra-high resolution Orbitrap platform, proved not only facile, but opened up a wealth of potential applications. Here, we lay out a historical, tutorial description of the interfacing and the evolution of the methodology regarding IRMS of uranium. Practical challenges and opportunities are described, which hopefully provide guidance to further applications in high resolution IRMS. It is hoped that, while detailed and lengthy, the didactic nature of the presentation provides experimental insights and tips, and also serves as an homage to our very good friend, Professor Gary M. Hieftje, whose scientific inspiration and comradery have been immeasurably important in our own careers.

Koppenaal, David W.↗
DOE OSTI2020

A control-oriented combustion model framework for compression ignition engines operating on low-reactivity fuel

This work focuses on zero-dimensional modeling of the heat release rate in a compression ignition engine operating on gasoline-like fuels. Due to the properties of gasoline, such as high volatility and longer ignition delay than diesel, the injection strategies can vary significantly from the operation with conventional diesel fuel. Different injection strategies are commonly used to achieve varying degrees of in-cylinder stratification in order to shape the combustion event and maximize efficiency. The proposed zero-dimensional combustion model was developed to account for the different stages in combustion caused by the fuel stratification. As the ignition delay model is an integral part of the entire combustion process and significantly affects the prediction accuracy, special attention has been paid to local phenomena influencing ignition delay. A one-dimensional spray model by Musculus and Kattke was employed in conjunction with a Lagrangian tracking approach in order to estimate the local air–fuel ratio within the spray tip, as a proxy for reactivity. The local air–fuel ratio, in-cylinder temperature and pressure were used in an integral fashion to estimate the ignition delay. Heat release rates were modeled using first-order non-linear differential equations. The proposed combustion model was validated against experimental data of a heavy-duty compression ignition engine with up to three injection events at mostly 1038 r/min and 14 bar brake mean effective pressure. Further validation of the model was carried out at other engine loads and speeds. Model prediction errors in CA50 of less than 1 °CA across all conditions were found. Modeling results of other combustion metrics such as combustion duration and indicated mean effective pressure are also highly satisfactory. In addition, the model has been shown to be capable of estimating the ringing intensity for most conditions.

Pamminger, Michael↗
DOE OSTI2023

Parametric evaluation of ducted fuel injection in an optically accessible mixing-controlled compression-ignition engine with two- and four-duct assemblies

Ducted fuel injection (DFI) is a strategy to improve fuel/charge-gas mixing in direct-injection compression-ignition engines. DFI involves injecting fuel along the axis of a small tube in the combustion chamber, which promotes the formation of locally leaner mixtures in the autoignition zone relative to conventional diesel combustion. Previous work has demonstrated that DFI is effective at curtailing engine-out soot emissions across a wide range of operating conditions. This study extends previous investigations, presenting engine-out emissions and efficiency trends between ducted two-orifice and ducted four-orifice injector tip configurations. For each configuration, parameters investigated include injection pressure, injection duration, intake manifold pressure, intake manifold temperature, start of combustion timing, and intake-oxygen mole fraction. For both configurations and across all parameters, DFI reduced engine-out soot emissions compared to conventional diesel combustion, with little effect on other emissions and engine efficiency. Emissions trends for both configurations were qualitatively the same across the parameters investigated. The four-duct configuration had higher thermal efficiency and indicated-specific engine-out nitrogen oxide emissions but lower indicated-specific engine-out hydrocarbon and carbon monoxide emissions than the two-duct assembly. Both configurations achieved indicated-specific engine-out emissions for both soot and nitrogen oxides that comply with current on- and off-road heavy-duty regulations in the United States without exhaust-gas aftertreatment at an intake-oxygen mole fraction of 12%. High-speed in-cylinder imaging of natural soot luminosity shows that some conditions include a second soot-production phase late in the cycle. The probability of these late-cycle events is sensitive to both the number of ducted sprays and the operating conditions.

Yraguen, Boni Frances↗
DOE OSTI2023

Measurement of needle and armature dynamics in a gasoline direct injector by high-speed neutron imaging

In modern spark ignition engines, precise delivery of fuel with gasoline direct injection has become increasingly important in the effort to meet ever stricter efficiency and emissions regulations. Use of multiple small close-coupled injections has become more common in attempt to precisely control fuel distribution in the cylinder, but these strategies are hindered by nonlinear injection effects due to operation in the ballistic region of the solenoid-operated valve and due to armature bounce at the end of injection. Understanding the internal dynamics of the injector is crucial to minimizing and controlling non-linearity and shot-to-shot variation, but the experimental techniques available to date are capable only of tracking the position of either the top of the needle (via laser sensors or by monitoring current and voltage in the solenoid coil) or the bottom of the needle (via transparent nozzles or high-speed x-ray imaging). Furthermore, a complete picture of the axial and radial motion of valve needle has until now remained elusive. In this work, we present high-speed ensemble neutron transmission imaging of an entire 8-hole gasoline direct injector operating at 200 bar, allowing for both visualization and quantification of the actuation dynamics including lift and wobble of the valve ball, oscillation and bending of the valve needle, lift, rocking, and bounce of the armature, compression of the springs, and radial swelling of the solenoid during energization. Because neutrons offer high penetration through the metal injector while also being sensitive to the 1 H nuclei in fuel molecules, it is also possible to simultaneously see the fluid dynamics of the injection process, including filling of the sac volume, emanation of the spray through the nozzle holes and into the downstream gas, and the formation and evolution of fuel films on the tip of the injector and the walls of the spray container.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana

Background: H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction. Results: H2A.X is encoded by two genes in Arabidopsis genome, HTA3 and HTA5. We generated h2a.x double mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However, h2a.x mutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under the H2A.X promoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation in h2a.x developing seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide in h2a.x mutant endosperm. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling. h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA. Conclusions: Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Overall, our data suggest that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

In-vivo Raman microspectroscopy reveals differential nitrate concentration in different developmental zones in Arabidopsis roots

Abstract Background Nitrate (NO 3 − ) is one of the two major forms of inorganic nitrogen absorbed by plant roots, and the tissue nitrate concentration in roots is considered important for optimizing developmental programs. Technologies to quantify the expression levels of nitrate transporters and assimilating enzymes at the cellular level have improved drastically in the past decade. However, a technological gap remains for detecting nitrate at a high spatial resolution. Using extraction-based methods, it is challenging to reliably estimate nitrate concentration from a small volume of cells (i.e., with high spatial resolution), since targeting a small or specific group of cells is physically difficult. Alternatively, nitrate detection with microelectrodes offers subcellular resolution with high cell specificity, but this method has some limitations on cell accessibility and detection speed. Finally, optical nitrate biosensors have very good ( in-vivo ) sensitivity (below 1 mM) and cellular-level spatial resolution, but require plant transformation, limiting their applicability. In this work, we apply Raman microspectroscopy for high-dynamic range in-vivo mapping of nitrate in different developmental zones of Arabidopsis thaliana roots in-situ . Results As a proof of concept, we have used Raman microspectroscopy for in-vivo mapping of nitrate content in roots of Arabidopsis seedlings grown on agar media with different nitrate concentrations. Our results revealed that the root nitrate concentration increases gradually from the meristematic zone (~ 250 µm from the root cap) to the maturation zone (~ 3 mm from the root cap) in roots grown under typical growth conditions used for Arabidopsis, a trend that has not been previously reported. This trend was observed for plants grown in agar media with different nitrate concentrations (0.5–10 mM). These results were validated through destructive measurement of nitrate concentration. Conclusions We present a methodology based on Raman microspectroscopy for in-vivo label-free mapping of nitrate within small root tissue volumes in Arabidopsis. Measurements are done in-situ without additional sample preparation. Our measurements revealed nitrate concentration changes from lower to higher concentration from tip to mature root tissue. Accumulation of nitrate in the maturation zone tissue shows a saturation behavior. The presented Raman-based approach allows for in-situ non-destructive measurements of Raman-active compounds.

Fernández González, Alma↗
DOE OSTI2025

Laser damage of crazed electron-beam high-reflectors following infrared and ultraviolet irradiation in the nanosecond pulse regime

Laser damage of optical components can be a limiting factor in scaling the energetics of high-peak and average power laser systems. Specifically for optical coatings, damage under nanosecond pulsed irradiation is initiated by pre-existing defects in the coating layers, including those that cause discontinuities in the structure, like craze lines. Crazing or cracking in a multilayer dielectric optical coating is induced when the overall coating stress is sufficiently tensile, and is an occasionally observed issue when employing more porous deposition techniques like electron-beam evaporation. Here, in this study, electron-beam high-reflectors were fabricated utilizing process parameters that are known to induce crazing based on prior processing history to systematically evaluate the impact of crazing on reflector damage performance for 1064 and 355 nm lasers. The crazing that was observed was apparently nucleated at nodular defects. When the cross-section of these nodules was investigated, it was observed that there were cracks into the fused silica substrate of approximately 5 µm in depth. The craze lines were irradiated with 1064 and 355 nm light at fluences slightly above the onset of damage initiation fluence of the coating. The 1064 nm irradiated sub-apertures exhibit laser damage but with no spatial correlation with the craze line, whereas the 355 nm irradiated area exhibited many damage sites along the craze line. Finite-difference time-domain electric-field simulations were conducted, and ∼2× field amplification in hafnia was observed for the 355 nm wavelength case. The laser damage can be attributed to a slight electric-field intensification coincidental with an area where UV damage-prone precursors are known to occur. The 355 nm laser damage in uncoated fused silica substrates has been previously correlated to initiate through localized UV absorption at the broken silica bonds in the tips of fractures.

Harthcock, Colin [Lawrence Livermore National Labo↗
DOE OSTI2021

Rapid simulations of hyperspectral near-field images of three-dimensional heterogeneous surfaces

The scattering-type scanning near-field optical microscope (s-SNOM) has emerged as a powerful tool for resolving nanoscale inhomogeneities in laterally heterogeneous samples. However, most analytical models used to predict the scattering near-field signals are assuming homogenous landscapes (bulk materials), resulting in inconsistencies when applied to samples with more complex configurations. In this work, we combine the point-dipole model (PDM) to the finite-element method (FEM) to account for the lateral and vertical heterogeneities while keeping the computation time manageable. Full images, spectra, or hyperspectral line profiles can be simulated by calculating the self-consistent dipole radiation demodulated at higher harmonics of the tip oscillation, mimicking real experimental procedures. Using this formalism, we clarify several important yet puzzling experimental observations in near-field images on samples with rich typography and complex material compositions, heterostructures of two-dimensional material flakes, and plasmonic antennas. The developed method serves as a basis for future investigations of nano-systems with nontrivial topography.

36 MATERIALS SCIENCE↗